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Yi X, Qiu Y, Tang X, Xie P, Xu C, Sun X. Immunoglobulin gene loci structure and diversity of raccoon dog (Nyctereutes procyonoides). BMC Genomics 2025; 26:424. [PMID: 40301716 PMCID: PMC12042606 DOI: 10.1186/s12864-025-11574-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 04/04/2025] [Indexed: 05/01/2025] Open
Abstract
In this study, we analyzed the loci structure of raccoon dog genes using a comparative genomics approach. We investigated the mechanism of expression diversity and its preference using the Next-generation sequencing. The results indicated that the raccoon dog gene loci structure were similar to that of most mammals, with a relative abundance of V(D)J genes, which ensures its expression diversity. We identified the following potentially functional genes: 7 VH genes, 6 Vκ genes, 23 Vλ genes, 24 DH genes, 5 JH genes, 4 Jκ genes, and 6 Jλ genes, arranged in a manner similar to that of other mammals. Analysis of the raccoon dog expression diversity mechanism showed that raccoon dog have a strong preference for the use of V genes, and the same was true for DH genes. The main modes of expression diversity in raccoon dog were V(D)J recombination and somatic hypermutation, in which the high mutation region of somatic hypermutation was not only concentrated in the CDR region, but also has a high mutation in the FR region, and the main types of somatic hypermutation were G > A, C > T, T > C, and A > G. Interestingly, we compared the expression differences between normal and diseased raccoon dogs, and the results showed that there were significant differences in the expression of the same gene (P < 0.05), whereas there were no significant differences in the types of gene expression, gene utilization preference, V(D)J recombination, and somatic hypermutation mutation types. In summary, we have described the IgH and IgL gene loci structure of raccoon dog, mapped the gene loci, and analyzed the mechanism of expression diversity and its preference using PE300 Next-generation sequencing. The results of this study could provide a theoretical basis for an in-depth understanding of raccoon dog immunoglobulins, and provide theoretical references for raccoon dog disease-resistant breeding.
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Affiliation(s)
- Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
- School of Medicine, Westlake University, Hangzhou, 310024, China
| | - Yanbo Qiu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Xiaoqin Tang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Puhang Xie
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Chao Xu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130112, China
| | - Xiuzhu Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China.
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Walsh ES, Yang K, Tollison TS, Seenu S, Adams N, Zeitoun G, Sideri I, Folch G, Brochu HN, Chou H, Kossida S, York IA, Peng X. Development of ferret immune repertoire reference resources and single-cell-based high-throughput profiling assays. J Virol 2025; 99:e0018125. [PMID: 40116504 PMCID: PMC11998538 DOI: 10.1128/jvi.00181-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2025] [Accepted: 02/18/2025] [Indexed: 03/23/2025] Open
Abstract
Domestic ferrets (Mustela putorius furo) are important for modeling human respiratory diseases. However, ferret B and T cell receptors have not been completely identified or annotated, limiting immune repertoire studies. Here, we performed long-read transcriptome sequencing of ferret splenocyte and lymph node samples to obtain over 120,000 high-quality full-length immunoglobin (Ig) and T cell receptor (TCR) transcripts. We constructed a complete reference set of the constant regions of ferret Ig and TCR isotypes and chain types. We also systematically annotated germline Ig and TCR variable (V), diversity (D), joining (J), and constant (C) genes on a recent ferret reference genome assembly. We designed new ferret-specific immune repertoire profiling assays by targeting positions in constant regions without allelic diversity across 11 ferret genome assemblies and experimentally validated them using a commercially compatible single-cell-based platform. These improved resources and assays will enable future studies to fully capture ferret immune repertoire diversity.IMPORTANCEDomestic ferrets (Mustela putorius furo) are an increasingly common model organism to study human respiratory diseases such as influenza infections. However, researchers lack ferret-specific reagents and resources to study the immune system and immune response in ferrets. In this study, we developed comprehensive ferret immune repertoire reference resources and assays, which will enable more accurate analyses of the ferret immune system in the future.
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Affiliation(s)
- Evan S. Walsh
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, North Carolina, USA
| | - Kui Yang
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tammy S. Tollison
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Sujatha Seenu
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nicole Adams
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, North Carolina, USA
| | - Guilhem Zeitoun
- IMGT, The International ImMunoGeneTics Information System, Institute of Human Genetics, National Center for Scientific Research (CNRS), University of Montpellier (UM), Montpellier, France
| | - Ifigeneia Sideri
- IMGT, The International ImMunoGeneTics Information System, Institute of Human Genetics, National Center for Scientific Research (CNRS), University of Montpellier (UM), Montpellier, France
| | - Geraldine Folch
- IMGT, The International ImMunoGeneTics Information System, Institute of Human Genetics, National Center for Scientific Research (CNRS), University of Montpellier (UM), Montpellier, France
| | - Hayden N. Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, North Carolina, USA
| | - Hsuan Chou
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Sofia Kossida
- IMGT, The International ImMunoGeneTics Information System, Institute of Human Genetics, National Center for Scientific Research (CNRS), University of Montpellier (UM), Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | - Ian A. York
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, North Carolina, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, North Carolina, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
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Holt CM, Janke AK, Amlashi P, Jamieson PJ, Marinov TM, Georgiev IS. Contrastive Learning Enables Epitope Overlap Predictions for Targeted Antibody Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.25.640114. [PMID: 40060439 PMCID: PMC11888244 DOI: 10.1101/2025.02.25.640114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/14/2025]
Abstract
Computational epitope prediction remains an unmet need for therapeutic antibody development. We present three complementary approaches for predicting epitope relationships from antibody amino acid sequences. First, we analyze ~18 million antibody pairs targeting ~250 protein families and establish that a threshold of >70% CDRH3 sequence identity among antibodies sharing both heavy and light chain V-genes reliably predicts overlapping-epitope antibody pairs. Next, we develop a supervised contrastive fine-tuning framework for antibody large language models which results in embeddings that better correlate with epitope information than those from pretrained models. Applying this contrastive learning approach to SARS-CoV-2 receptor binding domain antibodies, we achieve 82.7% balanced accuracy in distinguishing same-epitope versus different-epitope antibody pairs and demonstrate the ability to predict relative levels of structural overlap from learning on functional epitope bins (Spearman ρ = 0.25). Finally, we create AbLang-PDB, a generalized model for predicting overlapping-epitope antibodies for a broad range of protein families. AbLang-PDB achieves five-fold improvement in average precision for predicting overlapping-epitope antibody pairs compared to sequence-based methods, and effectively predicts the amount of epitope overlap among overlapping-epitope pairs (ρ = 0.81). In an antibody discovery campaign searching for overlapping-epitope antibodies to the HIV-1 broadly neutralizing antibody 8ANC195, 70% of computationally selected candidates demonstrated HIV-1 specificity, with 50% showing competitive binding with 8ANC195. Together, the computational models presented here provide powerful tools for epitope-targeted antibody discovery, while demonstrating the efficacy of contrastive learning for improving epitope-representation.
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Affiliation(s)
- Clinton M Holt
- Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Alexis K Janke
- Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Parastoo Amlashi
- Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Parker J Jamieson
- Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Toma M Marinov
- Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ivelin S Georgiev
- Vanderbilt Center for Antibody Therapeutics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Program in Chemical and Physical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Computational Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Computer Science, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN 37232, USA
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37232, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
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Cuinat S, Chatron N, Petit F, Brunelle P, Dincuff E, Aubert Mucca M, Bieth E, Schmetz A, Rieder H, Wollnik B, Kaulfuß S, Yigit G, McKeown C, Savage T, Mulligan MR, Bicknell LS, Corsten-Janssen N, Edery P, Lesca G, de Villartay JP, Putoux A. XRCC4-related microcephalic primordial dwarfism: description of a clinical series of 7 cases, phenotype expansion and new diagnostic approaches. Eur J Hum Genet 2025:10.1038/s41431-025-01821-0. [PMID: 40114033 DOI: 10.1038/s41431-025-01821-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 01/13/2025] [Accepted: 02/13/2025] [Indexed: 03/22/2025] Open
Abstract
The non-homologous end joining (NHEJ) pathway is essential to repair DNA double-strand breaks. XRCC4 acts as a stabilizer of the DNA ligase LIG4 in the NHEJ process. In humans, XRCC4 pathogenic variants are responsible for a microcephalic primordial dwarfism syndrome (MPD). Currently, 17 patients have been reported with XRCC4-related MPD and we report 7 new patients from 6 different families, including one fetus. The patients present with short stature, severe microcephaly, neurodevelopmental disorder and additional features, such as transient increase in nuchal translucency, congenital glaucoma, thumb anomalies, hepatic steatosis, seizures, essential tremor and oligodontia which have not been previously described. Hyper- and hypopigmented skin macules, dermatofibrosarcoma, mandibular osteoid osteoma and pancytopenia are also new features, reminiscent of cancer susceptibility syndromes. Functional studies were performed on two patients carrying the known pathogenic p.(Trp43Arg) variant in homozygous state, using a fast, cost-effective and non-invasive approach on PBMCs: (1) Survival analyses after ionizing radiation confirm important radiosensitivity. (2) Flow cytometry showed the lack of TCR-Va7+ T-lymphocytes, suggesting recombination defect of V(D)J coding segments. (3) This was confirmed by multiplexed RT-PCR (PROMIDISα biomarker), analyzing the diversity of V(D)J coding segments in a subset of the TCRα repertoire. We therefore extend the phenotype of XRCC4-related MPD and suggest a combination of three functional assays, based on radiosensitivity and V(D)J recombination defect, to improve the interpretation of XRCC4 variants in fast, cost-effective and non-invasive manner. These findings will improve the diagnosis, genetic counselling, follow-up and management of these patients.
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Affiliation(s)
- Silvestre Cuinat
- Hospices Civils de Lyon, Service de Génétique, Centre Labélisé Anomalies du Développement CLAD Sud-Est, Lyon, France.
- Centre de Recherche en Neurosciences de Lyon, équipe GENDEV, INSERM U1028 CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France.
| | - Nicolas Chatron
- Hospices Civils de Lyon, Service de Génétique, Centre Labélisé Anomalies du Développement CLAD Sud-Est, Lyon, France
- Institut Neuromyogène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Florence Petit
- Univ. Lille, CHU Lille, ULR 7364 - RADEME, F-59000, Lille, France
| | - Perrine Brunelle
- Univ. Lille, CHU Lille, ULR 7364 - RADEME, F-59000, Lille, France
| | - Etienne Dincuff
- Laboratory « Genome Dynamics in the Immune System », INSERM UMR 1163, DGSI, Equipe labellisée La Ligue Nationale Contre le Cancer, Institut Imagine, Université Paris Descartes Sorbonne Paris Cité, 75015, Paris, France
| | | | - Eric Bieth
- Service de Génétique Médicale, Hôpital Purpan, CHU, 31059, Toulouse, France
| | - Ariane Schmetz
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Harald Rieder
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Lower Saxony, Gottingen, Germany
- University of Göttingen, Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), Göttingen, Deutschland
| | - Silke Kaulfuß
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Lower Saxony, Gottingen, Germany
| | - Colina McKeown
- Genetic Health Service, Wellington Children's Hospital, Wellington, New Zealand
| | - Tim Savage
- General Pediatrics, Diabetes and Endocrinology, Wellington Children's Hospital, Wellington, New Zealand
| | - Meghan R Mulligan
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Nicole Corsten-Janssen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrick Edery
- Hospices Civils de Lyon, Service de Génétique, Centre Labélisé Anomalies du Développement CLAD Sud-Est, Lyon, France
- Centre de Recherche en Neurosciences de Lyon, équipe GENDEV, INSERM U1028 CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Gaetan Lesca
- Hospices Civils de Lyon, Service de Génétique, Centre Labélisé Anomalies du Développement CLAD Sud-Est, Lyon, France
- Institut Neuromyogène, Laboratoire Physiopathologie et Génétique du Neurone et du Muscle, Equipe Métabolisme énergétique et développement neuronal, CNRS UMR 5310, INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Jean-Pierre de Villartay
- Laboratory « Genome Dynamics in the Immune System », INSERM UMR 1163, DGSI, Equipe labellisée La Ligue Nationale Contre le Cancer, Institut Imagine, Université Paris Descartes Sorbonne Paris Cité, 75015, Paris, France
| | - Audrey Putoux
- Hospices Civils de Lyon, Service de Génétique, Centre Labélisé Anomalies du Développement CLAD Sud-Est, Lyon, France.
- Centre de Recherche en Neurosciences de Lyon, équipe GENDEV, INSERM U1028 CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France.
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Platt JL, Zhao C, Chicca J, Pianko MJ, Han J, The S, Rao A, Keller ET, Garcia de Mattos Barbosa M, Naing L, Pasieka-Axenov T, Axenov L, Schaefer S, Farkash E, Cascalho M. Complement C3d enables cell-mediated immunity capable of distinguishing spontaneously transformed from nontransformed cells. Proc Natl Acad Sci U S A 2024; 121:e2405824121. [PMID: 39693340 DOI: 10.1073/pnas.2405824121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 10/19/2024] [Indexed: 12/20/2024] Open
Abstract
Immune surveillance depends in part on the recognition of peptide variants by T cell antigen receptors. Given that both normal B cells and malignant B cells accumulate mutations we chose a murine model of multiple myeloma to test conditions to induce cell-mediated immunity targeting malignant plasma cell (PC) clones but sparing of normal PCs. Revealing a previously unknown function for intracellular C3d, we found that C3d engaged T cell responses against malignant PC in the bone marrow of mice that had developed multiple myeloma spontaneously. Our results show that C3d internalized by cells augments immune surveillance by several mechanisms. In one, C3d induces a master transcription regulator, E2f1, to increase the expression of long noncoding (lnc) RNAs, to generate peptides for MHC-I presentation, and increase MHC-I expression. In another, C3d increases expression of RNAs encoding ribosomal proteins linked to processing of defective ribosomal products that arise from noncanonical translation and known to promote immunosurveillance. Cancer cells are uniquely susceptible to increased expression and presentation of mutant peptides given the extent of protein misfolding and accumulation of somatic mutations. Accordingly, although C3d can be internalized by any cell, C3d preferentially targets malignant clones by evoking specific T cell-mediated immunity and sparing most nontransformed polyclonal B cells and PC with lower mutation loads. Malignant PC deletion was blocked by cyclosporin or by CD8 depletion confirming that endogenous T cells mediated malignant clone clearance. Besides the potential for therapeutic application our results highlight how intracellular C3d modifies cellular metabolism to augment immune surveillance.
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Affiliation(s)
- Jeffrey L Platt
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Chong Zhao
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Jeffrey Chicca
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Matthew J Pianko
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Joshua Han
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Stephanie The
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
- Cancer Data Science Shared Research Core, University of Michigan Rogel Cancer Center, Ann Arbor, MI 48109
| | - Arvind Rao
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
- Cancer Data Science Shared Research Core, University of Michigan Rogel Cancer Center, Ann Arbor, MI 48109
| | - Evan T Keller
- Department of Urology and the Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | | | - Lwar Naing
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, Graduate Program in Molecular and Cellular Biology, Ann Arbor, MI 48109
| | | | - Lev Axenov
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
| | - Simon Schaefer
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen 91054, Germany
| | - Evan Farkash
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Marilia Cascalho
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
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Platt JL, Zhao C, Chicca J, Pianko MJ, Han J, The S, Rao A, Keller E, de Mattos Barbosa MG, Naing L, Pasieka-Axenov T, Axenov L, Schaefer S, Farkash E, Cascalho M. Complement C3d enables protective immunity capable of distinguishing spontaneously transformed from non-transformed cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.606044. [PMID: 39211250 PMCID: PMC11360951 DOI: 10.1101/2024.07.31.606044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Immune-surveillance depends in part on the recognition of peptide variants by T cell antigen receptors. Given that both normal B cells and malignant B cells accumulate mutations we chose a murine model of multiple myeloma to test conditions to induce cell-mediated immunity targeting malignant plasma cell (PC) clones but sparing of normal PCs. Revealing a novel function for intracellular C3d, we discovered that C3d engaged T cell responses against malignant plasma cells in the bone marrow of mice that had developed multiple myeloma spontaneously. Our results show that C3d internalized by cells augments immune surveillance by several mechanisms. In one, C3d induces a master transcription regulator, E2f1, to increase the expression of long non-coding (lnc) RNAs, to generate peptides for MHC-I presentation and increase MHC-I expression. In another, C3d increases expression of RNAs encoding ribosomal proteins linked to processing of defective ribosomal products (DRiPs) that arise from non-canonical translation and known to promote immunosurveillance. Cancer cells are uniquely susceptible to increased expression and presentation of mutant peptides given the extent of protein misfolding and accumulation of somatic mutations. Accordingly, although C3d can be internalized by any cell, C3d preferentially targets malignant clones by evoking specific T cell mediated immunity (CMI) and sparing most non-transformed polyclonal B cells and plasma cells with lower mutation loads. Malignant plasma cell deletion was blocked by cyclosporin or by CD8 depletion confirming that endogenous T cells mediated malignant clone clearance. Besides the potential for therapeutic application our results highlight how intracellular C3d modifies cellular metabolism to augment immune surveillance. One Sentence Summary We show that intracellular soluble fragment 3d of complement (C3d) induces regression of spontaneous multiple myeloma in mice reducing tumor burden by 10 fold, after 8 weeks. C3d enables cell-mediated immunity to target multiple myeloma clones sparing non-transformed polyclonal B cells and plasma cells with lower mutation loads. We show that C3d increases the expression of ribosomal subunits associated with the translation of defective ribosomal products (DRiPs). C3d also decreases expression of protein arginine methyl transferase (PRMT) 5 which in turn relieves E2f1 repression increasing the expression of Lnc RNAs and derived peptides that evoke anti-tumor cellular immunity. The approach increases MHC-I expression by tumor cells and generates a CMI response that overcomes tumor immune-evasion strategies. Significance Tumors are immunogenic in part because of somatic mutations that originate novel peptides that once presented on MHC engage cell-mediated immunity (CMI). However, in spite of the higher mutation load most tumors evade immunity. We discovered that a component of the complement system (C3d) overcomes tumor immune evasion by augmenting expression of ribosomal proteins and lncRNAs linked to the presentation of novel peptides by tumor cells. C3d induced CMI targets cancer cells sparing non transformed cells uncovering a novel function for complement in immune surveillance.
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Györkei Á, Johansen FE, Qiao SW. Systematic characterization of immunoglobulin loci and deep sequencing of the expressed repertoire in the Atlantic cod (Gadus morhua). BMC Genomics 2024; 25:663. [PMID: 38961347 PMCID: PMC11223323 DOI: 10.1186/s12864-024-10571-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 06/26/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND The Atlantic cod is a prolific species in the Atlantic, despite its inconsistent specific antibody response. It presents a peculiar case within vertebrate immunology due to its distinct immune system, characterized by the absence of MHCII antigen presentation pathway, required for T cell-dependent antibody responses. Thorough characterisation of immunoglobulin loci and analysis of the antibody repertoire is necessary to further our understanding of the Atlantic cod's immune response on a molecular level. RESULTS A comprehensive search of the cod genome (gadmor3.0) identified the complete set of IgH genes organized into three sequential translocons on chromosome 2, while IgL genes were located on chromosomes 2 and 5. The Atlantic cod displayed a moderate germline V gene diversity, comprising four V gene families for both IgH and IgL, each with distinct chromosomal locations and organizational structures. 5'RACE sequencing revealed a diverse range of heavy chain CDR3 sequences and relatively limited CDR3 diversity in light chains. The analysis highlighted a differential impact of V-gene germline CDR3 length on receptor CDR3 length between heavy and light chains, underlining different recombination processes. CONCLUSIONS This study reveals that the Atlantic cod, despite its inconsistent antibody response, maintains a level of immunoglobulin diversity comparable to other fish species. The findings suggest that the extensive recent duplications of kappa light chain genes do not result in increased repertoire diversity. This research provides a comprehensive view of the Atlantic cod's immunoglobulin gene organization and repertoire, necessary for future studies of antibody responses at the molecular level.
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Affiliation(s)
- Ádám Györkei
- Department of Biosciences, Section for Physiology and Cell Biology, University of Oslo, Oslo, Norway
| | - Finn-Eirik Johansen
- Department of Biosciences, Section for Physiology and Cell Biology, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- Department of Immunology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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Dumonteil E, Tu W, Desale H, Goff K, Marx P, Ortega-Lopez J, Herrera C. Immunoglobulin and T cell receptor repertoire changes induced by a prototype vaccine against Chagas disease in naïve rhesus macaques. J Biomed Sci 2024; 31:58. [PMID: 38824576 PMCID: PMC11143712 DOI: 10.1186/s12929-024-01050-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/27/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND A vaccine against Trypanosoma cruzi, the agent of Chagas disease, would be an excellent additional tool for disease control. A recombinant vaccine based on Tc24 and TSA1 parasite antigens was found to be safe and immunogenic in naïve macaques. METHODS We used RNA-sequencing and performed a transcriptomic analysis of PBMC responses to vaccination of naïve macaques after each vaccine dose, to shed light on the immunogenicity of this vaccine and guide the optimization of doses and formulation. We identified differentially expressed genes and pathways and characterized immunoglobulin and T cell receptor repertoires. RESULTS RNA-sequencing analysis indicated a clear transcriptomic response of PBMCs after three vaccine doses, with the up-regulation of several immune cell activation pathways and a broad non-polarized immune profile. Analysis of the IgG repertoire showed that it had a rapid turnover with novel IgGs produced following each vaccine dose, while the TCR repertoire presented several persisting clones that were expanded after each vaccine dose. CONCLUSIONS These data suggest that three vaccine doses may be needed for optimum immunogenicity and support the further evaluation of the protective efficacy of this vaccine.
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Affiliation(s)
- Eric Dumonteil
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA.
| | - Weihong Tu
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
| | - Hans Desale
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
| | - Kelly Goff
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Preston Marx
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Jaime Ortega-Lopez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico, México
| | - Claudia Herrera
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
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9
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Salem GM, Galula JU, Wu SR, Liu JH, Chen YH, Wang WH, Wang SF, Song CS, Chen FC, Abarientos AB, Chen GW, Wang CI, Chao DY. Antibodies from dengue patients with prior exposure to Japanese encephalitis virus are broadly neutralizing against Zika virus. Commun Biol 2024; 7:15. [PMID: 38267569 PMCID: PMC10808242 DOI: 10.1038/s42003-023-05661-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/01/2023] [Indexed: 01/26/2024] Open
Abstract
Exposure to multiple mosquito-borne flaviviruses within a lifetime is not uncommon; however, how sequential exposures to different flaviviruses shape the cross-reactive humoral response against an antigen from a different serocomplex has yet to be explored. Here, we report that dengue-infected individuals initially primed with the Japanese encephalitis virus (JEV) showed broad, highly neutralizing potencies against Zika virus (ZIKV). We also identified a rare class of ZIKV-cross-reactive human monoclonal antibodies with increased somatic hypermutation and broad neutralization against multiple flaviviruses. One huMAb, K8b, binds quaternary epitopes with heavy and light chains separately interacting with overlapping envelope protein dimer units spanning domains I, II, and III through cryo-electron microscopy and structure-based mutagenesis. JEV virus-like particle immunization in mice further confirmed that such cross-reactive antibodies, mainly IgG3 isotype, can be induced and proliferate through heterologous dengue virus (DENV) serotype 2 virus-like particle stimulation. Our findings highlight the role of prior immunity in JEV and DENV in shaping the breadth of humoral response and provide insights for future vaccination strategies in flavivirus-endemic countries.
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Affiliation(s)
- Gielenny M Salem
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung City, 402, Taiwan
| | - Jedhan Ucat Galula
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung City, 402, Taiwan
| | - Shang-Rung Wu
- Institute of Oral Medicine, School of Dentistry, College of Medicine, National Cheng Kung University, Tainan City, 701, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Jyung-Hurng Liu
- Graduate Institute of Genomics and Bioinformatics, College of Life Sciences, National Chung Hsing University, Taichung City, 40227, Taiwan
| | - Yen-Hsu Chen
- School of Medicine, College of Medicine, National Sun Yat-Sen University, Kaohsiung City, 80424, Taiwan
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan
| | - Wen-Hung Wang
- School of Medicine, College of Medicine, National Sun Yat-Sen University, Kaohsiung City, 80424, Taiwan
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan
| | - Sheng-Fan Wang
- Center for Tropical Medicine and Infectious Disease Research, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung City, 80708, Taiwan
| | - Cheng-Sheng Song
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung City, 402, Taiwan
| | - Fan-Chi Chen
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung City, 402, Taiwan
| | - Adrian B Abarientos
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung City, 402, Taiwan
| | - Guan-Wen Chen
- Institute of Oral Medicine, School of Dentistry, College of Medicine, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Cheng-I Wang
- Singapore Immunology Network, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, Immunos, Singapore, 138648, Singapore
| | - Day-Yu Chao
- Graduate Institute of Microbiology and Public Health, College of Veterinary Medicine, National Chung Hsing University, Taichung City, 402, Taiwan.
- Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taichung City, 402, Taiwan.
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung City, 402, Taiwan.
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10
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Fang Y, Shen B, Dai Q, Xie Q, Li X, Wu W, Wang M. Composition and diversity analysis of the TCR CDR3 repertoire in patients with idiopathic orbital inflammation using high-throughput sequencing. BMC Ophthalmol 2023; 23:491. [PMID: 38044453 PMCID: PMC10694961 DOI: 10.1186/s12886-023-03248-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023] Open
Abstract
BACKGROUND Idiopathic orbital inflammation (IOI) is a nonspecific orbital inflammatory disease with the third highest prevalence among orbital diseases, and its pathogenesis is associated with T-cell-mediated immune responses. This study aimed to investigate the differences in T-cell receptor (TCR) expression between IOI patients and healthy subjects by high-throughput sequencing and to characterize TCR expression in patients with IOI and with respect to glucocorticoid response. METHODS A total of 19 subjects were enrolled in this study and were divided into the idiopathic orbital inflammation group (IOI group, n = 13) and the healthy control group (HC group, n = 6), and within the IOI group were further divided into the glucocorticoid therapy sensitive group (IOI(EF) group, n = 6) and the glucocorticoid therapy ineffective group (IOI(IN) group, n = 7) based on the degree of effectiveness to glucocorticoid therapy. High-throughput TCR sequencing was performed on peripheral blood mononuclear cells of IOI patients and healthy control individuals using 5' RACE technology combined with Unique Identifier (UID) digital tag correction technology. The TCR CDR3 region diversity, sharing patterns, and differential sequences between the IOI and HC groups, and between the IOI(EF) and IOI(IN) groups were analyzed. RESULTS It was found that the diversity of TCR CDR3 in the IOI group was significantly lower than that in the HC group, and the frequency of V gene use was significantly different between groups. The diversity of TCR CDR3 in patients in the IOI(EF) group was significantly lower than that in patients in the IOI(IN) group, and the frequency of V and J gene use was significantly different between the IOI(EF) group and the IOI(IN) group. Additionally, we found 133 nucleotide sequences shared in all IOI samples and screened two sequences with higher expression from them. CONCLUSIONS Our results suggested that abnormal clonal expansion of specific T-cells exists in IOI patients and that TCR diversity may had an impact on the prognosis of glucocorticoid-treated IOI. This study may contribute to a better understanding of the immune status of IOI and provide new insights for T-cell -associated IOI pathogenesis, diagnosis and treatment prediction.
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Affiliation(s)
- Yenan Fang
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- Department of Ophthalmology, Children's Hospital of Fudan University, National Children's Medical Center, No. 399 Wanyuan Road, Shanghai, 201102, China
| | - Bingyan Shen
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qin Dai
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qiqi Xie
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xinyu Li
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Wencan Wu
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
| | - Min Wang
- National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
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11
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Gervásio J, Ferreira A, Felicori LF. Yclon: Ultrafast clustering of B cell clones from high-throughput immunoglobulin repertoire sequencing data. J Immunol Methods 2023; 523:113576. [PMID: 37966818 DOI: 10.1016/j.jim.2023.113576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
MOTIVATION The next-generation sequencing technologies have transformed our understanding of immunoglobulin (Ig) profiles in various immune states. Clonotyping, which groups Ig sequences into B cell clones, is crucial in investigating the diversity of repertoires and changes in antigen exposure. Despite its importance, there is no widely accepted method for clonotyping, and existing methods are computationally intensive for large sequencing datasets. RESULTS To address this challenge, we introduce YClon, a fast and efficient approach for clonotyping Ig repertoire data. YClon uses a hierarchical clustering approach, similar to other methods, to group Ig sequences into B cell clones in a highly sensitive and specific manner. Notably, our approach outperforms other methods by being more than 30 to 5000 times faster in processing the repertoires analyzed. Astonishingly, YClon can effortlessly handle up to 2 million Ig sequences on a standard laptop computer. This enables in-depth analysis of large and numerous antibody repertoires. AVAILABILITY AND IMPLEMENTATION YClon was implemented in Python3 and is freely available on GitHub.
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Affiliation(s)
- João Gervásio
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Alice Ferreira
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil
| | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
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12
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Dumonteil E, Tu W, Desale H, Goff K, Marx P, Ortega-Lopez J, Herrera C. Immunoglobin and T cell receptor repertoire changes induced by a prototype vaccine against Chagas disease in naïve rhesus macaques. RESEARCH SQUARE 2023:rs.3.rs-3453582. [PMID: 37961272 PMCID: PMC10635379 DOI: 10.21203/rs.3.rs-3453582/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A vaccine against Trypanosoma cruzi, the agent of Chagas disease, would be an excellent additional tool for disease control. A recombinant vaccine based on Tc24 and TSA1 parasite antigens was found to be safe and immunogenic in naïve macaques. Here we performed a transcriptomic analysis of PBMC responses to vaccination, to shed light on the immunogenicity of this vaccine and guide the optimization of doses and formulation. RNA-sequencing analysis indicated a clear transcriptomic response of PBMCs from macaques after three vaccine doses, with the up-regulation of several immune cell activation pathways and a broad non-polarized immune profile. Analysis of the IgG repertoire showed that it had a rapid turnover with novel IgGs produced following each vaccine dose, while the TCR repertoire presented several persisting clones that were expanded after each vaccine dose. These data suggest that three vaccine doses may be needed for optimum immunogenecity and support the further evaluation of the protective efficacy of this vaccine.
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13
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Zhou H, Li J, Zhou D, Wu Y, Wang X, Zhou J, Ma Q, Yao X, Ma L. New insights into the germline genes and CDR3 repertoire of the TCRβ chain in Chiroptera. Front Immunol 2023; 14:1147859. [PMID: 37051236 PMCID: PMC10083501 DOI: 10.3389/fimmu.2023.1147859] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
IntroductionBats are recognized as natural reservoirs for many viruses, and their unique immune system enables them to coexist with these viruses without frequently exhibiting disease symptoms. However, the current understanding of the bat adaptive immune system is limited due to the lack of a database or tool capable of processing T-cell receptor (TCR) sequences for bats.MethodsWe performed germline gene annotation in three bat species using homologous genes and RSSs (Recombinational Signal Sequences) scanning method. Then we used the conserved C gene to construct the TCRβ chain receptor library of the Intermediate Horseshoe Bat. Bats' TCRβ data will be analyzed using MiXCR and constructed reference library.ResultsRegarding the annotation results, we found that the Pale Spear-nosed Bat has 37 members in the TRBV12 family, which is more than the total number of TRBV genes in the Greater Horseshoe Bat. The average number of unique TCRβ chain receptor sequences in each Intermediate Horseshoe Bat sample reached 24,904.DiscussionThe distinct variations in the distribution of TRBV genes among the three types of bats could have a direct impact on the diversity of the TCR repertoire, as evidenced by the presence of conserved amino acids that indicate the T-cell recognition of antigens in bats is MHC-restricted. The bats’ TCRβ repertoire is formed through the rearrangement of the V-D-J-C genes, with D-J/V-D deletions and insertions resulting in high diversity.
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Affiliation(s)
- Hao Zhou
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Jun Li
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Dewei Zhou
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Yingjie Wu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xingliang Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Jiang Zhou
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qingqing Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
- *Correspondence: Xinsheng Yao, ; Long Ma,
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
- *Correspondence: Xinsheng Yao, ; Long Ma,
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14
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Mejias-Gomez O, Madsen AV, Skovgaard K, Pedersen LE, Morth JP, Jenkins TP, Kristensen P, Goletz S. A window into the human immune system: comprehensive characterization of the complexity of antibody complementary-determining regions in functional antibodies. MAbs 2023; 15:2268255. [PMID: 37876265 PMCID: PMC10601506 DOI: 10.1080/19420862.2023.2268255] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
The human immune system uses antibodies to neutralize foreign antigens. They are composed of heavy and light chains, both with constant and variable regions. The variable region has six hypervariable loops, also known as complementary-determining regions (CDRs) that determine antibody diversity and antigen specificity. Knowledge of their significance, and certain residues present in these areas, is vital for antibody therapeutics development. This study includes an analysis of more than 11,000 human antibody sequences from the International Immunogenetics information system (IMGT). The analysis included parameters such as length distribution, overall amino acid diversity, amino acid frequency per CDR and residue position within antibody chains. Overall, our findings confirm existing knowledge, such as CDRH3's high length diversity and amino acid variability, increased aromatic residue usage, particularly tyrosine, charged and polar residues like aspartic acid, serine, and the flexible residue glycine. Specific residue positions within each CDR influence these occurrences, implying a unique amino acid type distribution pattern. We compared amino acid type usage in CDRs and non-CDR regions, both in globular and transmembrane proteins, which revealed distinguishing features, such as increased frequency of tyrosine, serine, aspartic acid, and arginine. These findings should prove useful for future optimization, improvement of affinity, synthetic antibody library design, or the creation of antibodies de-novo in silico.
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Affiliation(s)
- Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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15
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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: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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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16
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Porciello N, Franzese O, D’Ambrosio L, Palermo B, Nisticò P. T-cell repertoire diversity: friend or foe for protective antitumor response? JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:356. [PMID: 36550555 PMCID: PMC9773533 DOI: 10.1186/s13046-022-02566-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Profiling the T-Cell Receptor (TCR) repertoire is establishing as a potent approach to investigate autologous and treatment-induced antitumor immune response. Technical and computational breakthroughs, including high throughput next-generation sequencing (NGS) approaches and spatial transcriptomics, are providing unprecedented insight into the mechanisms underlying antitumor immunity. A precise spatiotemporal variation of T-cell repertoire, which dynamically mirrors the functional state of the evolving host-cancer interaction, allows the tracking of the T-cell populations at play, and may identify the key cells responsible for tumor eradication, the evaluation of minimal residual disease and the identification of biomarkers of response to immunotherapy. In this review we will discuss the relationship between global metrics characterizing the TCR repertoire such as T-cell clonality and diversity and the resultant functional responses. In particular, we will explore how specific TCR repertoires in cancer patients can be predictive of prognosis or response to therapy and in particular how a given TCR re-arrangement, following immunotherapy, can predict a specific clinical outcome. Finally, we will examine current improvements in terms of T-cell sequencing, discussing advantages and challenges of current methodologies.
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Affiliation(s)
- Nicla Porciello
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Ornella Franzese
- grid.6530.00000 0001 2300 0941Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Lorenzo D’Ambrosio
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Belinda Palermo
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Paola Nisticò
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
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17
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Yang P, He Y, Qing P, Xu W, Xie D, Cazier J, Liu X, Varnai C, Zhou Y, Zhao Y, Tang H, Yin X, Liu Y. Application of T-cell receptor repertoire as a novel monitor in dynamic tracking and assessment: A cohort-study based on RA patients. J Cell Mol Med 2022; 26:6042-6055. [PMID: 36440548 PMCID: PMC9753462 DOI: 10.1111/jcmm.17623] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/19/2022] [Accepted: 10/21/2022] [Indexed: 11/29/2022] Open
Abstract
T-cell receptor repertoire (TCRR) sequencing has been widely applied in many fields as a novel tool. This study explored characteristics of TCRR in detail with a cohort of 598 rheumatoid arthritis (RA) patients before and after anti-rheumatic treatments. We highlighted the abnormal TCRR distribution in RA characterized by decreased diversity and increased proportion of hyperexpanded clones (HECs), which was potentially attributed to skewed usage of global V/J segments but not a few certain ones. Enriched motifs analysis in RA community demonstrated the huge heterogeneity of CDR3 sequences, so that individual factors are strongly recommended to be taken into consideration when it comes to clinical application of TCRR. Disease-modifying antirheumatic drugs (DMARDs) can regulate immune system through recovery of TCRR richness to relieve symptoms. Remarkably, sensitive gene profile and advantageous gene profile were identified in this study as new biomarkers for different DMARDs regimens.
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Affiliation(s)
- Peiqing Yang
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina
| | - Yijing He
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine CenterWest China Hospital, Sichuan UniversityChengduChina,Laboratory of Nervous System Disease and Brain Functions, Clinical Research InstituteThe Affiliated Hospital of Southwest Medical UniversityLuzhouChina
| | - Pingying Qing
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina
| | - Wangdong Xu
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina,Department of Evidence‐Based MedicineSchool of Public Health, Southwest Medical UniversityLuzhouChina
| | - Dan Xie
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine CenterWest China Hospital, Sichuan UniversityChengduChina
| | | | - Xiao Liu
- BGI‐Shenzhen and Shenzhen Key Laboratory of Transomics BiotechnologiesBGI‐ShenzhenShenzhenChina
| | - Csilla Varnai
- Center for Computational BiologyUniversity of BirminghamBirminghamUK
| | - Yi Zhou
- Department of Medical Affairs, West China HospitalSichuan UniversityChengduChina
| | - Yi Zhao
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina
| | - Huairong Tang
- Health Management CenterWest China Hospital of Sichuan UniversityChengduChina
| | | | - Yi Liu
- Department of Rheumatology, West China HospitalSichuan UniversityChengduChina
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18
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Xu Z, Ismanto HS, Zhou H, Saputri DS, Sugihara F, Standley DM. Advances in antibody discovery from human BCR repertoires. FRONTIERS IN BIOINFORMATICS 2022; 2:1044975. [PMID: 36338807 PMCID: PMC9631452 DOI: 10.3389/fbinf.2022.1044975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it possible to search for antibodies targeting a given antigen within the repertoires of B cells in humans. Here we group these innovations into four broad categories: cell sorting allows the collection of cells enriched in specificity to one or more antigens; BCR sequencing can be performed on bulk mRNA, genomic DNA or on paired (heavy-light) mRNA; BCR repertoire analysis generally involves clustering BCRs into specificity groups or more in-depth modeling of antibody-antigen interactions, such as antibody-specific epitope predictions; validation of antibody-antigen interactions requires expression of antibodies, followed by antigen binding assays or epitope mapping. Together with innovations in Deep learning these technologies will contribute to the future discovery of diagnostic and therapeutic antibodies directly from humans.
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Affiliation(s)
- Zichang Xu
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hao Zhou
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Department Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
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19
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Lefranc MP, Lefranc G. IMGT ® Nomenclature of Engineered IGHG Variants Involved in Antibody Effector Properties and Formats. Antibodies (Basel) 2022; 11:65. [PMID: 36278618 PMCID: PMC9624366 DOI: 10.3390/antib11040065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
The constant region of the immunoglobulin (IG) or antibody heavy gamma chain is frequently engineered to modify the effector properties of the therapeutic monoclonal antibodies. These variants are classified in regards to their effects on effector functions, antibody-dependent cytotoxicity (ADCC), antibody-dependent phagocytosis (ADCP), complement-dependent cytotoxicity (CDC) enhancement or reduction, B cell inhibition by the coengagement of antigen and FcγR on the same cell, on half-life increase, and/or on structure such as prevention of IgG4 half-IG exchange, hexamerisation, knobs-into-holes and the heteropairing H-H of bispecific antibodies, absence of disulfide bridge inter H-L, absence of glycosylation site, and site-specific drug attachment engineered cysteine. The IMGT engineered variant identifier is comprised of the species and gene name (and eventually allele), the letter 'v' followed by a number (assigned chronologically), and for each concerned domain (e.g, CH1, h, CH2 and CH3), the novel AA (single letter abbreviation) and IMGT position according to the IMGT unique numbering for the C-domain and between parentheses, the Eu numbering. IMGT engineered variants are described with detailed amino acid changes, visualized in motifs based on the IMGT numbering bridging genes, sequences, and structures for higher order description.
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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), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), UMR 9002 CNRS-UM, CEDEX 5, 34396 Montpellier, France
| | - Gérard 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), UMR 9002 CNRS-UM, CEDEX 5, 34396 Montpellier, France
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20
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Garrido-Mesa J, Brown MA. T cell Repertoire Profiling and the Mechanism by which HLA-B27 Causes Ankylosing Spondylitis. Curr Rheumatol Rep 2022; 24:398-410. [PMID: 36197645 PMCID: PMC9666335 DOI: 10.1007/s11926-022-01090-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2022] [Indexed: 11/25/2022]
Abstract
Purpose of Review Ankylosing spondylitis (AS) is strongly associated with the HLA-B27 gene. The canonical function of HLA-B27 is to present antigenic peptides to CD8 lymphocytes, leading to adaptive immune responses. The ‘arthritogenic peptide’ theory as to the mechanism by which HLA-B27 induces ankylosing spondylitis proposes that HLA-B27 presents peptides derived from exogenous sources such as bacteria to CD8 lymphocytes, which subsequently cross-react with antigens at the site of inflammation of the disease, causing inflammation. This review describes findings of studies in AS involving profiling of T cell expansions and discusses future research opportunities based on these findings. Recent Findings Consistent with this theory, there is an expanding body of data showing that expansion of a restricted pool of CD8 lymphocytes is found in most AS patients yet only in a small proportion of healthy HLA-B27 carriers. Summary These exciting findings strongly support the theory that AS is driven by presentation of antigenic peptides to the adaptive immune system by HLA-B27. They point to new potential approaches to identify the exogenous and endogenous antigens involved and to potential therapies for the disease.
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Affiliation(s)
- Jose Garrido-Mesa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, England.
- Genomics England, Charterhouse Square, London, EC1M 6BQ, England.
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21
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Zaragoza-Infante L, Junet V, Pechlivanis N, Fragkouli SC, Amprachamian S, Koletsa T, Chatzidimitriou A, Papaioannou M, Stamatopoulos K, Agathangelidis A, Psomopoulos F. IgIDivA: immunoglobulin intraclonal diversification analysis. Brief Bioinform 2022; 23:bbac349. [PMID: 36044248 PMCID: PMC9487589 DOI: 10.1093/bib/bbac349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/14/2022] Open
Abstract
Intraclonal diversification (ID) within the immunoglobulin (IG) genes expressed by B cell clones arises due to ongoing somatic hypermutation (SHM) in a context of continuous interactions with antigen(s). Defining the nature and order of appearance of SHMs in the IG genes can assist in improved understanding of the ID process, shedding light into the ontogeny and evolution of B cell clones in health and disease. Such endeavor is empowered thanks to the introduction of high-throughput sequencing in the study of IG gene repertoires. However, few existing tools allow the identification, quantification and characterization of SHMs related to ID, all of which have limitations in their analysis, highlighting the need for developing a purpose-built tool for the comprehensive analysis of the ID process. In this work, we present the immunoglobulin intraclonal diversification analysis (IgIDivA) tool, a novel methodology for the in-depth qualitative and quantitative analysis of the ID process from high-throughput sequencing data. IgIDivA identifies and characterizes SHMs that occur within the variable domain of the rearranged IG genes and studies in detail the connections between identified SHMs, establishing mutational pathways. Moreover, it combines established and new graph-based metrics for the objective determination of ID level, combined with statistical analysis for the comparison of ID level features for different groups of samples. Of importance, IgIDivA also provides detailed visualizations of ID through the generation of purpose-built graph networks. Beyond the method design, IgIDivA has been also implemented as an R Shiny web application. IgIDivA is freely available at https://bio.tools/igidiva.
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Affiliation(s)
- Laura Zaragoza-Infante
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
- Hematology Unit, 1st Dept of Internal Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki
| | - Valentin Junet
- Anaxomics Biotech SL, Barcelona, Spain
- Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nikos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Serovpe Amprachamian
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Maria Papaioannou
- Hematology Unit, 1st Dept of Internal Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
- Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
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22
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Scheepers C, Kgagudi P, Mzindle N, Gray ES, Moyo-Gwete T, Lambson BE, Oosthuysen B, Mabvakure B, Garrett NJ, Abdool Karim SS, Morris L, Moore PL. Dependence on a variable residue limits the breadth of an HIV MPER neutralizing antibody, despite convergent evolution with broadly neutralizing antibodies. PLoS Pathog 2022; 18:e1010450. [PMID: 36054228 PMCID: PMC9477419 DOI: 10.1371/journal.ppat.1010450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/15/2022] [Accepted: 08/14/2022] [Indexed: 11/18/2022] Open
Abstract
Broadly neutralizing antibodies (bNAbs) that target the membrane-proximal external region (MPER) of HIV gp41 envelope, such as 4E10, VRC42.01 and PGZL1, can neutralize >80% of viruses. These three MPER-directed monoclonal antibodies share germline antibody genes (IGHV1-69 and IGKV3-20) and form a bNAb epitope class. Furthermore, convergent evolution within these two lineages towards a 111.2GW111.3 motif in the CDRH3 is known to enhance neutralization potency. We have previously isolated an MPER neutralizing antibody, CAP206-CH12, that uses these same germline heavy and light chain genes but lacks breadth (neutralizing only 6% of heterologous viruses). Longitudinal sequencing of the CAP206-CH12 lineage over three years revealed similar convergent evolution towards 111.2GW111.3 among some lineage members. Mutagenesis of CAP206-CH12 from 111.2GL111.3 to 111.2GW111.3 and the introduction of the double GWGW motif into CAP206-CH12 modestly improved neutralization potency (2.5–3-fold) but did not reach the levels of potency of VRC42.01, 4E10 or PGZL1. To explore the lack of potency/breadth, viral mutagenesis was performed to map the CAP206-CH12 epitope. This indicated that CAP206-CH12 is dependent on D674, a highly variable residue at the solvent-exposed elbow of MPER. In contrast, VRC42.01, PGZL1 and 4E10 were dependent on highly conserved residues (W672, F673, T676, and W680) facing the hydrophobic patch of the MPER. Therefore, while CAP206-CH12, VRC42.01, PGZL1 and 4E10 share germline genes and show some evidence of convergent evolution, their dependence on different amino acids, which impacts orientation of binding to the MPER, result in differences in breadth and potency. These data have implications for the design of HIV vaccines directed at the MPER epitope. Germline-targeting immunogens are a promising HIV vaccine design strategy. This approach is reliant on the identification of broadly neutralizing antibody (bNAb) classes, which use the same germline antibody genes to target the same viral epitopes. Here, we compare four HIV Envelope MPER-directed antibodies (4E10, VRC42.01, PGZL1 and CAP206-CH12) that despite having shared antibody genes, show distinct neutralization profiles. We show that CAP206-CH12 is dependent on a highly variable residue in the MPER, which results in low neutralization breadth. In contrast, the 4E10, PGZL1 and VRC42.01 mAbs are dependent on highly conserved residues in the MPER, resulting in exceptional neutralization breadth. Our data suggest that while shared germline genes within bNAb epitope classes are required, in some cases these are not sufficient to produce neutralization breadth, and MPER immunogens will need to trigger responses to conserved sites.
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Affiliation(s)
- Cathrine Scheepers
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Prudence Kgagudi
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Nonkululeko Mzindle
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Elin S. Gray
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Bronwen E. Lambson
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Brent Oosthuysen
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Batsirai Mabvakure
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Nigel J. Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal, South Africa
| | - Salim S. Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal, South Africa
- Department of Epidemiology, Columbia University, New York City, New York, United States of America
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal, South Africa
- * E-mail: (LM); (PLM)
| | - Penny L. Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- SA MRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- * E-mail: (LM); (PLM)
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23
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Grace BE, Backlund CM, Morgan DM, Kang BH, Singh NK, Huisman BD, Rappazzo CG, Moynihan KD, Maiorino L, Dobson CS, Kyung T, Gordon KS, Holec PV, Mbah OCT, Garafola D, Wu S, Love JC, Wittrup KD, Irvine DJ, Birnbaum ME. Identification of Highly Cross-Reactive Mimotopes for a Public T Cell Response in Murine Melanoma. Front Immunol 2022; 13:886683. [PMID: 35812387 PMCID: PMC9260506 DOI: 10.3389/fimmu.2022.886683] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022] Open
Abstract
While immune checkpoint blockade results in durable responses for some patients, many others have not experienced such benefits. These treatments rely upon reinvigorating specific T cell-antigen interactions. However, it is often unknown what antigens are being recognized by T cells or how to potently induce antigen-specific responses in a broadly applicable manner. Here, we characterized the CD8+ T cell response to a murine model of melanoma following combination immunotherapy to determine the basis of tumor recognition. Sequencing of tumor-infiltrating T cells revealed a repertoire of highly homologous TCR sequences that were particularly expanded in treated mice and which recognized an antigen from an endogenous retrovirus. While vaccination against this peptide failed to raise a protective T cell response in vivo, engineered antigen mimotopes induced a significant expansion of CD8+ T cells cross-reactive to the original antigen. Vaccination with mimotopes resulted in killing of antigen-loaded cells in vivo yet showed modest survival benefit in a prophylactic vaccine paradigm. Together, this work demonstrates the identification of a dominant tumor-associated antigen and generation of mimotopes which can induce robust functional T cell responses that are cross-reactive to the endogenous antigen across multiple individuals.
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Affiliation(s)
- Beth E. Grace
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Coralie M. Backlund
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Duncan M. Morgan
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Byong H. Kang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Nishant K. Singh
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Brooke D. Huisman
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - C. Garrett Rappazzo
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Kelly D. Moynihan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Laura Maiorino
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Connor S. Dobson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Taeyoon Kyung
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Khloe S. Gordon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Patrick V. Holec
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | - Daniel Garafola
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Shengwei Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - J. Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - K. Dane Wittrup
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Darrell J. Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
| | - Michael E. Birnbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, United States
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, United States
- *Correspondence: Michael E. Birnbaum,
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24
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Bunnoy A, Na-Nakorn U, Srisapoome P. Mystifying Molecular Structure, Expression and Repertoire Diversity of IgM Heavy Chain Genes (Ighμ) in Clarias Catfish and Hybrids: Two Novel Transcripts in Vertebrates. Front Immunol 2022; 13:884434. [PMID: 35784299 PMCID: PMC9247300 DOI: 10.3389/fimmu.2022.884434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
Two novel immunoglobulin heavy chain (Ighμ) transcripts encoding membrane-bound forms of IgM (mIgM) were discovered in bighead catfish, Clarias macrocephalus. The first transcript contains four constant and two transmembrane domains [Cμ1-Cμ2-Cμ3-Cμ4-TM1-TM2] that have never been reported in teleosts, and the second transcript is an unusual mIgM that has never been identified in any vertebrate [Cμ1-(Cδ2-Cδ3-Cδ4-Cδ5)-Cμ2-Cμ3-TM1-TM2]. Fluorescence in situ hybridization (FISH) in bighead catfish, North African catfish (C. gariepinus) and hybrid catfish revealed a single copy of Ighμ in individual parent catfish, while two gene copies were found in diploid hybrid catfish. Intensive sequence analysis demonstrated multiple distinct structural variabilities in the VH domain in Clarias, and hybrid catfish were defined and used to generate diversity with various mechanisms. Expression analysis of Ighμ in Aeromonas hydrophila infection of the head kidney, peripheral blood leukocytes and spleen revealed significantly higher levels in North African catfish and hybrid catfish than in bighead catfish.
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Affiliation(s)
- Anurak Bunnoy
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Uthairat Na-Nakorn
- Laboratory of Aquatic Animal Genetics, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Prapansak Srisapoome
- Laboratory of Aquatic Animal Health Management, Department of Aquaculture, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- Center of Excellence in Aquatic Animal Health Management, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
- *Correspondence: Prapansak Srisapoome,
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25
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Worth AN, Palmer VL, Schabla NM, Perry GA, Fraser-Philbin AN, Swanson PC. Receptor editing constrains development of phosphatidyl choline-specific B cells in V H12-transgenic mice. Cell Rep 2022; 39:110899. [PMID: 35705027 DOI: 10.1016/j.celrep.2022.110899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/22/2022] [Accepted: 05/10/2022] [Indexed: 11/03/2022] Open
Abstract
B1 B cells reactive to phosphatidyl choline (PtC) exhibit restricted immunoglobulin heavy chain (HC) and light chain (LC) combinations, exemplified by VH12/Vκ4/5H. Two checkpoints are thought to focus PtC+ B cell maturation in VH12-transgenic mice (VH12 mice): V-J rearrangements encoding a "permissive" LC capable of VH12 HC pairing are selected first, followed by positive selection based on PtC binding, often requiring LC receptor editing to salvage PtC- B cells and acquire PtC reactivity. However, evidence obtained from breeding VH12 mice to editing-defective dnRAG1 mice and analyzing LC sequences from PtC+ and PtC- B cell subsets instead suggests that receptor editing functions after initial positive selection to remove PtC+ B cells in VH12 mice. This offers a mechanism to constrain natural, polyreactive B cells to limit their frequency. Sequencing also reveals occasional in-frame hybrid LC genes, reminiscent of type 2 gene replacement, that, testing suggests, arise via a recombination-activating gene (RAG)-independent mechanism.
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Affiliation(s)
- Alexandra N Worth
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Victoria L Palmer
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - N Max Schabla
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; Shoreline Biosciences, San Diego, CA 92121, USA
| | - Greg A Perry
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Anna N Fraser-Philbin
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Patrick C Swanson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA.
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26
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Galigalidou C, Zaragoza-Infante L, Chatzidimitriou A, Stamatopoulos K, Psomopoulos F, Agathangelidis A. Purpose-Built Immunoinformatics for BcR IG/TR Repertoire Data Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:585-603. [PMID: 35622343 DOI: 10.1007/978-1-0716-2115-8_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The study of antigen receptor gene repertoires using next-generation sequencing (NGS) technologies has disclosed an unprecedented depth of complexity, requiring novel computational and analytical solutions. Several bioinformatics workflows have been developed to this end, including the T-cell receptor/immunoglobulin profiler (TRIP), a web application implemented in R shiny, specifically designed for the purposes of comprehensive repertoire analysis, which is the focus of this chapter. TRIP has the potential to perform robust immunoprofiling analysis through the extraction and processing of the IMGT/HighV-Quest output, via a series of functions, ensuring the analysis of high-quality, biologically relevant data through a multilevel process of data filtering. Subsequently, it provides in-depth analysis of antigen receptor gene rearrangements, including (a) clonality assessment; (b) extraction of variable (V), diversity (D), and joining (J) gene repertoires; (c) CDR3 characterization at both the nucleotide and amino acid level; and (d) somatic hypermutation analysis, in the case of immunoglobulin gene rearrangements. Relevant to mention, TRIP enables a high level of customization through the integration of various options in key aspects of the analysis, such as clonotype definition and computation, hence allowing for flexibility without compromising on accuracy.
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Affiliation(s)
- Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Biology and Genetics (MBG), Democritus University of Thrace, Alexandroupolis, Greece
| | - Laura Zaragoza-Infante
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,First Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece. .,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
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Lefranc MP, Lefranc G. IMGT/3Dstructure-DB: T-Cell Receptor TR Paratope and Peptide/Major Histocompatibility pMH Contact Sites and Epitope. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:533-570. [PMID: 35622341 DOI: 10.1007/978-1-0716-2115-8_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
T-cell receptors (TR), the antigen receptors of T cells, specifically recognize peptides presented by the major histocompatibility (MH) proteins, as peptide/MH (pMH), on the cell surface. The structure characterization of the trimolecular TR/pMH complexes is crucial to the fields of immunology, vaccination, and immunotherapy. IMGT/3Dstructure-DB is the three-dimensional (3-D) structure database of IMGT®, the international ImMunoGenetics information system®. By its creation, IMGT® marks the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. The IMGT® immunoglobulin (IG) and TR gene and allele nomenclature (CLASSIFICATION axiom) and the IMGT unique numbering and IMGT/Collier-de-Perles (NUMEROTATION axiom) are the two founding breakthroughs of immunoinformatics. IMGT-ONTOLOGY concepts and IMGT Scientific chart rules generated from these axioms allowed IMGT® bridging genes, structures, and functions. IMGT/3Dstructure-DB contains 3-D structures of IG or antibodies, TR and MH proteins of the adaptive immune responses of jawed vertebrates (gnathostomata), IG or TR complexes with antigens (IG/Ag, TR/pMH), related proteins of the immune system of any species belonging to the IG and MH superfamilies, and fusion proteins for immune applications. The focus of this chapter is on the TR V domains and MH G domains and the contact analysis comparison in TR/pMH interactions. Standardized molecular characterization includes "IMGT pMH contact sites" for peptide and MH groove interactions and "IMGT paratopes and epitopes" for TR/pMH complexes. Data are available in the IMGT/3Dstructure database, at the IMGT Home page http://www.imgt.org .
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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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28
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Teng YHF, Quah HS, Suteja L, Dias JML, Mupo A, Bashford-Rogers RJM, Vassiliou GS, Chua MLK, Tan DSW, Lim DWT, Iyer NG. Analysis of T cell receptor clonotypes in tumor microenvironment identifies shared cancer-type-specific signatures. Cancer Immunol Immunother 2022; 71:989-998. [PMID: 34580764 PMCID: PMC8476067 DOI: 10.1007/s00262-021-03047-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 08/25/2021] [Indexed: 12/02/2022]
Abstract
Despite the conventional view that a truly random V(D)J recombination process should generate a highly diverse immune repertoire, emerging reports suggest that there is a certain bias toward the generation of shared/public immune receptor chains. These studies were performed in viral diseases where public T cell receptors (TCR) appear to confer better protective responses. Selective pressures generating common TCR clonotypes are currently not well understood, but it is believed that they confer a growth advantage. As very little is known about public TCR clonotypes in cancer, here we set out to determine the extent of shared TCR clonotypes in the intra-tumor microenvironments of virus- and non-virus-driven head and neck cancers using TCR sequencing. We report that tumor-infiltrating T cell clonotypes were indeed shared across individuals with the same cancer type, where the majority of shared sequences were specific to the cancer type (i.e., viral versus non-viral). These shared clonotypes were not particularly enriched in EBV-associated nasopharynx cancer but, in both cancers, exhibited distinct characteristics, namely shorter CDR3 lengths, restricted V- and J-gene usages, and also demonstrated convergent V(D)J recombination. Many of these shared TCRs were expressed in patients with a shared HLA background. Pattern recognition of CDR3 amino acid sequences revealed strong convergence to specific pattern motifs, and these motifs were uniquely found to each cancer type. This suggests that they may be enriched for specificity to common antigens found in the tumor microenvironment of different cancers. The identification of shared TCRs in infiltrating tumor T cells not only adds to our understanding of the tumor-adaptive immune recognition but could also serve as disease-specific biomarkers and guide the development of future immunotherapies.
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Affiliation(s)
- Yvonne H. F. Teng
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Hong Sheng Quah
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Lisda Suteja
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - João M. L. Dias
- Hutchison/MRC Research Centre, MRC Cancer Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ UK
| | | | | | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge Biomedical Campus, Puddicombe Way, Cambridge, CB2 0AW UK
| | - Melvin L. K. Chua
- Duke-NUS Medical School, Singapore, Singapore
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Daniel S. W. Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Darren W. T. Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Institute of Molecular and Cell Biology, A-STAR, Singapore, Singapore
| | - N. Gopalakrishna Iyer
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 11 Hospital Crescent, Singapore, 169610 Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Department of Head and Neck Surgery, National Cancer Centre Singapore, Singapore, Singapore
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29
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Hanke L, Sheward DJ, Pankow A, Vidakovics LP, Karl V, Kim C, Urgard E, Smith NL, Astorga-Wells J, Ekström S, Coquet JM, McInerney GM, Murrell B. Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies. SCIENCE ADVANCES 2022; 8:eabm0220. [PMID: 35333580 PMCID: PMC8956255 DOI: 10.1126/sciadv.abm0220] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Conventional approaches to isolate and characterize nanobodies are laborious. We combine phage display, multivariate enrichment, next-generation sequencing, and a streamlined screening strategy to identify numerous anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nanobodies. We characterize their potency and specificity using neutralization assays and hydrogen/deuterium exchange mass spectrometry (HDX-MS). The most potent nanobodies bind to the receptor binding motif of the receptor binding domain (RBD), and we identify two exceptionally potent members of this category (with monomeric half-maximal inhibitory concentrations around 13 and 16 ng/ml). Other nanobodies bind to a more conserved epitope on the side of the RBD and are able to potently neutralize the SARS-CoV-2 founder virus (42 ng/ml), the Beta variant (B.1.351/501Y.V2) (35 ng/ml), and also cross-neutralize the more distantly related SARS-CoV-1 (0.46 μg/ml). The approach presented here is well suited for the screening of phage libraries to identify functional nanobodies for various biomedical and biochemical applications.
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Affiliation(s)
- Leo Hanke
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Daniel J. Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Division of Medical Virology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Alec Pankow
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura Perez Vidakovics
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Vivien Karl
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Changil Kim
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Egon Urgard
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Natalie L. Smith
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Juan Astorga-Wells
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Simon Ekström
- Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
| | - Jonathan M. Coquet
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Gerald M. McInerney
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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30
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Al-Diwani A, Theorell J, Damato V, Bull J, McGlashan N, Green E, Kienzler AK, Harrison R, Hassanali T, Campo L, Browne M, Easton A, Soleymani majd H, Tenaka K, Iorio R, Dale RC, Harrison P, Geddes J, Quested D, Sharp D, Lee ST, Nauen DW, Makuch M, Lennox B, Fowler D, Sheerin F, Waters P, Leite MI, Handel AE, Irani SR. Cervical lymph nodes and ovarian teratomas as germinal centres in NMDA receptor-antibody encephalitis. Brain 2022; 145:2742-2754. [PMID: 35680425 PMCID: PMC9486890 DOI: 10.1093/brain/awac088] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/22/2021] [Accepted: 01/24/2022] [Indexed: 01/14/2023] Open
Abstract
Autoantibodies against the extracellular domain of the N-methyl-d-aspartate receptor (NMDAR) NR1 subunit cause a severe and common form of encephalitis. To better understand their generation, we aimed to characterize and identify human germinal centres actively participating in NMDAR-specific autoimmunization by sampling patient blood, CSF, ovarian teratoma tissue and, directly from the putative site of human CNS lymphatic drainage, cervical lymph nodes. From serum, both NR1-IgA and NR1-IgM were detected more frequently in NMDAR-antibody encephalitis patients versus controls (both P < 0.0001). Within patients, ovarian teratoma status was associated with a higher frequency of NR1-IgA positivity in serum (OR = 3.1; P < 0.0001) and CSF (OR = 3.8, P = 0.047), particularly early in disease and before ovarian teratoma resection. Consistent with this immunoglobulin class bias, ovarian teratoma samples showed intratumoral production of both NR1-IgG and NR1-IgA and, by single cell RNA sequencing, contained expanded highly-mutated IgA clones with an ovarian teratoma-restricted B cell population. Multiplex histology suggested tertiary lymphoid architectures in ovarian teratomas with dense B cell foci expressing the germinal centre marker BCL6, CD21+ follicular dendritic cells, and the NR1 subunit, alongside lymphatic vessels and high endothelial vasculature. Cultured teratoma explants and dissociated intratumoral B cells secreted NR1-IgGs in culture. Hence, ovarian teratomas showed structural and functional evidence of NR1-specific germinal centres. On exploring classical secondary lymphoid organs, B cells cultured from cervical lymph nodes of patients with NMDAR-antibody encephalitis produced NR1-IgG in 3/7 cultures, from patients with the highest serum NR1-IgG levels (P < 0.05). By contrast, NR1-IgG secretion was observed neither from cervical lymph nodes in disease controls nor in patients with adequately resected ovarian teratomas. Our multimodal evaluations provide convergent anatomical and functional evidence of NMDAR-autoantibody production from active germinal centres within both intratumoral tertiary lymphoid structures and traditional secondary lymphoid organs, the cervical lymph nodes. Furthermore, we develop a cervical lymph node sampling protocol that can be used to directly explore immune activity in health and disease at this emerging neuroimmune interface.
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Affiliation(s)
- Adam Al-Diwani
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK,University Department of Psychiatry, University of Oxford, Oxford, UK
| | - Jakob Theorell
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK,Department of Clinical Neurosciences, Karolinska Institutet, Stockholm, Sweden
| | - Valentina Damato
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK,UOC Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Joshua Bull
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, UK
| | - Nicholas McGlashan
- Department of Radiology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, UK
| | - Edward Green
- Department of Radiology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, UK
| | - Anne Kathrin Kienzler
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Ruby Harrison
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Tasneem Hassanali
- Translational Histopathology Laboratory, Department of Oncology, University of Oxford, Oxford, UK
| | - Leticia Campo
- Translational Histopathology Laboratory, Department of Oncology, University of Oxford, Oxford, UK
| | - Molly Browne
- Translational Histopathology Laboratory, Department of Oncology, University of Oxford, Oxford, UK
| | - Alistair Easton
- Translational Histopathology Laboratory, Department of Oncology, University of Oxford, Oxford, UK
| | | | - Keiko Tenaka
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Raffaele Iorio
- UOC Neurologia, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy,Università Cattolica del Sacro Cuore, Rome, Italy
| | - Russell C Dale
- Kids Neuroscience Centre, Children’s Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Paul Harrison
- University Department of Psychiatry, University of Oxford, Oxford, UK
| | - John Geddes
- University Department of Psychiatry, University of Oxford, Oxford, UK
| | - Digby Quested
- University Department of Psychiatry, University of Oxford, Oxford, UK
| | - David Sharp
- Computational, Cognitive and Clinical Neuroimaging Laboratory, Division of Brain Sciences, Imperial College London, London, UK
| | - Soon Tae Lee
- Department of Neurology, Seoul National University Hospital, Seoul, South Korea
| | - David W Nauen
- Department of Pathology, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Mateusz Makuch
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Belinda Lennox
- University Department of Psychiatry, University of Oxford, Oxford, UK
| | - Darren Fowler
- Department of Pathology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, UK
| | - Fintan Sheerin
- Department of Radiology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, UK
| | - Patrick Waters
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - M Isabel Leite
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK,Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, UK
| | - Adam E Handel
- Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK,Department of Neurology, John Radcliffe Hospital, Oxford University Hospitals, Oxford, UK
| | - Sarosh R Irani
- Correspondence to: Professor Sarosh Irani Oxford Autoimmune Neurology Group West Wing, Level 6, John Radcliffe Hospital Oxford OX3 9DU, UK E-mail:
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31
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Chang AJ, Baron S, Hoffman J, Hicar MD. Clonal expansion and markers of directed mutation of IGHV4-34 B cells in plasmablasts during Kawasaki disease. Mol Immunol 2022; 145:67-77. [PMID: 35303530 PMCID: PMC9166636 DOI: 10.1016/j.molimm.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/18/2022] [Accepted: 03/06/2022] [Indexed: 11/26/2022]
Abstract
Kawasaki disease (KD) is the leading cause of acquired heart disease in children. The cause remains unknown; however, epidemiologic and demographic data support a single preceding infectious agent may lead to KD. A variety of pathophysiologic responses have been proposed, including direct invasion of the coronary arteries, a superantigen response, and a post-infectious autoimmune phenomenon. A role for B cell responses during KD are supported by numerous findings including B cell specific markers identified in genome wide association studies. We have recently published data showing children with KD have similar plasmablast (PB) responses to children with infections. Since during other infections, cells expressing antibodies against the preceding infection are enriched in PBs, we sought to explore the specific antibodies encoded by PBs during KD. In one child we see a massive expansion in IGHV4-34 utilizing antibodies, which has been associated with autoimmunity in the past. We further explored this expansion of IGHV4-34 utilization during the peripheral PB rise with next generation sequencing (NGS) analysis and utilizing newer techniques of chromium chip single cell separation (10x Genomics®). We also utilized peptide array screening to attempt to identify an antigen to the most prolific clones.
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Affiliation(s)
| | - Sarah Baron
- University at Buffalo, Department of Pediatrics, USA
| | | | - Mark D Hicar
- University at Buffalo, Department of Pediatrics, USA.
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32
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Lefranc MP, Lefranc G. IMGT ®Homo sapiens IG and TR Loci, Gene Order, CNV and Haplotypes: New Concepts as a Paradigm for Jawed Vertebrates Genome Assemblies. Biomolecules 2022; 12:381. [PMID: 35327572 PMCID: PMC8945572 DOI: 10.3390/biom12030381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 02/04/2023] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®, created in 1989, by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science which emerged at the interface between immunogenetics and bioinformatics for the study of the adaptive immune responses. IMGT® is based on a standardized nomenclature of the immunoglobulin (IG) and T cell receptor (TR) genes and alleles from fish to humans and on the IMGT unique numbering for the variable (V) and constant (C) domains of the immunoglobulin superfamily (IgSF) of vertebrates and invertebrates, and for the groove (G) domain of the major histocompatibility (MH) and MH superfamily (MhSF) proteins. IMGT® comprises 7 databases, 17 tools and more than 25,000 pages of web resources for sequences, genes and structures, based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts. IMGT® reference directories are used for the analysis of the NGS high-throughput expressed IG and TR repertoires (natural, synthetic and/or bioengineered) and for bridging sequences, two-dimensional (2D) and three-dimensional (3D) structures. This manuscript focuses on the IMGT®Homo sapiens IG and TR loci, gene order, copy number variation (CNV) and haplotypes new concepts, as a paradigm for jawed vertebrates genome assemblies.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d’Immuno Génétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), UMR 9002 CNRS-UM, 141 rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
| | - Gérard Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d’Immuno Génétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), UMR 9002 CNRS-UM, 141 rue de la Cardonille, CEDEX 5, 34396 Montpellier, France
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33
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Tian G, Li M, Lv G. Analysis of T-Cell Receptor Repertoire in Transplantation: Fingerprint of T Cell-mediated Alloresponse. Front Immunol 2022; 12:778559. [PMID: 35095851 PMCID: PMC8790170 DOI: 10.3389/fimmu.2021.778559] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
T cells play a key role in determining allograft function by mediating allogeneic immune responses to cause rejection, and recent work pointed their role in mediating tolerance in transplantation. The unique T-cell receptor (TCR) expressed on the surface of each T cell determines the antigen specificity of the cell and can be the specific fingerprint for identifying and monitoring. Next-generation sequencing (NGS) techniques provide powerful tools for deep and high-throughput TCR profiling, and facilitate to depict the entire T cell repertoire profile and trace antigen-specific T cells in circulation and local tissues. Tailing T cell transcriptomes and TCR sequences at the single cell level provides a full landscape of alloreactive T-cell clones development and biofunction in alloresponse. Here, we review the recent advances in TCR sequencing techniques and computational tools, as well as the recent discovery in overall TCR profile and antigen-specific T cells tracking in transplantation. We further discuss the challenges and potential of using TCR sequencing-based assays to profile alloreactive TCR repertoire as the fingerprint for immune monitoring and prediction of rejection and tolerance.
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Affiliation(s)
| | - Mingqian Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
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34
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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: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [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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35
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Wang Y, Mai G, Zou M, Long H, Chen YQ, Sun L, Tian D, Zhao Y, Jiang G, Cao Z, Du X. Heavy chain sequence-based classifier for the specificity of human antibodies. Brief Bioinform 2021; 23:6483065. [PMID: 34953464 DOI: 10.1093/bib/bbab516] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/07/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Antibodies specifically bind to antigens and are an essential part of the immune system. Hence, antibodies are powerful tools in research and diagnostics. High-throughput sequencing technologies have promoted comprehensive profiling of the immune repertoire, which has resulted in large amounts of antibody sequences that remain to be further analyzed. In this study, antibodies were downloaded from IMGT/LIGM-DB and Sequence Read Archive databases. Contributing features from antibody heavy chains were formulated as numerical inputs and fed into an ensemble machine learning classifier to classify the antigen specificity of six classes of antibodies, namely anti-HIV-1, anti-influenza virus, anti-pneumococcal polysaccharide, anti-citrullinated protein, anti-tetanus toxoid and anti-hepatitis B virus. The classifier was validated using cross-validation and a testing dataset. The ensemble classifier achieved a macro-average area under the receiver operating characteristic curve (AUC) of 0.9246 from the 10-fold cross-validation, and 0.9264 for the testing dataset. Among the contributing features, the contribution of the complementarity-determining regions was 53.1% and that of framework regions was 46.9%, and the amino acid mutation rates occupied the first and second ranks among the top five contributing features. The classifier and insights provided in this study could promote the mechanistic study, isolation and utilization of potential therapeutic antibodies.
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Affiliation(s)
- Yaqi Wang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Guoqin Mai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Min Zou
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Haoyu Long
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Litao Sun
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Dechao Tian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Yang Zhao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Guozhi Jiang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Zicheng Cao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China
| | - Xiangjun Du
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, P.R. China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou 510275, P.R. China.,Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, 510030, P.R. China
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36
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Manso T, Folch G, Giudicelli V, Jabado-Michaloud J, Kushwaha A, Nguefack Ngoune V, Georga M, Papadaki A, Debbagh C, Pégorier P, Bertignac M, Hadi-Saljoqi S, Chentli I, Cherouali K, Aouinti S, El Hamwi A, Albani A, Elazami Elhassani M, Viart B, Goret A, Tran A, Sanou G, Rollin M, Duroux P, Kossida S. IMGT® databases, related tools and web resources through three main axes of research and development. Nucleic Acids Res 2021; 50:D1262-D1272. [PMID: 34875068 PMCID: PMC8728119 DOI: 10.1093/nar/gkab1136] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/26/2021] [Accepted: 11/28/2021] [Indexed: 11/15/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org/, is at the forefront of the immunogenetics and immunoinformatics fields with more than 30 years of experience. IMGT® makes available databases and tools to the scientific community pertaining to the adaptive immune response, based on the IMGT-ONTOLOGY. We focus on the recent features of the IMGT® databases, tools, reference directories and web resources, within the three main axes of IMGT® research and development. Axis I consists in understanding the adaptive immune response, by deciphering the identification and characterization of the immunoglobulin (IG) and T cell receptor (TR) genes in jawed vertebrates. It is the starting point of the two other axes, namely the analysis and exploration of the expressed IG and TR repertoires based on comparison with IMGT reference directories in normal and pathological situations (Axis II) and the analysis of amino acid changes and functions of 2D and 3D structures of antibody and TR engineering (Axis III).
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Affiliation(s)
- Taciana Manso
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Géraldine Folch
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Joumana Jabado-Michaloud
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Anjana Kushwaha
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Viviane Nguefack Ngoune
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Maria Georga
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Ariadni Papadaki
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Chahrazed Debbagh
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Perrine Pégorier
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Morgane Bertignac
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Saida Hadi-Saljoqi
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Imène Chentli
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Karima Cherouali
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Safa Aouinti
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Amar El Hamwi
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Alexandre Albani
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Merouane Elazami Elhassani
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Benjamin Viart
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Agathe Goret
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Anna Tran
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Gaoussou Sanou
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Maël Rollin
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Patrice Duroux
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
| | - Sofia Kossida
- IMGT®, the international ImMunoGeneTics Information System®, Scientific Research National Center (CNRS), Institute of Human Genetics (IGH), University of Montpellier (UM), Montpellier, France
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Porritt RA, Binek A, Paschold L, Rivas MN, McArdle A, Yonker LM, Alter G, Chandnani HK, Lopez M, Fasano A, Van Eyk JE, Binder M, Arditi M. The autoimmune signature of hyperinflammatory multisystem inflammatory syndrome in children. J Clin Invest 2021; 131:e151520. [PMID: 34437303 PMCID: PMC8516454 DOI: 10.1172/jci151520] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
Multisystem inflammatory syndrome in children (MIS-C) manifests as a severe and uncontrolled inflammatory response with multiorgan involvement, occurring weeks after SARS-CoV-2 infection. Here, we utilized proteomics, RNA sequencing, autoantibody arrays, and B cell receptor (BCR) repertoire analysis to characterize MIS-C immunopathogenesis and identify factors contributing to severe manifestations and intensive care unit admission. Inflammation markers, humoral immune responses, neutrophil activation, and complement and coagulation pathways were highly enriched in MIS-C patient serum, with a more hyperinflammatory profile in severe than in mild MIS-C cases. We identified a strong autoimmune signature in MIS-C, with autoantibodies targeted to both ubiquitously expressed and tissue-specific antigens, suggesting autoantigen release and excessive antigenic drive may result from systemic tissue damage. We further identified a cluster of patients with enhanced neutrophil responses as well as high anti-Spike IgG and autoantibody titers. BCR sequencing of these patients identified a strong imprint of antigenic drive with substantial BCR sequence connectivity and usage of autoimmunity-associated immunoglobulin heavy chain variable region (IGHV) genes. This cluster was linked to a TRBV11-2 expanded T cell receptor (TCR) repertoire, consistent with previous studies indicating a superantigen-driven pathogenic process. Overall, we identify a combination of pathogenic pathways that culminate in MIS-C and may inform treatment.
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Affiliation(s)
- Rebecca A. Porritt
- Departments of Pediatrics, Division of Infectious Diseases and Immunology, and Infectious and Immunologic Diseases Research Center (IIDRC), Department of Biomedical Sciences and
| | - Aleksandra Binek
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lisa Paschold
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Magali Noval Rivas
- Departments of Pediatrics, Division of Infectious Diseases and Immunology, and Infectious and Immunologic Diseases Research Center (IIDRC), Department of Biomedical Sciences and
| | - Angela McArdle
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lael M. Yonker
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center and Department of Pediatrics, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Galit Alter
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center and Department of Pediatrics, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Ragon Institute of MIT, MGH and Harvard, Cambridge, Massachusetts, USA
| | | | - Merrick Lopez
- Department of Pediatrics, Loma Linda University Hospital, California, USA
| | - Alessio Fasano
- Massachusetts General Hospital, Mucosal Immunology and Biology Research Center and Department of Pediatrics, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Barbra Streisand Women’s Heart Center, Cedars-Sinai Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Mascha Binder
- Department of Internal Medicine IV, Oncology/Hematology, Martin-Luther-University Halle-Wittenberg, Halle (Saale), Germany
| | - Moshe Arditi
- Departments of Pediatrics, Division of Infectious Diseases and Immunology, and Infectious and Immunologic Diseases Research Center (IIDRC), Department of Biomedical Sciences and
- Cedars-Sinai Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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38
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Next Generation Sequencing of Cerebrospinal Fluid B Cell Repertoires in Multiple Sclerosis and Other Neuro-Inflammatory Diseases-A Comprehensive Review. Diagnostics (Basel) 2021; 11:diagnostics11101871. [PMID: 34679570 PMCID: PMC8534365 DOI: 10.3390/diagnostics11101871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022] Open
Abstract
During the last few decades, the role of B cells has been well established and redefined in neuro-inflammatory diseases, including multiple sclerosis and autoantibody-associated diseases. In particular, B cell maturation and trafficking across the blood–brain barrier (BBB) has recently been deciphered with the development of next-generation sequencing (NGS) approaches, which allow the assessment of representative cerebrospinal fluid (CSF) and peripheral blood B cell repertoires. In this review, we perform literature research focusing on NGS studies that allow further insights into B cell pathophysiology during neuro-inflammation. Besides the analysis of CSF B cells, the paralleled assessment of peripheral blood B cell repertoire provides deep insights into not only the CSF compartment, but also in B cell trafficking patterns across the BBB. In multiple sclerosis, CSF-specific B cell maturation, in combination with a bidirectional exchange of B cells across the BBB, is consistently detectable. These data suggest that B cells most likely encounter antigen(s) within the CSF and migrate across the BBB, with further maturation also taking place in the periphery. Autoantibody-mediated diseases, such as neuromyelitis optica spectrum disorder and LGI1 / NMDAR encephalitis, also show features of a CSF-specific B cell maturation and clonal connectivity with peripheral blood. In conclusion, these data suggest an intense exchange of B cells across the BBB, possibly feeding autoimmune circuits. Further developments in sequencing technologies will help to dissect the exact pathophysiologic mechanisms of B cells during neuro-inflammation.
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Zhang Y, Yang X, Zhang Y, Zhang Y, Wang M, Ou JX, Zhu Y, Zeng H, Wu J, Lan C, Zhou HW, Yang W, Zhang Z. Tools for fundamental analysis functions of TCR repertoires: a systematic comparison. Brief Bioinform 2021; 21:1706-1716. [PMID: 31624828 PMCID: PMC7947996 DOI: 10.1093/bib/bbz092] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 12/30/2022] Open
Abstract
The full set of T cell receptors (TCRs) in an individual is known as his or her TCR repertoire. Defining TCR repertoires under physiological conditions and in response to a disease or vaccine may lead to a better understanding of adaptive immunity and thus has great biological and clinical value. In the past decade, several high-throughput sequencing-based tools have been developed to assign TCRs to germline genes and to extract complementarity-determining region 3 (CDR3) sequences using different algorithms. Although these tools claim to be able to perform the full range of fundamental TCR repertoire analyses, there is no clear consensus of which tool is best suited to particular projects. Here, we present a systematic analysis of 12 available TCR repertoire analysis tools using simulated data, with an emphasis on fundamental analysis functions. Our results shed light on the detailed functions of TCR repertoire analysis tools and may therefore help researchers in the field to choose the right tools for their particular experimental design.
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Affiliation(s)
- Yanfang Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China.,Center for Precision Medicine, Shunde Hospital, Southern Medical University, Foshan, Guangdong, 528399, China
| | - Xiujia Yang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
| | - Yanxia Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yan Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Minhui Wang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Jin Xia Ou
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yan Zhu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huikun Zeng
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaqi Wu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Chunhong Lan
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China.,Center for Precision Medicine, Shunde Hospital, Southern Medical University, Foshan, Guangdong, 528399, China
| | - Hong-Wei Zhou
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Zhenhai Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China.,Center for Precision Medicine, Shunde Hospital, Southern Medical University, Foshan, Guangdong, 528399, China
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40
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Liu H, Pan W, Tang C, Tang Y, Wu H, Yoshimura A, Deng Y, He N, Li S. The methods and advances of adaptive immune receptors repertoire sequencing. Theranostics 2021; 11:8945-8963. [PMID: 34522220 PMCID: PMC8419057 DOI: 10.7150/thno.61390] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
The adaptive immune response is a powerful tool, capable of recognizing, binding to, and neutralizing a vast number of internal and external threats via T or B lymphatic receptors with widespread sets of antigen specificities. The emergence of high-throughput sequencing technology and bioinformatics provides opportunities for research in the fields of life sciences and medicine. The analysis and annotation for immune repertoire data can reveal biologically meaningful information, including immune prediction, target antigens, and effective evaluation. Continuous improvements of the immunological repertoire sequencing methods and analysis tools will help to minimize the experimental and calculation errors and realize the immunological information to meet the clinical requirements. That said, the clinical application of adaptive immune repertoire sequencing requires appropriate experimental methods and standard analytical tools. At the population cell level, we can acquire the overview of cell groups, but the information about a single cell is not obtained accurately. The information that is ignored may be crucial for understanding the heterogeneity of each cell, gene expression and drug response. The combination of high-throughput sequencing and single-cell technology allows us to obtain single-cell information with low-cost and high-throughput. In this review, we summarized the current methods and progress in this area.
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Affiliation(s)
- Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Congli Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Yujie Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hu-nan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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Zhan Q, Xu JH, Yu YY, Lo KK E, El-Nezami H, Zeng Z. Human immune repertoire in hepatitis B virus infection. World J Gastroenterol 2021; 27:3790-3801. [PMID: 34321844 PMCID: PMC8291018 DOI: 10.3748/wjg.v27.i25.3790] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/08/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatitis B virus (HBV) infection is a public health threat that affects 257 million people worldwide and can progress to liver cirrhosis, liver failure, and hepatocellular carcinoma. The HBV antigen- induced adaptive immune response plays an important role in HBV clearance. Immune repertoire sequencing (IRS) has been used to investigate the molecular mechanisms behind the immune system, find novel ways to treat HBV infection, and evaluate the genetic responses and immune characteristics of individuals infected by HBV or immunized by HBV vaccine. This review summarizes the human immune repertoire analysis methodology, and the application of the IRS in the prediction of HBV infection progression, treatment, and vaccination.
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Affiliation(s)
- Qiao Zhan
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China
| | - Jing-Hang Xu
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China
| | - Yan-Yan Yu
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China
| | - Emily Lo KK
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Felicianna
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Hani El-Nezami
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
- Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio FI-70211, Finland
| | - Zheng Zeng
- Department of Infectious Diseases, Peking University First Hospital, Beijing 100034, China
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Yermanos A, Agrafiotis A, Kuhn R, Robbiani D, Yates J, Papadopoulou C, Han J, Sandu I, Weber C, Bieberich F, Vazquez-Lombardi R, Dounas A, Neumeier D, Oxenius A, Reddy ST. Platypus: an open-access software for integrating lymphocyte single-cell immune repertoires with transcriptomes. NAR Genom Bioinform 2021; 3:lqab023. [PMID: 33884369 PMCID: PMC8046018 DOI: 10.1093/nargab/lqab023] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/05/2021] [Accepted: 03/17/2021] [Indexed: 12/12/2022] Open
Abstract
High-throughput single-cell sequencing (scSeq) technologies are revolutionizing the ability to molecularly profile B and T lymphocytes by offering the opportunity to simultaneously obtain information on adaptive immune receptor repertoires (VDJ repertoires) and transcriptomes. An integrated quantification of immune repertoire parameters, such as germline gene usage, clonal expansion, somatic hypermutation and transcriptional states opens up new possibilities for the high-resolution analysis of lymphocytes and the inference of antigen-specificity. While multiple tools now exist to investigate gene expression profiles from scSeq of transcriptomes, there is a lack of software dedicated to single-cell immune repertoires. Here, we present Platypus, an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. Platypus provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. To showcase the capabilities of Platypus, we use it to analyze and visualize single-cell immune repertoires and transcriptomes from B and T cells from convalescent COVID-19 patients, revealing unique insight into the repertoire features and transcriptional profiles of clonally expanded lymphocytes. Platypus will expedite progress by facilitating the analysis of single-cell immune repertoire and transcriptome sequencing.
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Affiliation(s)
- Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
- Department of Pathology and Immunology, University of Geneva, 1211 Geneva, Switzerland
| | - Andreas Agrafiotis
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Raphael Kuhn
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Damiano Robbiani
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Josephine Yates
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Chrysa Papadopoulou
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Ioana Sandu
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Cédric Weber
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Florian Bieberich
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | | | - Andreas Dounas
- Institute for Biomedical Engineering, University and ETH Zurich, 8092 Zurich, Switzerland
| | - Daniel Neumeier
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Annette Oxenius
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
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Li A, Thwaite R, Kellie S, Barnes AC. Serum IgM heavy chain sub-isotypes and light chain variants revealed in giant grouper (Epinephelus lanceolatus) via protein A affinity purification, mass spectrometry and genome sequencing. FISH & SHELLFISH IMMUNOLOGY 2021; 113:42-50. [PMID: 33794338 DOI: 10.1016/j.fsi.2021.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Two IgM heavy (H) chain sub-isotypes (80 and 40 kDa) and two light (L) chain variants (25 and 30 kDa) were detected in the serum of giant grouper (Epinephelus lanceolatus), purified by ammonium sulphate precipitation followed by protein A affinity chromatography. This method yielded 5.6 mg/mL high purity IgM from grouper serum, with efficiency estimated at 39.5% recovery from crude serum. The H and L chains were identified by SDS-PAGE and mass spectrometry (MS). Nanopore long-read sequencing was used to generate a genomic contig (MW768935), containing Cμ, Cδ loci, VH regions, and a H chain Joining segment. cDNA sequencing of Cμ transcripts (MW768933 and MW768934) were used to polish the genomic contig and determine the exons and introns of the corresponding locus. MS peptide mapping revealed that the 80 kDa H chain consisted of CH1-4 domains while peptides from the 40 kDa H chain only mapped to CH1-2 domains. Our genomic contig showed the Cμ locus has a Cμ1-Cμ2-Cμ3-Cμ4 arrangement on the same strand as the other Ig loci identified in this genomic sequence. Our study corrects the NCBI annotations of the opposing Cμ loci (LOC117268697 and LOC117268550) in chromosome 16 (NC_047006). Further, we identified both κ and λ L chain isotypes in serum IgM. The molecular weight differences observed may result from different combinations of CL and VL genes. Putative IgM sub-isotypes have also been reported in Epinephelus itajara and Epinephelus coioides. The presence of IgM sub-isotypes may be a conserved trait among Epinephelus species.
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Affiliation(s)
- Angus Li
- The University of Queensland, School of Biological Sciences, Australia
| | - Rosemary Thwaite
- The University of Queensland, School of Biological Sciences, Australia
| | - Stuart Kellie
- School of Chemistry and Molecular Biosciences, Brisbane, QLD4072, Australia
| | - Andrew C Barnes
- The University of Queensland, School of Biological Sciences, Australia.
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Trück J, Eugster A, Barennes P, Tipton CM, Luning Prak ET, Bagnara D, Soto C, Sherkow JS, Payne AS, Lefranc MP, Farmer A, Bostick M, Mariotti-Ferrandiz E. Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife 2021; 10:e66274. [PMID: 34037521 PMCID: PMC8154019 DOI: 10.7554/elife.66274] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/15/2021] [Indexed: 12/15/2022] Open
Abstract
Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community's Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work.
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Affiliation(s)
- Johannes Trück
- University Children’s Hospital and the Children’s Research Center, University of ZurichZurichSwitzerland
| | - Anne Eugster
- CRTD Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität DresdenDresdenGermany
| | - Pierre Barennes
- Sorbonne Université U959, Immunology-Immunopathology-Immunotherapy (i3)ParisFrance
- AP-HP Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi)ParisFrance
| | - Christopher M Tipton
- Lowance Center for Human Immunology, Emory University School of MedicineAtlantaUnited States
| | - Eline T Luning Prak
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Davide Bagnara
- University of Genoa, Department of Experimental MedicineGenoaItaly
| | - Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical CenterNashvilleUnited States
- Department of Pediatrics, Vanderbilt University Medical CenterNashvilleUnited States
| | - Jacob S Sherkow
- College of Law, University of IllinoisChampaignUnited States
- Center for Advanced Studies in Biomedical Innovation Law, University of Copenhagen Faculty of LawCopenhagenDenmark
- Carl R. Woese Institute for Genomic Biology, University of IllinoisUrbana, IllinoisUnited States
| | - Aimee S Payne
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of MontpellierMontpellierFrance
- Laboratoire d'ImmunoGénétique Moléculaire (LIGM) CNRS, University of MontpellierMontpellierFrance
- Institut de Génétique Humaine (IGH), CNRS, University of MontpellierMontpellierFrance
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Magadan S, Mondot S, Palti Y, Gao G, Lefranc MP, Boudinot P. Genomic analysis of a second rainbow trout line (Arlee) leads to an extended description of the IGH VDJ gene repertoire. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 118:103998. [PMID: 33450314 DOI: 10.1016/j.dci.2021.103998] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 01/07/2021] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
High-throughput sequencing technologies brought a renewed interest for immune repertoires. Fish Ab and B cell repertoires are no exception, and their comprehensive analysis can both provide new insights into poorly understood immune mechanisms, and identify markers of protection after vaccination. However, the lack of genomic description and standardized nomenclature of IG genes hampers accurate annotation of Ig mRNA deep sequencing data. Complete genome sequences of Atlantic salmon and rainbow trout (Swanson line) recently allowed us to establish a comprehensive and coherent annotation of Salmonid IGH genes following IMGT standards. Here we analyzed the IGHV, D, and J genes from the newly released genome of a second rainbow trout line (Arlee). We confirmed the validity of salmonid IGHV subgroups, and extended the description of the rainbow trout IGH gene repertoire with novel sequences, while keeping nomenclature continuity. This work provides an important resource for annotation of high-throughput Ab repertoire sequencing data.
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Affiliation(s)
- Susana Magadan
- Centro de Investigaciones Biomédicas, Universidade de Vigo, Campus Universitario Lagoas Marcosende, 36310, Vigo, Spain.
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Yniv Palti
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV, 25430, USA
| | - Guangtu Gao
- USDA-ARS National Center for Cool and Cold Water Aquaculture, 11861 Leetown Road, Kearneysville, WV, 25430, USA
| | - Marie Paule Lefranc
- IMGT®, The International ImMunoGeneTics Information System®, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UMR9002 CNRS, Université de Montpellier, Montpellier, France
| | - Pierre Boudinot
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France.
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Forgacs D, Abreu RB, Sautto GA, Kirchenbaum GA, Drabek E, Williamson KS, Kim D, Emerling DE, Ross TM. Convergent antibody evolution and clonotype expansion following influenza virus vaccination. PLoS One 2021; 16:e0247253. [PMID: 33617543 PMCID: PMC7899375 DOI: 10.1371/journal.pone.0247253] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/03/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in high-throughput single cell sequencing have opened up new avenues into the investigation of B cell receptor (BCR) repertoires. In this study, PBMCs were collected from 17 human participants vaccinated with the split-inactivated influenza virus vaccine during the 2016-2017 influenza season. A combination of Immune Repertoire Capture (IRCTM) technology and IgG sequencing was performed on ~7,800 plasmablast (PB) cells and preferential IgG heavy-light chain pairings were investigated. In some participants, a single expanded clonotype accounted for ~22% of their PB BCR repertoire. Approximately 60% (10/17) of participants experienced convergent evolution, possessing public PBs that were elicited independently in multiple participants. Binding profiles of one private and three public PBs confirmed they were all subtype-specific, cross-reactive hemagglutinin (HA) head-directed antibodies. Collectively, this high-resolution antibody repertoire analysis demonstrated the impact evolution can have on BCRs in response to influenza virus vaccination, which can guide future universal influenza prophylactic approaches.
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Affiliation(s)
- David Forgacs
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Rodrigo B. Abreu
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Giuseppe A. Sautto
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Greg A. Kirchenbaum
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Elliott Drabek
- Atreca, Inc., South San Francisco, CA, United States of America
| | | | - Dongkyoon Kim
- Atreca, Inc., South San Francisco, CA, United States of America
| | | | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- * E-mail:
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Genetic Bias, Diversity Indices, Physiochemical Properties and CDR3 Motifs Divide Auto-Reactive from Allo-Reactive T-Cell Repertoires. Int J Mol Sci 2021; 22:ijms22041625. [PMID: 33562731 PMCID: PMC7915266 DOI: 10.3390/ijms22041625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/30/2021] [Accepted: 01/31/2021] [Indexed: 12/26/2022] Open
Abstract
The distinct properties of allo-reactive T-cell repertoires are not well understood. To investigate whether auto-reactive and allo-reactive T-cell repertoires encoded distinct properties, we used dextramer enumeration, enrichment, single-cell T-cell receptor (TCR) sequencing and multiparameter analysis. We found auto-reactive and allo-reactive T-cells differed in mean ex vivo frequency which was antigen dependent. Allo-reactive T-cells showed clear differences in TCR architecture, with enriched usage of specific T-cell receptor variable (TRBJ) genes and broader use of T-cell receptor variable joining (TRBJ) genes. Auto-reactive T-cell repertoires exhibited complementary determining regions three (CDR3) lengths using a Gaussian distribution whereas allo-reactive T-cell repertoires exhibited distorted patterns in CDR3 length. CDR3 loops from allo-reactive T-cells showed distinct physical-chemical properties, tending to encode loops that were more acidic in charge. Allo-reactive T-cell repertoires differed in diversity metrics, tending to show increased overall diversity and increased homogeneity between repertoires. Motif analysis of CDR3 loops showed allo-reactive T-cell repertoires differed in motif preference which included broader motif use. Collectively, these data conclude that allo-reactive T-cell repertoires are indeed different to auto-reactive repertoires and provide tangible metrics for further investigations and validation. Given that the antigens studied here are overexpressed on multiple cancers and that allo-reactive TCRs often show increased ligand affinity, this new TCR bank also has translational potential for adoptive cell therapy, soluble TCR-based therapy and rational TCR design.
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Lim B, Kydd L, Jaworski J. Engineering a reporter cell line to mimic the high oligomannose presenting surface immunoglobulin of follicular lymphoma B cells. Sci Rep 2021; 11:87. [PMID: 33420165 PMCID: PMC7794505 DOI: 10.1038/s41598-020-79862-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/10/2020] [Indexed: 11/28/2022] Open
Abstract
Subtypes of B cell non-Hodgkin’s lymphomas, including follicular lymphomas, have shown a unique high oligomannose presentation on their immunoglobulins that will interact with natural receptors of the innate immunity, reportedly causing stimulation and proliferation. From deep sequencing of the variable heavy and light chain sequences of follicular lymphoma involved tissue sections, we identified the consensus variable sequences possessing glycosylation sites at the complementarity determining region. Using this information, we developed a cell line, referred to here as BZ, which displays the consensus variable segments as part of a surface antibody (IgM) and confirmed its presentation of high oligomannose on the heavy chain both in vitro and in vivo. An mCherry expressing variant provided a reporter cell line displaying the high oligomannose surface biomarker while affording clear fluorescent signals for FACS screening as well as for fluorescent in vivo imaging of ectopic xenograft tumors. In developing this reporter cell line that displays the biomarker glycan of follicular lymphoma, we provide a tool that may be used for future screening and validation of receptive moieties for selectively binding high oligomannose for development of targeted diagnostics or therapeutics to such B cell malignancies that display this unique glycan.
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Affiliation(s)
- Butaek Lim
- Department of Bioengineering, University of Texas at Arlington, 500 UTA Blvd., Arlington, TX, 76019, USA
| | - LeNaiya Kydd
- Department of Bioengineering, University of Texas at Arlington, 500 UTA Blvd., Arlington, TX, 76019, USA
| | - Justyn Jaworski
- Department of Bioengineering, University of Texas at Arlington, 500 UTA Blvd., Arlington, TX, 76019, USA.
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Immunoglobulin variable domain high-throughput sequencing reveals specific novel mutational patterns in POEMS syndrome. Blood 2020; 135:1750-1758. [PMID: 32243509 DOI: 10.1182/blood.2019004197] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/13/2020] [Indexed: 12/22/2022] Open
Abstract
Polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes (POEMS) syndrome is a rare multisystem disease resulting from an underlying plasma cell (PC) dyscrasia. The pathophysiology of the disease remains unclear, but the role of the monoclonal immunoglobulin (Ig) light chain (LC) is strongly suspected because of the highly restrictive usage of 2 λ variable (V) domains (IGLV1-40 and IGLV1-44) and the general improvement of clinical manifestations after PC clone-targeted treatment. However, the diagnostic value of Ig LC sequencing, especially in the case of incomplete forms of the disease, remains to be determined. Using a sensitive high-throughput Ig repertoire sequencing on RNA (rapid amplification of cDNA ends-based repertoire sequencing [RACE-RepSeq]), we detected a λ LC monoclonal expansion in the bone marrow (BM) of 83% of patients with POEMS syndrome, including some in whom BM tests routinely performed to diagnose plasma cell dyscrasia failed to detect λ+ monoclonal PCs. Twenty-four (83%) of the 29 LC clonal sequences found were derived from the IGLV1-40 and IGLV1-44 germline genes, as well as 2 from the closely related IGLV1-36 gene, and all were associated with an IGLJ3*02 junction (J) gene, confirming the high restriction of VJ region usage in POEMS syndrome. RACE-RepSeq VJ full-length sequencing additionally revealed original mutational patterns, the strong specificity of which might crucially help establish or eliminate the diagnosis of POEMS syndrome in uncertain cases. Thus, RACE-RepSeq appears as a sensitive, rapid, and specific tool to detect low-abundance PC clones in BM and assign them to POEMS syndrome, with all the consequences for therapeutic options.
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50
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Lee S, Song S, Yoon SS, Koh Y, Yun H. Proper Read Filtering Method to Adequately Analyze Whole-Transcriptome Sequencing and RNA Based Immune Repertoire Sequencing Data for Tumor Milieu Research. Cancers (Basel) 2020; 12:cancers12123693. [PMID: 33317041 PMCID: PMC7763492 DOI: 10.3390/cancers12123693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The recent advancement in high-throughput sequencing has become indispensable for immune-genomics and profiling the T- and B-cell receptor repertoires. Immune repertoire sequencing (IR-seq) and whole transcriptome sequencing (WTS) can be implemented to investigate and quantitatively characterize the complex pattern of the CDR3 region. We conducted T-cell diversity analysis result comparisons of these sequencing methods and suggest an intuitive approach to discriminate reliable TCR sequences and clonotype patterns from capturing errors. Although bulk-RNA sequencing is commonly used for cancer analysis, we confirmed capturing highly enriched TCR transcripts with IR-seq is more reliable for accurate immune repertoire discovery, and singleton read filtering criteria should be applied to capture true clonotypes from error-prone sequencing data. The use of such well-established data and analytical methodologies can broaden understanding of antigen specificity in immunity and enabling efficient therapeutic antibody finding. Abstract Analysis of the T-cell receptor (TCR) repertoire is essential to characterize the extensive collections of T-cell populations with recognizing antigens in cancer research, and whole transcriptome sequencing (WTS) and immune repertoire sequencing (IR-seq) are commonly used for this measure. To date, no standard read filtering method for IR measurement has been presented. We assessed the diversity of the TCR repertoire results from the paired WTS and IR-seq data of 31 multiple myeloma (MM) patients. To invent an adequate read filtering strategy for IR analysis, we conducted comparisons with WTS results. First, our analyses for determining an optimal threshold for selecting clonotypes showed that the clonotypes supported by a single read largely affected the shared clonotypes and manifested distinct patterns of mapping qualities, unlike clonotypes with multiple reads. Second, although IR-seq could reflect a wider TCR region with a higher capture rate than WTS, an adequate comparison with the removal of unwanted bias from potential sequencing errors was possible only after applying our read filtering strategy. As a result, we suggest that TCR repertoire analysis be carried out through IR-seq to produce reliable and accurate results, along with the removal of single-read clonotypes, to conduct immune research in cancer using high-throughput sequencing.
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Affiliation(s)
- Sungyoung Lee
- Center for Precision Medicine, Seoul National University Hospital, Seoul 03082, Korea;
| | - Seulki Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (S.S.); (S.-S.Y.)
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (S.S.); (S.-S.Y.)
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea
| | - Youngil Koh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea; (S.S.); (S.-S.Y.)
- Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Korea
- Correspondence: (Y.K.); (H.Y.)
| | - Hongseok Yun
- Center for Precision Medicine, Seoul National University Hospital, Seoul 03082, Korea;
- Correspondence: (Y.K.); (H.Y.)
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