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Zong F, Long C, Hu W, Chen S, Dai W, Xiao ZX, Cao Y. Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires. Nucleic Acids Res 2023:7173809. [PMID: 37207341 DOI: 10.1093/nar/gkad400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/23/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these experiments presents a challenge in data processing. Specifically, multiple sequence alignment (MSA), a critical aspect of BCR analysis, remains inadequate for handling massive BCR sequencing data and lacks the ability to provide immunoglobulin-specific information. To address this gap, we introduce Abalign, a standalone program specifically designed for ultrafast MSA of BCR/antibody sequences. Benchmark tests demonstrate that Abalign achieves comparable or even better accuracy than state-of-the-art MSA tools, and shows remarkable advantages in terms of speed and memory consumption, reducing the time required for high-throughput analysis from weeks to hours. In addition to its alignment capabilities, Abalign offers a broad range of BCR analysis features, including extracting BCRs, constructing lineage trees, assigning VJ genes, analyzing clonotypes, profiling mutations, and comparing BCR immune repertoires. With its user-friendly graphic interface, Abalign can be easily run on personal computers instead of computing clusters. Overall, Abalign is an easy-to-use and effective tool that enables researchers to analyze massive BCR/antibody sequences, leading to new discoveries in the field of immunoinformatics. The software is freely available at http://cao.labshare.cn/abalign/.
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Affiliation(s)
- Fanjie Zong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Chenyu Long
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Wanxin Hu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Shuang Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wentao Dai
- NHC Key Laboratory of Reproduction Regulation & Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
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Aranburu A, Engström E, Gerasimcik N, Alsén S, Camponeschi A, Yrlid U, Grimsholm O, Mårtensson IL. Clonal relationships of memory B cell subsets in autoimmune mice. Front Immunol 2023; 14:1129234. [PMID: 36936947 PMCID: PMC10015592 DOI: 10.3389/fimmu.2023.1129234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
Immunological memory protects our body from re-infection and it is composed of a cellular and a humoral arm. The B-cell branch with its memory B cells (MBCs), plasma cells and antibodies, formed either in a germinal centre (GC) -dependent or -independent manner, ensure that we can rapidly mount a recall immune response. Previous work in immunised wildtype (WT) mice have identified several subsets of MBCs whereas less is known under autoimmune conditions. Here, we have investigated the heterogeneity of the MBC compartment in autoimmune mouse models and examined the clonal relationships between MBC subsets and GC B cells in one of the models. We demonstrate the presence of at least four different MBC subsets based on their differential expression pattern of CD73, CD80 and PD-L2 in surrogate light chain-deficient (SLC-/-), MRL+/+ and MRLlpr/lpr mice, where most of the MBCs express IgM. Likewise, four MBC subsets could be identified in WT immunised mice. In SLC-/- mice, high-throughput sequencing of Ig heavy chains demonstrates that the two CD73-positive subsets are generally more mutated. Lineage tree analyses on expanded clones show overlaps between all MBC subsets and GC B cells primarily in the IgM sequences. Moreover, each of the three IgM MBC subsets could be found both as ancestor and progeny to GC B cells. This was also observed in the IgG sequences except for the CD73-negative subset. Thus, our findings demonstrate that several MBC subsets are present in autoimmune and WT mice. In SLC-/- mice, these MBC subsets are clonally related to each other and to GC B cells. Our results also indicate that different MBC subsets can seed the GC reaction.
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Affiliation(s)
- Alaitz Aranburu
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Engström
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Natalija Gerasimcik
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Samuel Alsén
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Sahlgrenska Cancer Center, Department of Surgery, Institute of Clinical Sciences, University of Gothenburg and Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Alessandro Camponeschi
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ulf Yrlid
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ola Grimsholm
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Inga-Lill Mårtensson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- *Correspondence: Inga-Lill Mårtensson,
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Krohn S, Boje AS, Gehlert CL, Lutz S, Darzentas N, Knecht H, Herrmann D, Brüggemann M, Scheidig AJ, Weisel K, Gramatzki M, Peipp M, Klausz K. Identification of New Antibodies Targeting Malignant Plasma Cells for Immunotherapy by Next-Generation Sequencing-Assisted Phage Display. Front Immunol 2022; 13:908093. [PMID: 35784366 PMCID: PMC9248769 DOI: 10.3389/fimmu.2022.908093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
To identify new antibodies for the treatment of plasma cell disorders including multiple myeloma (MM), a single-chain Fragment variable (scFv) antibody library was generated by immunizing mice with patient-derived malignant plasma cells. To enrich antibodies binding myeloma antigens, phage display with cellular panning was performed. After depleting the immune library with leukocytes of healthy donors, selection of antibodies was done with L-363 plasma cell line in two consecutive panning rounds. Monitoring the antibodies’ enrichment throughout the panning by next-generation sequencing (NGS) identified several promising candidates. Initially, 41 unique scFv antibodies evolving from different B cell clones were selected. Nine of these antibodies strongly binding to myeloma cells and weakly binding to peripheral blood mononuclear cells (PBMC) were characterized. Using stably transfected Chinese hamster ovary cells expressing individual myeloma-associated antigens revealed that two antibodies bind CD38 and intercellular adhesion molecule-1 (ICAM-1), respectively, and 7 antibodies target yet unknown antigens. To evaluate the therapeutic potential of our new antibodies, in a first proof-of-concept study the CD38 binding scFv phage antibody was converted into a chimeric IgG1. Further analyses revealed that #5-CD38-IgG1 shared an overlapping epitope with daratumumab and isatuximab and had potent anti-myeloma activity comparable to the two clinically approved CD38 antibodies. These results indicate that by phage display and deep sequencing, new antibodies with therapeutic potential for MM immunotherapy can be identified.
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Affiliation(s)
- Steffen Krohn
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Ammelie Svea Boje
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Carina Lynn Gehlert
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Sebastian Lutz
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Nikos Darzentas
- Unit for Hematological Diagnostics, Department of Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Henrik Knecht
- Unit for Hematological Diagnostics, Department of Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Dietrich Herrmann
- Unit for Hematological Diagnostics, Department of Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Monika Brüggemann
- Unit for Hematological Diagnostics, Department of Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Axel J. Scheidig
- Zoological Institute, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Katja Weisel
- Department of Oncology, Hematology, Bone Marrow Transplant (BMT) with Section of Pneumology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Martin Gramatzki
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Matthias Peipp
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
| | - Katja Klausz
- Division of Antibody-Based Immunotherapy, Department of Internal Medicine II, University Hospital Schleswig-Holstein and Christian-Albrechts-University Kiel, Kiel, Germany
- *Correspondence: Katja Klausz,
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4
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Su Z, Jin Y, Zhang Y, Guan Z, Li H, Chen X, Xie C, Zhang C, Liu X, Li P, Ye P, Zhang L, Kong Y, Luo W. The Diagnostic and Prognostic Potential of the B-Cell Repertoire in Membranous Nephropathy. Front Immunol 2021; 12:635326. [PMID: 34122405 PMCID: PMC8190383 DOI: 10.3389/fimmu.2021.635326] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
Membranous nephropathy (MN), an autoimmune glomerular disease, is one of the most common causes of nephrotic syndrome in adults. In current clinical practice, the diagnosis is dependent on renal tissue biopsy. A new method for diagnosis and prognosis surveillance is urgently needed for patients. In the present study, we recruited 66 MN patients before any treatment and 11 healthy control (HC) and analyzed multiple aspects of the immunoglobulin heavy chain (IGH) repertoire of these samples using high-throughput sequencing. We found that the abnormalities of CDR-H3 length, hydrophobicity, somatic hypermutation (SHM), and germ line index were progressively more prominent in patients with MN, and the frequency of IGHV3-66 in post-therapy patients was significantly lower than that in pre-therapy patients. Moreover, we found that the IGHV3-38 gene was significantly related to PLA2R, which is the most commonly used biomarker. The most important discovery was that several IGHV, IGHD transcripts, CDR-H3 length, and SHM rate in pre-therapy patients had the potential to predict the therapeutic effect. Our study further demonstrated that the IGH repertoire could be a potential biomarker for prognosis prediction of MN. The landscape of circulating B-lymphocyte repertoires sheds new light on the detection and surveillance of MN.
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Affiliation(s)
- Zuhui Su
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - Yabin Jin
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - Yu Zhang
- Nephrology Department, The First People's Hospital of Foshan, Foshan, China
| | - Zhanwen Guan
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - Huishi Li
- Nephrology Department, The First People's Hospital of Foshan, Foshan, China
| | - Xiangping Chen
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - Chao Xie
- Nephrology Department, The First People's Hospital of Foshan, Foshan, China
| | - Chuling Zhang
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - Xiaofen Liu
- Nephrology Department, The First People's Hospital of Foshan, Foshan, China
| | - Peixian Li
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - Peiyi Ye
- Nephrology Department, The First People's Hospital of Foshan, Foshan, China
| | - Lifang Zhang
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - Yaozhong Kong
- Nephrology Department, The First People's Hospital of Foshan, Foshan, China
| | - Wei Luo
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
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Li H, Dement-Brown J, Liao PJ, Mazo I, Mills F, Kraus Z, Fitzsimmons S, Tolnay M. Fc receptor-like 4 and 5 define human atypical memory B cells. Int Immunol 2020; 32:755-770. [DOI: 10.1093/intimm/dxaa053] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/04/2020] [Indexed: 11/14/2022] Open
Abstract
Abstract
Atypical memory B cells accumulate in chronic infections and autoimmune conditions, and commonly express FCRL4 and FCRL5, respective IgA and IgG receptors. We characterized memory cells from tonsils on the basis of both FCRL4 and FCRL5 expression, defining three subsets with distinct surface proteins and gene expression. Atypical FCRL4+FCRL5+ memory cells had the most discrete surface protein expression and were enriched in cell adhesion pathways, consistent with functioning as tissue-resident cells. Atypical FCRL4−FCRL5+ memory cells expressed transcription factors and immunoglobulin genes that suggest poised differentiation into plasma cells. Accordingly, the FCRL4−FCRL5+ memory subset was enriched in pathways responding to endoplasmic reticulum stress and IFN-γ. We reconstructed ongoing B-cell responses as lineage trees, providing crucial in vivo developmental context. Each memory subset typically maintained its lineage, denoting mechanisms enforcing their phenotypes. Classical FCRL4−FCRL5− memory cells were infrequently detected in lineage trees, suggesting the majority were in a quiescent state. FCRL4−FCRL5+ cells were the most represented memory subset in lineage trees, indicating robust participation in ongoing responses. Together, these differences suggest FCRL4 and FCRL5 are unlikely to be passive markers but rather active drivers of human memory B-cell development and function.
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Affiliation(s)
- Huifang Li
- Office of Biotechnology Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Jessica Dement-Brown
- Office of Biotechnology Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Pei-Jyun Liao
- Office of Biotechnology Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Ilya Mazo
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
- Argentys Informatics LLC, Gaithersburg, MD, USA
| | - Frederick Mills
- Office of Biotechnology Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Zachary Kraus
- Office of Biotechnology Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Sean Fitzsimmons
- Office of Biotechnology Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Mate Tolnay
- Office of Biotechnology Products, Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
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6
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Minervina A, Pogorelyy M, Mamedov I. T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity. Transpl Int 2019; 32:1111-1123. [DOI: 10.1111/tri.13475] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/09/2019] [Accepted: 06/25/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Anastasia Minervina
- Department of Genomics of Adaptive Immunity M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Russia
| | - Mikhail Pogorelyy
- Department of Genomics of Adaptive Immunity M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Russia
- Institute of Translational Medicine Pirogov Russian National Research Medical University Moscow Russia
| | - Ilgar Mamedov
- Department of Genomics of Adaptive Immunity M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Russia
- Institute of Translational Medicine Pirogov Russian National Research Medical University Moscow Russia
- Laboratory of Molecular Biology Rogachev Federal Scientific and Clinical Centre of Pediatric Hematology Oncology and Immunology Moscow Russia
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7
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Lee NK, Su Y, Bidlingmaier S, Liu B. Manipulation of Cell-Type Selective Antibody Internalization by a Guide-Effector Bispecific Design. Mol Cancer Ther 2019; 18:1092-1103. [PMID: 30962321 DOI: 10.1158/1535-7163.mct-18-1313] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/25/2019] [Accepted: 03/27/2019] [Indexed: 02/07/2023]
Abstract
Cell-type-specific intracellular payload delivery is desired for antibody-based-targeted therapy development. However, tumor-specific internalizing antigens are rare to find, and even rarer for those that are expressed at uniformly high levels. We constructed a bispecific antibody that is composed of a rapidly internalizing antibody binding to a tumor-associated antigen, ephrin receptor A2 (EphA2), and a noninternalizing antibody binding to a highly expressed tumor-associated antigen, activated leukocyte cell adhesion molecule (ALCAM). We found that the overall internalization property of the bispecific is profoundly impacted by the relative surface expression level (antigen density ratio) of EphA2 versus ALCAM. When the EphA2-to-ALCAM ratio is greater than a threshold level (1:5), the amount of the bispecific taken into the tumor cell exceeds what is achieved by either the monoclonal internalizing antibody or a mixture of the two antibodies, showing a bispecific-dependent amplification effect where a small amount of the internalizing antigen EphA2 induces internalization of a larger amount of the noninternalizing antigen ALCAM. When the ratio is below the threshold, EphA2 can be rendered noninternalizing by the presence of excess ALCAM on the same cell surface. We constructed a bispecific antibody-drug conjugate (ADC) based on the above bispecific design and found that the bispecific ADC is more potent than monospecific ADCs in tumor cell killing both in vitro and in vivo Thus, the internalizing property of a cell surface antigen can be manipulated in either direction by a neighboring antigen, and this phenomenon can be exploited for therapeutic targeting.
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Affiliation(s)
- Nam-Kyung Lee
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Yang Su
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Scott Bidlingmaier
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Bin Liu
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California.
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Manso TC, Groenner-Penna M, Minozzo JC, Antunes BC, Ippolito GC, Molina F, Felicori LF. Next-generation sequencing reveals new insights about gene usage and CDR-H3 composition in the horse antibody repertoire. Mol Immunol 2018; 105:251-259. [PMID: 30562645 DOI: 10.1016/j.molimm.2018.11.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 11/11/2018] [Accepted: 11/30/2018] [Indexed: 12/26/2022]
Abstract
Horse serum antibodies have been used for greater than a century for the treatment and prophylaxis of infectious diseases and envenomations. Little is known, however, about the immunogenetic diversity that produces horse serum antibodies. Here, we employed next-generation sequencing for a first-in-kind comprehensive analysis of the equine B-cell repertoire. Nearly 45,000 and 30,000 clonotypes were obtained for the heavy-chain (IGH) and lambda light-chain (IGL) loci, respectively. We observed skewed use of the common subgroups IGHV2 (92.49%) and IGLV8 (82.50%), consistent with previous reports, but also novel use of the rare genes IGHV6S1 and IGLV4S2. CDR-H3 amino acid composition revealed different amino acid patterns at positions 106 and 116 compared to human, rabbit, and mouse, suggesting that an extended conformation predominates among horse CDR-H3 loops. Our analysis provides new insights regarding the mechanisms employed to generate antibody diversity in the horse, and could be applicable to the optimized design of synthetic antibodies intended for future therapeutic use.
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Affiliation(s)
- Taciana Conceição Manso
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Michele Groenner-Penna
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - João Carlos Minozzo
- Production and Research Centre of Immunobiological Products, Department of Health of the State of Paraná, Piraquara 83302-200, Brazil
| | - Bruno Cesar Antunes
- Production and Research Centre of Immunobiological Products, Department of Health of the State of Paraná, Piraquara 83302-200, Brazil
| | - Gregory C Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, 100 E. 24th Street, Stop A5000, Austin, TX, 78712, USA
| | | | - Liza F Felicori
- Laboratory of Synthetic Biology and Biomimetics, Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas - ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Lee NK, Bidlingmaier S, Su Y, Liu B. Modular Construction of Large Non-Immune Human Antibody Phage-Display Libraries from Variable Heavy and Light Chain Gene Cassettes. Methods Mol Biol 2018; 1701:61-82. [PMID: 29116500 DOI: 10.1007/978-1-4939-7447-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Monoclonal antibodies and antibody-derived therapeutics have emerged as a rapidly growing class of biological drugs for the treatment of cancer, autoimmunity, infection, and neurological diseases. To support the development of human antibodies, various display techniques based on antibody gene repertoires have been constructed over the last two decades. In particular, scFv-antibody phage display has been extensively utilized to select lead antibodies against a variety of target antigens. To construct a scFv phage display that enables efficient antibody discovery, and optimization, it is desirable to develop a system that allows modular assembly of highly diverse variable heavy chain and light chain (Vκ and Vλ) repertoires. Here, we describe modular construction of large non-immune human antibody phage-display libraries built on variable gene cassettes from heavy chain and light chain repertoires (Vκ- and Vλ-light can be made into independent cassettes). We describe utility of such libraries in antibody discovery and optimization through chain shuffling.
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Affiliation(s)
- Nam-Kyung Lee
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, 1001 Potrero Avenue, 1305, San Francisco, CA, 94110, USA
| | - Scott Bidlingmaier
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, 1001 Potrero Avenue, 1305, San Francisco, CA, 94110, USA
| | - Yang Su
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, 1001 Potrero Avenue, 1305, San Francisco, CA, 94110, USA
| | - Bin Liu
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, 1001 Potrero Avenue, 1305, San Francisco, CA, 94110, USA.
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10
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Leighton PA, Morales J, Harriman WD, Ching KH. V(D)J Rearrangement Is Dispensable for Producing CDR-H3 Sequence Diversity in a Gene Converting Species. Front Immunol 2018; 9:1317. [PMID: 29951062 PMCID: PMC6008532 DOI: 10.3389/fimmu.2018.01317] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/28/2018] [Indexed: 12/20/2022] Open
Abstract
An important characteristic of chickens is that the antibody repertoire is based on a single framework, with diversity found mainly in the CDRs of the light and heavy chain variable regions. Despite this apparent limitation in the antibody repertoire, high-affinity antibodies can be raised to a wide variety of targets, including those that are highly conserved. Transgenic chickens have previously been generated that express a humanized antibody repertoire, with a single framework that incorporates diversity by the process of gene conversion, as in wild-type chickens. Here, we compare the sequences and antibodies that are generated purely by gene conversion/somatic hypermutation of a pre-rearranged heavy chain, with the diversity obtained by V(D)J rearrangement followed by gene conversion and somatic hypermutation. In a gene converting species, CDR-H3 lengths are more variable with V(D)J rearrangement, but similar levels of amino acid diversity are obtainable with gene conversion/somatic hypermutation alone.
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Abstract
Somatic assembly of T cell receptor and B cell receptor (BCR) genes produces a vast diversity of lymphocyte antigen recognition capacity. The advent of efficient high-throughput sequencing of lymphocyte antigen receptor genes has recently generated unprecedented opportunities for exploration of adaptive immune responses. With these opportunities have come significant challenges in understanding the analysis techniques that most accurately reflect underlying biological phenomena. In this regard, sample preparation and sequence analysis techniques, which have largely been borrowed and adapted from other fields, continue to evolve. Here, we review current methods and challenges of library preparation, sequencing and statistical analysis of lymphocyte receptor repertoire studies. We discuss the general steps in the process of immune repertoire generation including sample preparation, platforms available for sequencing, processing of sequencing data, measurable features of the immune repertoire, and the statistical tools that can be used for analysis and interpretation of the data. Because BCR analysis harbors additional complexities, such as immunoglobulin (Ig) (i.e., antibody) gene somatic hypermutation and class switch recombination, the emphasis of this review is on Ig/BCR sequence analysis.
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Affiliation(s)
- Neha Chaudhary
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Duane R. Wesemann
- Division of Rheumatology, Department of Medicine, Immunology and Allergy, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
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12
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Prohaska TA, Que X, Diehl CJ, Hendrikx S, Chang MW, Jepsen K, Glass CK, Benner C, Witztum JL. Massively Parallel Sequencing of Peritoneal and Splenic B Cell Repertoires Highlights Unique Properties of B-1 Cell Antibodies. THE JOURNAL OF IMMUNOLOGY 2018; 200:1702-1717. [PMID: 29378911 PMCID: PMC5821571 DOI: 10.4049/jimmunol.1700568] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 01/03/2018] [Indexed: 12/26/2022]
Abstract
B-1 cells are a unique subset of B cells that are positively selected for expressing autoreactive BCRs. We isolated RNA from peritoneal (B-1a, B-1b, B-2) and splenic (B-1a, marginal zone, follicular) B cells from C57BL/6 mice and used 5'-RACE to amplify the IgH V region using massively parallel sequencing. By analyzing 379,000 functional transcripts, we demonstrate that B-1a cells use a distinct and restricted repertoire. All B-1 cell subsets, especially peritoneal B-1a cells, had a high proportion of sequences without N additions, suggesting predominantly prenatal development. Their transcripts differed markedly and uniquely contained VH11 and VH12 genes, which were rearranged only with a restricted selection of D and J genes, unlike other V genes. Compared to peritoneal B-1a, the peritoneal B-1b repertoire was larger, had little overlap with B-1a, and most sequences contained N additions. Similarly, the splenic B-1a repertoire differed from peritoneal B-1a sequences, having more unique sequences and more frequent N additions, suggesting influx of B-1a cells into the spleen from nonperitoneal sites. Two CDR3s, previously described as Abs to bromelain-treated RBCs, comprised 43% of peritoneal B-1a sequences. We show that a single-chain variable fragment designed after the most prevalent B-1a sequence bound oxidation-specific epitopes such as the phosphocholine of oxidized phospholipids. In summary, we provide the IgH V region library of six murine B cell subsets, including, to our knowledge for the first time, a comparison between B-1a and B-1b cells, and we highlight qualities of B-1 cell Abs that indicate unique selection processes.
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Affiliation(s)
- Thomas A Prohaska
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Xuchu Que
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Cody J Diehl
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Sabrina Hendrikx
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Max W Chang
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093; and
| | - Christopher K Glass
- Department of Medicine, University of California San Diego, La Jolla, CA 92093.,Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
| | - Christopher Benner
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Joseph L Witztum
- Department of Medicine, University of California San Diego, La Jolla, CA 92093;
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13
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Abstract
Next-generation sequencing is making it possible to study the antibody repertoire of an organism in unprecedented detail, and, by so doing, to characterize its behavior in the response to infection and in pathological conditions such as autoimmunity and cancer. The polymorphic nature of the repertoire poses unique challenges that rule out the use of many commonly used NGS methods and require tradeoffs to be made when considering experimental design.We outline the main contexts in which antibody repertoire analysis has been used, and summarize the key tools that are available. The humoral immune response to vaccination has been a particular focus of repertoire analyses, and we review the key conclusions and methods used in these studies.
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Affiliation(s)
- William D Lees
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK
| | - Adrian J Shepherd
- Department of Biological Sciences and Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London, WC1E 7HX, UK.
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14
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Aranburu A, Höök N, Gerasimcik N, Corleis B, Ren W, Camponeschi A, Carlsten H, Grimsholm O, Mårtensson IL. Age-associated B cells expanded in autoimmune mice are memory cells sharing H-CDR3-selected repertoires. Eur J Immunol 2018; 48:509-521. [PMID: 29266242 DOI: 10.1002/eji.201747127] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 11/07/2017] [Accepted: 12/07/2017] [Indexed: 11/10/2022]
Abstract
Age-associated B cells (ABCs) represent a distinct cell population expressing low levels of CD21 (CD21-/low ). The Ig repertoire expressed by ABCs in aged mice is diverse and exhibits signs of somatic hypermutation (SHM). A CD21-/low B-cell population is expanded in autoimmune diseases, e.g. systemic lupus erythematosus, as well as in lupus-prone NZB/W mice and in mice lacking a pre-B cell receptor (SLC-/- ). However, the nature of the CD21-/low B cells (hereafter ABCs) in autoimmunity is not well understood. Here we show that in young SLC-/- mice, the vast majority of the ABCs express memory B-cell (MBC) markers in contrast to wild-type controls. A similar population is present in lupus-prone MRL mice before and at disease onset. In SLC-/- mice, a majority of the ABCs are IgM+ , their VH genes have undergone SHM, show clonal diversification and clonal restriction at the H-CDR3 level. ABC hybridomas, established from SLC-/- mice, secrete typical lupus autoantibodies, e.g. anti-Smith antigen, and some of those that bind to DNA comprise a H-CDR3 that is identical to previously described IgM anti-DNA antibodies from lupus-prone mice. Together, these results reveal that ABCs in autoimmune mice are comprised of autoreactive MBCs expressing highly restricted H-CDR3 repertoires.
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Affiliation(s)
- Alaitz Aranburu
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
| | - Nina Höök
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
| | - Natalija Gerasimcik
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
| | - Bjorn Corleis
- Ragon Institute of MGH, MIT and Harvard, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Weicheng Ren
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Alessandro Camponeschi
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
| | - Hans Carlsten
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
| | - Ola Grimsholm
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden.,B Cell Physiopathology Unit, Immunology Research Area, Bambino Gesù Children's Hospital IRCCS, Rome, Italy
| | - Inga-Lill Mårtensson
- Department of Rheumatology and Inflammation Research, University of Gothenburg, Gothenburg, Sweden
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15
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Abstract
Bloom's syndrome (BS) is an autosomal recessive disease, caused by mutations in the BLM gene. This gene codes for BLM protein, which is a helicase involved in DNA repair. DNA repair is especially important for the development and maturation of the T and B cells. Since BLM is involved in DNA repair, we aimed to study if BLM deficiency affects T and B cell development and especially somatic hypermutation (SHM) and class switch recombination (CSR) processes. Clinical data of six BS patients was collected, and immunoglobulin serum levels were measured at different time points. In addition, we performed immune phenotyping of the B and T cells and analyzed the SHM and CSR in detail by analyzing IGHA and IGHG transcripts using next-generation sequencing. The serum immunoglobulin levels were relatively low, and patients had an increased number of infections. The absolute number of T, B, and NK cells were low but still in the normal range. Remarkably, all BS patients studied had a high percentage (20-80%) of CD4+ and CD8+ effector memory T cells. The process of SHM seems normal; however, the Ig subclass distribution was not normal, since the BS patients had more IGHG1 and IGHG3 transcripts. In conclusion, BS patients have low number of lymphocytes, but the immunodeficiency seems relatively mild since they have no severe or opportunistic infections. Most changes in the B cell development were seen in the CSR process; however, further studies are necessary to elucidate the exact role of BLM in CSR.
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16
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Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol 2017; 8:1418. [PMID: 29163494 PMCID: PMC5671925 DOI: 10.3389/fimmu.2017.01418] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/12/2017] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1–3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community’s founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org).
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Florian Rubelt
- Department of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Christian E Busse
- Division of B Cell Immunology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Jason A Vander Heiden
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | | | - Adrian Thorogood
- entre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Frederick A Matsen Iv
- Public Health Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Uri Laserson
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David Klatzmann
- Immunology-Immunopathology-Immunotherapy (i3 & i2B), Sorbonne Université, Paris, France
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Marie-Paule Lefranc
- IMGT, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Tania Bubela
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jamie K Scott
- Faculty of Health Sciences, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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17
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Omar N, Hamidon NH, Yunus MH, Noordin R, Choong YS, Lim TS. Generation and selection of naïve Fab library for parasitic antigen: Anti‐
Bm
SXP antibodies for lymphatic filariasis. Biotechnol Appl Biochem 2017; 65:346-354. [DOI: 10.1002/bab.1591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Accepted: 08/16/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Noorsharmimi Omar
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Nurul Hamizah Hamidon
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Muhammad Hafiznur Yunus
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Rahmah Noordin
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular MedicineUniversiti Sains Malaysia Minden Penang Malaysia
- Analytical Biochemistry Research CentreUniversiti Sains Malaysia Penang Malaysia
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18
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Cortegano I, Rodríguez M, Martín I, Prado MC, Ruíz C, Hortigüela R, Alía M, Vilar M, Mira H, Cano E, Domínguez M, de Andrés B, Gaspar ML. Altered marginal zone and innate-like B cells in aged senescence-accelerated SAMP8 mice with defective IgG1 responses. Cell Death Dis 2017; 8:e3000. [PMID: 28817118 PMCID: PMC5596542 DOI: 10.1038/cddis.2017.351] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/27/2017] [Accepted: 07/02/2017] [Indexed: 12/31/2022]
Abstract
Aging has a strong impact on the activity of the immune system, enhancing susceptibility to pathogens and provoking a predominant pre-inflammatory status, whereas dampening responses to vaccines in humans and mice. Here, we demonstrate a loss of marginal zone B lymphocytes (MZ, CD19+CD45R+CD21++CD23lo) and a decrease of naive B cells (CD19+IgD+), whereas there is an enhancement of a CD19+CD45Rlo innate-like B cell population (B1REL) and the so-called aged B cell compartment (ABC, CD45R+CD21loCD23loCD5-CD11b-) in aged senescence-accelerated (SAMP8) mice but not in aged senescence-resistant (SAMR1) mice. These changes in aged SAMP8 mice were associated with lower IgG isotype levels, displaying low variable gene usage repertoires of the immunoglobulin heavy chain (VH) diversity, with a diminution on IgG1-memory B cells (CD11b-Gr1-CD138-IgM-IgD-CD19+CD38+IgG1+), an increase in T follicular helper (TFH, CD4+CXCR5+PD1+) cell numbers, and an altered MOMA-1 (metallophilic macrophages) band in primary follicles. LPS-mediated IgG1 responses were impaired in the B1REL and ABC cell compartments, both in vitro and in vivo. These data demonstrate the prominent changes to different B cell populations and in structural follicle organization that occur upon aging in SAMP8 mice. These novel results raise new questions regarding the importance of the cellular distribution in the B cell layers, and their effector functions needed to mount a coordinated and effective humoral response.
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MESH Headings
- Aging/genetics
- Aging/immunology
- Animals
- Antigens, CD/genetics
- Antigens, CD/immunology
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Cell Death/drug effects
- Cell Proliferation/drug effects
- Gene Expression Regulation, Developmental
- IgG Deficiency/genetics
- IgG Deficiency/metabolism
- IgG Deficiency/pathology
- Immunity, Humoral
- Immunity, Innate
- Immunoglobulin D/genetics
- Immunoglobulin D/metabolism
- Immunoglobulin G/genetics
- Immunoglobulin G/metabolism
- Immunoglobulin Heavy Chains
- Immunoglobulin M/genetics
- Immunoglobulin M/metabolism
- Immunologic Memory
- Lipopolysaccharides/pharmacology
- Mice, Inbred C57BL
- Mice, Transgenic
- Primary Cell Culture
- Signal Transduction
- Spleen/cytology
- Spleen/drug effects
- Spleen/immunology
- T-Lymphocytes, Helper-Inducer/cytology
- T-Lymphocytes, Helper-Inducer/drug effects
- T-Lymphocytes, Helper-Inducer/immunology
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Affiliation(s)
- Isabel Cortegano
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Mercedes Rodríguez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Isabel Martín
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Maria Carmen Prado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Carolina Ruíz
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Rafael Hortigüela
- Unidad Funcional de Investigación en Enfermedades Crónicas, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
| | - Mario Alía
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Marçal Vilar
- Instituto de Biomedicina de Valencia, Valencia 46010, Spain
| | - Helena Mira
- Instituto de Biomedicina de Valencia, Valencia 46010, Spain
| | - Eva Cano
- Unidad Funcional de Investigación en Enfermedades Crónicas, Instituto de Salud Carlos III (ISCIII), Majadahonda, 28220 Madrid, Spain
| | - Mercedes Domínguez
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - Belén de Andrés
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
| | - María Luisa Gaspar
- Centro Nacional de Microbiología, Instituto de Salud Carlos III (ISCIII), Majadahonda, Madrid, Spain
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19
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Khavrutskii IV, Chaudhury S, Stronsky SM, Lee DW, Benko JG, Wallqvist A, Bavari S, Cooper CL. Quantitative Analysis of Repertoire-Scale Immunoglobulin Properties in Vaccine-Induced B-Cell Responses. Front Immunol 2017; 8:910. [PMID: 28855898 PMCID: PMC5557726 DOI: 10.3389/fimmu.2017.00910] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/17/2017] [Indexed: 12/15/2022] Open
Abstract
Recent advances in the next-generation sequencing of B-cell receptors (BCRs) enable the characterization of humoral responses at a repertoire-wide scale and provide the capability for identifying unique features of immune repertoires in response to disease, vaccination, or infection. Immunosequencing now readily generates 103–105 sequences per sample; however, statistical analysis of these repertoires is challenging because of the high genetic diversity of BCRs and the elaborate clonal relationships among them. To date, most immunosequencing analyses have focused on reporting qualitative trends in immunoglobulin (Ig) properties, such as usage or somatic hypermutation (SHM) percentage of the Ig heavy chain variable (IGHV) gene segment family, and on reducing complex Ig property distributions to simple summary statistics. However, because Ig properties are typically not normally distributed, any approach that fails to assess the distribution as a whole may be inadequate in (1) properly assessing the statistical significance of repertoire differences, (2) identifying how two repertoires differ, and (3) determining appropriate confidence intervals for assessing the size of the differences and their potential biological relevance. To address these issues, we have developed a technique that uses Wilcox’ robust statistics toolbox to identify statistically significant vaccine-specific differences between Ig repertoire properties. The advantage of this technique is that it can determine not only whether but also where the distributions differ, even when the Ig repertoire properties are non-normally distributed. We used this technique to characterize murine germinal center (GC) B-cell repertoires in response to a complex Ebola virus-like particle (eVLP) vaccine candidate with known protective efficacy. The eVLP-mediated GC B-cell responses were highly diverse, consisting of thousands of clonotypes. Despite this staggering diversity, we identified statistically significant differences between non-immunized, vaccine only, and vaccine-plus-adjuvant groups in terms of Ig properties, including IGHV-family usage, SHM percentage, and characteristics of the BCR complementarity-determining region. Most notably, our analyses identified a robust eVLP-specific feature—enhanced IGHV8-family usage in B-cell repertoires. These findings demonstrate the utility of our technique in identifying statistically significant BCR repertoire differences following vaccination. More generally, our approach is potentially applicable to a wide range of studies in infection, vaccination, auto-immunity, and cancer.
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Affiliation(s)
- Ilja V Khavrutskii
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Sidhartha Chaudhury
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Sabrina M Stronsky
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| | - Donald W Lee
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Jacqueline G Benko
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute (BHSAI), Telemedicine and Advanced Technology Research Center, United States Army Medical Research and Materiel Command, Fort Detrick, MD, United States
| | - Sina Bavari
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
| | - Christopher L Cooper
- Molecular and Translational Sciences, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, MD, United States
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20
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Henderson LA, Volpi S, Frugoni F, Janssen E, Kim S, Sundel RP, Dedeoglu F, Lo MS, Hazen MM, Beth Son M, Mathieu R, Zurakowski D, Yu N, Lebedeva T, Fuhlbrigge RC, Walter JE, Nee Lee Y, Nigrovic PA, Notarangelo LD. Next-Generation Sequencing Reveals Restriction and Clonotypic Expansion of Treg Cells in Juvenile Idiopathic Arthritis. Arthritis Rheumatol 2017; 68:1758-68. [PMID: 26815131 DOI: 10.1002/art.39606] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/19/2016] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Treg cell-mediated suppression of Teff cells is impaired in juvenile idiopathic arthritis (JIA); however, the basis for this dysfunction is incompletely understood. Animal models of autoimmunity and immunodeficiency demonstrate that a diverse Treg cell repertoire is essential to maintain Treg cell function. The present study was undertaken to investigate the Treg and Teff cell repertoires in JIA. METHODS Treg cells (CD4+CD25+CD127(low) ) and Teff cells (CD4+CD25-) were isolated from peripheral blood and synovial fluid obtained from JIA patients, healthy controls, and children with Lyme arthritis. Treg cell function was measured in suppressive assays. The T cell receptor β chain (TRB) was amplified by multiplex polymerase chain reaction and next-generation sequencing was performed, with amplicons sequenced using an Illumina HiSeq platform. Data were analyzed using ImmunoSEQ, International ImMunoGeneTics system, and the Immunoglobulin Analysis Tools. RESULTS Compared to findings in controls, the JIA peripheral blood Treg cell repertoire was restricted, and clonotypic expansions were found in both blood and synovial fluid Treg cells. Skewed usage and pairing of TRB variable and joining genes, including overuse of gene segments that have been associated with other autoimmune conditions, was observed. JIA patients shared a substantial portion of synovial fluid Treg cell clonotypes that were private to JIA and not identified in Lyme arthritis. CONCLUSION We identified restriction and clonotypic expansions in the JIA Treg cell repertoire with sharing of Treg cell clonotypes across patients. These findings suggest that abnormalities in the Treg cell repertoire, possibly engendered by shared antigenic triggers, may contribute to disease pathogenesis in JIA.
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Affiliation(s)
| | | | | | - Erin Janssen
- Boston Children's Hospital, Boston, Massachusetts
| | - Susan Kim
- Boston Children's Hospital, Boston, Massachusetts
| | | | | | - Mindy S Lo
- Boston Children's Hospital, Boston, Massachusetts
| | | | | | | | | | - Neng Yu
- American Red Cross Blood Services-East Division, New England HLA Services, Dedham, Massachusetts
| | - Tatiana Lebedeva
- American Red Cross Blood Services-East Division, New England HLA Services, Dedham, Massachusetts
| | - Robert C Fuhlbrigge
- Boston Children's Hospital and Brigham and Women's Hospital, Boston, Massachusetts
| | - Jolan E Walter
- Boston Children's Hospital and Massachusetts General Hospital for Children, Boston, Massachusetts
| | - Yu Nee Lee
- Boston Children's Hospital, Boston, Massachusetts
| | - Peter A Nigrovic
- Boston Children's Hospital and Brigham and Women's Hospital, Boston, Massachusetts
| | - Luigi D Notarangelo
- Boston Children's Hospital, Harvard Medical School, and Harvard Stem Cell Institute, Boston, Massachusetts
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21
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Longo NS, Rogosch T, Zemlin M, Zouali M, Lipsky PE. Mechanisms That Shape Human Antibody Repertoire Development in Mice Transgenic for Human Ig H and L Chain Loci. THE JOURNAL OF IMMUNOLOGY 2017; 198:3963-3977. [PMID: 28438896 DOI: 10.4049/jimmunol.1700133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/17/2017] [Indexed: 02/03/2023]
Abstract
To determine the impact of the milieu on the development of the human B cell repertoire, we carried out a comprehensive analysis of productive and nonproductive Ig gene rearrangements from transgenic mice engineered to express single copies of the unrearranged human H chain and L chain Ig gene loci. By examining the nonproductive repertoire as an indication of the immediate product of the rearrangement machinery without an impact of selection, we discovered that the distribution of human rearrangements arising in the mouse was generally comparable to that seen in humans. However, differences between the distribution of nonproductive and productive rearrangements that reflect the impact of selection suggested species-specific selection played a role in shaping the respective repertoires. Although expression of some VH genes was similar in mouse and human (IGHV3-23, IGHV3-30, and IGHV4-59), other genes behaved differently (IGHV3-33, IGHV3-48, IGHV4-31, IGHV4-34, and IGHV1-18). Gene selection differences were also noted in L chains. Notably, nonproductive human VH rearrangements in the transgenic mice expressed shorter CDRH3 with less N addition. Even the CDRH3s in the productive rearrangements were shorter in length than those of the normal human productive repertoire. Amino acids in the CDRH3s in both species showed positive selection of tyrosines and glycines, and negative selection of leucines. The data indicate that the environment in which B cells develop can affect the expressed Ig repertoire by exerting influences on the distribution of expressed VH and VL genes and by influencing the amino acid composition of the Ag binding site.
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Affiliation(s)
- Nancy S Longo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Tobias Rogosch
- Pediatric Immunology and Allergology, Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Michael Zemlin
- Klinik für Kinder-und Jugendmedizin, Universitätsklinikum Gießen und Marburg GmbH, Standort Marburg, D-35033 Marburg, Germany.,Department of General Pediatrics and Neonatology, Saarland University Medical School, D-66421 Homburg, Germany
| | - Moncef Zouali
- INSERM & Université Paris Diderot, Sorbonne Paris Cité Centre Viggo Petersen, Hôpital Lariboisière, 75475 Paris, France; and
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22
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Abstract
BACKGROUND Previous studies identified B cell gene signatures and predominance of specific B cell subsets as a marker of operational tolerance after kidney transplantation. These findings suggested a role for B cells in the establishment or maintenance of tolerance. Here we analyzed B cell recovery in 4 subjects, 3 of whom achieved tolerance after combined kidney/bone marrow transplantation. METHODS Peripheral B cell subsets were examined longitudinally by flow cytometry. Immunoglobulin heavy chain repertoire analysis was performed using next-generation sequencing. Lastly, the patients' serum reactivity to HLA was assessed by Luminex. RESULTS B cell counts recovered approximately 1 year posttransplant except for 1 subject who experienced delayed reconstitution. This subject resumed immunosuppression for acute rejection at 10 months posttransplant and underwent preemptive retransplantation at 3 years for chronic rejection. B cell recovery was accompanied by a high frequency of CD20 + CD24CD38 transitional B cells and a diversified clonal repertoire. However, all 4 subjects showed prevalence of CD20 + CD27+ memory B cells around 6 months posttransplant when B cell counts were still low and the clonal B cell repertoire very limited. The predominance of memory B cells was also associated with high levels of somatically mutated immunoglobulin heavy chain variable sequences and transient serum reactivity to HLA. CONCLUSIONS Our observations reveal the presence of memory B cells early posttransplant that likely escaped the preparative regimen at a time consistent with the establishment of tolerance. Further studies are warranted to characterize the functional properties of these persisting memory cells and evaluate their potential contribution to tolerance induction.
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23
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IJspeert H, van Schouwenburg PA, van Zessen D, Pico-Knijnenburg I, Stubbs AP, van der Burg M. Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data. THE JOURNAL OF IMMUNOLOGY 2017; 198:4156-4165. [PMID: 28416602 DOI: 10.4049/jimmunol.1601921] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 03/13/2017] [Indexed: 11/19/2022]
Abstract
Antigen Receptor Galaxy (ARGalaxy) is a Web-based tool for analyses and visualization of TCR and BCR sequencing data of 13 species. ARGalaxy consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, depending on the available data and the question of interest. The demultiplex tool allows data trimming and demultiplexing, whereas with the concatenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file. The immune repertoire pipeline is an extended version of our previously published ImmunoGlobulin Galaxy (IGGalaxy) virtual machine that was developed to visualize V(D)J gene usage. It allows analysis of both BCR and TCR rearrangements, visualizes CDR3 characteristics (length and amino acid usage) and junction characteristics, and calculates the diversity of the immune repertoire. Finally, ARGalaxy includes the newly developed SHM and CSR pipeline to analyze SHM and/or CSR in BCR rearrangements. It analyzes the frequency and patterns of SHM, Ag selection (including BASELINe), clonality (Change-O), and CSR. The functionality of the ARGalaxy tool is illustrated in several clinical examples of patients with primary immunodeficiencies. In conclusion, ARGalaxy is a novel tool for the analysis of the complete immune repertoire, which is applicable to many patient groups with disturbances in the immune repertoire such as autoimmune diseases, allergy, and leukemia, but it can also be used to address basic research questions in repertoire formation and selection.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and
| | | | - David van Zessen
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and.,Department of Bioinformatics, Erasmus University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus University Medical Center, 3015 CE Rotterdam, the Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Center, 3015 CN Rotterdam, the Netherlands; and
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24
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Amara K, Clay E, Yeo L, Ramsköld D, Spengler J, Sippl N, Cameron JA, Israelsson L, Titcombe PJ, Grönwall C, Sahbudin I, Filer A, Raza K, Malmström V, Scheel-Toellner D. B cells expressing the IgA receptor FcRL4 participate in the autoimmune response in patients with rheumatoid arthritis. J Autoimmun 2017; 81:34-43. [PMID: 28343748 PMCID: PMC5473332 DOI: 10.1016/j.jaut.2017.03.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/06/2017] [Accepted: 03/09/2017] [Indexed: 12/24/2022]
Abstract
The clinical efficacy of B cell targeting therapies highlights the pathogenic potential of B cells in inflammatory diseases. Expression of Fc Receptor like 4 (FcRL4) identifies a memory B cell subset, which is enriched in the joints of patients with rheumatoid arthritis (RA) and in mucosa-associated lymphoid tissue. The high level of RANKL production by this B cell subset indicates a unique pathogenic role. In addition, recent work has identified a role for FcRL4 as an IgA receptor, suggesting a potential function in mucosal immunity. Here, the contribution of FcRL4+ B cells to the specific autoimmune response in the joints of patients with RA was investigated. Single FcRL4+ and FcRL4- B cells were sorted from synovial fluid and tissue from RA patients and their immunoglobulin genes characterized. Levels of hypermutation in the variable regions in both populations were largely consistent with memory B cells selected by an antigen- and T cell-dependent process. Recombinant antibodies were generated based on the IgH and IgL variable region sequences and investigated for antigen specificity. A significantly larger proportion of the recombinant antibodies generated from individual synovial FcRL4+ B cells showed reactivity towards citrullinated autoantigens. Furthermore, both in analyses based on heavy chain sequences and flow cytometric detection, FcRL4+ B cells have significantly increased usage of the IgA isotype. Their low level of expression of immunoglobulin and plasma cell differentiation genes does not suggest current antibody secretion. We conclude that these activated B cells are a component of the local autoimmune response, and through their RANKL expression, can contribute to joint destruction. Furthermore, their expression of FcRL4 and their enrichment in the IgA isotype points towards a potential role for these cells in the link between mucosal and joint inflammation. Memory B cells expressing the IgA receptor FcRL4 are found in the joints of patients with RA. B cell receptors expressed on synovial FcRL4+ B cells more frequently belong to the IgA class. Among recombinant antibodies cloned from FcRL4+ B cells there is more reactivity with citrullinated proteins. The gene transcription profile of FcRL4+ B cells shows a low level of differentiation to plasma cells. These cells may be involved in the link between mucosal and joint autoimmunity.
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Affiliation(s)
- Khaled Amara
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-17176 Solna, Stockholm, Sweden
| | - Elizabeth Clay
- Rheumatology Research Group, RACE AR UK Centre of Excellence in RA Pathogenesis, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Lorraine Yeo
- Rheumatology Research Group, RACE AR UK Centre of Excellence in RA Pathogenesis, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Daniel Ramsköld
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-17176 Solna, Stockholm, Sweden
| | - Julia Spengler
- Rheumatology Research Group, RACE AR UK Centre of Excellence in RA Pathogenesis, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Natalie Sippl
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-17176 Solna, Stockholm, Sweden
| | - James A Cameron
- Rheumatology Research Group, RACE AR UK Centre of Excellence in RA Pathogenesis, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Lena Israelsson
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-17176 Solna, Stockholm, Sweden
| | - Philip J Titcombe
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-17176 Solna, Stockholm, Sweden
| | - Caroline Grönwall
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-17176 Solna, Stockholm, Sweden
| | - Ilfita Sahbudin
- Rheumatology Research Group, RACE AR UK Centre of Excellence in RA Pathogenesis, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Andrew Filer
- Rheumatology Research Group, RACE AR UK Centre of Excellence in RA Pathogenesis, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Karim Raza
- Rheumatology Research Group, RACE AR UK Centre of Excellence in RA Pathogenesis, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK; Department of Rheumatology, Sandwell and West Birmingham Hospitals NHS Trust, Birmingham UK
| | - Vivianne Malmström
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Karolinska Institutet, SE-17176 Solna, Stockholm, Sweden
| | - Dagmar Scheel-Toellner
- Rheumatology Research Group, RACE AR UK Centre of Excellence in RA Pathogenesis, Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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25
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Comparative analysis of the feline immunoglobulin repertoire. Biologicals 2017; 46:81-87. [PMID: 28131552 DOI: 10.1016/j.biologicals.2017.01.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/02/2016] [Accepted: 01/09/2017] [Indexed: 12/19/2022] Open
Abstract
Next-Generation Sequencing combined with bioinformatics is a powerful tool for analyzing the large number of DNA sequences present in the expressed antibody repertoire and these data sets can be used to advance a number of research areas including antibody discovery and engineering. The accurate measurement of the immune repertoire sequence composition, diversity and abundance is important for understanding the repertoire response in infections, vaccinations and cancer immunology and could also be useful for elucidating novel molecular targets. In this study 4 individual domestic cats (Felis catus) were subjected to antibody repertoire sequencing with total number of sequences generated 1079863 for VH for IgG, 1050824 VH for IgM, 569518 for VK and 450195 for VL. Our analysis suggests that a similar VDJ expression patterns exists across all cats. Similar to the canine repertoire, the feline repertoire is dominated by a single subgroup, namely VH3. The antibody paratope of felines showed similar amino acid variation when compared to human, mouse and canine counterparts. All animals show a similarly skewed VH CDR-H3 profile and, when compared to canine, human and mouse, distinct differences are observed. Our study represents the first attempt to characterize sequence diversity in the expressed feline antibody repertoire and this demonstrates the utility of using NGS to elucidate entire antibody repertoires from individual animals. These data provide significant insight into understanding the feline immune system function.
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26
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Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol 2017. [PMID: 29163494 DOI: 10.3389/fimmu.2017.01418/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1-3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community's founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org).
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Florian Rubelt
- Department of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Christian E Busse
- Division of B Cell Immunology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Jason A Vander Heiden
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | | | - Adrian Thorogood
- entre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Frederick A Matsen Iv
- Public Health Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Uri Laserson
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David Klatzmann
- Immunology-Immunopathology-Immunotherapy (i3 & i2B), Sorbonne Université, Paris, France
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Marie-Paule Lefranc
- IMGT, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Tania Bubela
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jamie K Scott
- Faculty of Health Sciences, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States
- Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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27
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Lee YN, Frugoni F, Dobbs K, Tirosh I, Du L, Ververs FA, Ru H, Ott de Bruin L, Adeli M, Bleesing JH, Buchbinder D, Butte MJ, Cancrini C, Chen K, Choo S, Elfeky RA, Finocchi A, Fuleihan RL, Gennery AR, El-Ghoneimy DH, Henderson LA, Al-Herz W, Hossny E, Nelson RP, Pai SY, Patel NC, Reda SM, Soler-Palacin P, Somech R, Palma P, Wu H, Giliani S, Walter JE, Notarangelo LD. Characterization of T and B cell repertoire diversity in patients with RAG deficiency. Sci Immunol 2016; 1:eaah6109. [PMID: 28783691 PMCID: PMC5586490 DOI: 10.1126/sciimmunol.aah6109] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/22/2016] [Indexed: 12/13/2022]
Abstract
Recombination-activating genes 1 and 2 (RAG1 and RAG2) play a critical role in T and B cell development by initiating the recombination process that controls the expression of T cell receptor (TCR) and immunoglobulin genes. Mutations in the RAG1 and RAG2 genes in humans cause a broad spectrum of phenotypes, including severe combined immunodeficiency (SCID) with lack of T and B cells, Omenn syndrome, leaky SCID, and combined immunodeficiency with granulomas or autoimmunity (CID-G/AI). Using next-generation sequencing, we analyzed the TCR and B cell receptor (BCR) repertoire in 12 patients with RAG mutations presenting with Omenn syndrome (n = 5), leaky SCID (n = 3), or CID-G/AI (n = 4). Restriction of repertoire diversity skewed usage of variable (V), diversity (D), and joining (J) segment genes, and abnormalities of CDR3 length distribution were progressively more prominent in patients with a more severe phenotype. Skewed usage of V, D, and J segment genes was present also within unique sequences, indicating a primary restriction of repertoire. Patients with Omenn syndrome had a high proportion of class-switched immunoglobulin heavy chain transcripts and increased somatic hypermutation rate, suggesting in vivo activation of these B cells. These data provide a framework to better understand the phenotypic heterogeneity of RAG deficiency.
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Affiliation(s)
- Yu Nee Lee
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Pediatric Department A and the Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Francesco Frugoni
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kerry Dobbs
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irit Tirosh
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Likun Du
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Francesca A Ververs
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Heng Ru
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lisa Ott de Bruin
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mehdi Adeli
- Pediatrics Department, Weill Cornell Medical College, Hamad Medical Corporation, Doha, Qatar
| | - Jacob H Bleesing
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - David Buchbinder
- Division of Hematology, Children's Hospital Orange County, Orange County, CA 92868, USA
| | - Manish J Butte
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Caterina Cancrini
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Karin Chen
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Sharon Choo
- Department of Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Reem A Elfeky
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Andrea Finocchi
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Ramsay L Fuleihan
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew R Gennery
- Department of Paediatric Immunology, Great North Children's Hospital, Newcastle Upon Tyne, U.K
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, U.K
| | - Dalia H El-Ghoneimy
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lauren A Henderson
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Elham Hossny
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Robert P Nelson
- Division of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sung-Yun Pai
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Niraj C Patel
- Division of Infectious Disease and Immunology, Department of Pediatrics, Levine Children's Hospital, Carolinas Medical Center, Charlotte, NC 28203, USA
| | - Shereen M Reda
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Pere Soler-Palacin
- Paediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Raz Somech
- Pediatric Department A and the Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Paolo Palma
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Silvia Giliani
- A. Nocivelli Institute for Molecular Medicine, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Section of Medical Genetics, Department of Pathology, Spedali Civili di Bresia, Brescia, Italy
| | - Jolan E Walter
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Pediatric Allergy/Immunology, University of South Florida, and Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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28
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IJspeert H, van Schouwenburg PA, van Zessen D, Pico-Knijnenburg I, Driessen GJ, Stubbs AP, van der Burg M. Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults. Front Immunol 2016; 7:410. [PMID: 27799928 PMCID: PMC5066086 DOI: 10.3389/fimmu.2016.00410] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/22/2016] [Indexed: 12/03/2022] Open
Abstract
Upon antigen recognition via their B cell receptor (BR), B cells migrate to the germinal center where they undergo somatic hypermutation (SHM) to increase their affinity for the antigen, and class switch recombination (CSR) to change the effector function of the secreted antibodies. These steps are essential to create an antigen-experienced BR repertoire that efficiently protects the body against pathogens. At the same time, the BR repertoire should be selected to protect against responses to self-antigen or harmless antigens. Insights into the processes of SHM, selection, and CSR can be obtained by studying the antigen-experienced BR repertoire. Currently, a large reference data set of healthy children and adults, which ranges from neonates to the elderly, is not available. In this study, we analyzed the antigen-experienced repertoire of 38 healthy donors (HD), ranging from cord blood to 74 years old, by sequencing IGA and IGG transcripts using next generation sequencing. This resulted in a large, freely available reference data set containing 412,890 IGA and IGG transcripts. We used this data set to study mutation levels, SHM patterns, antigenic selection, and CSR from birth to elderly HD. Only small differences were observed in SHM patterns, while the mutation levels increase in early childhood and stabilize at 6 years of age at around 7%. Furthermore, comparison of the antigen-experienced repertoire with sequences from the naive immune repertoire showed that features associated with autoimmunity such as long CDR3 length and IGHV4-34 usage are reduced in the antigen-experienced repertoire. Moreover, IGA2 and IGG2 usage was increased in HD in higher age categories, while IGG1 usage was decreased. In addition, we studied clonal relationship in the different samples. Clonally related sequences were found with different subclasses. Interestingly, we found transcripts with the same CDR1–CDR3 sequence, but different subclasses. Together, these data suggest that a single antigen can provoke a B-cell response with BR of different subclasses and that, during the course of an immune response, some B cells change their isotype without acquiring additional SHM or can directly switch to different isotypes.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | | | - David van Zessen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Gertjan J Driessen
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
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29
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Aouinti S, Giudicelli V, Duroux P, Malouche D, Kossida S, Lefranc MP. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST. Front Immunol 2016; 7:339. [PMID: 27667992 PMCID: PMC5016520 DOI: 10.3389/fimmu.2016.00339] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/22/2016] [Indexed: 11/25/2022] Open
Abstract
There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the “IMGT clonotype (AA)” (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for “IMGT clonotype (AA)” diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT® tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package “IMGTStatClonotype,” with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT®1 for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V–D–J associations, in immunoprofiles from normal or pathological immune responses.
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Affiliation(s)
- Safa Aouinti
- IMGT®, The international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University, Montpellier, France; Higher School of Statistics and Information Analysis, Unité Modélisation et Analyse Statistique et Economique, University of Carthage, Tunis, Tunisia
| | - Véronique Giudicelli
- IMGT®, The international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University , Montpellier , France
| | - Patrice Duroux
- IMGT®, The international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University , Montpellier , France
| | - Dhafer Malouche
- Higher School of Statistics and Information Analysis, Unité Modélisation et Analyse Statistique et Economique, University of Carthage , Tunis , Tunisia
| | - Sofia Kossida
- IMGT®, The international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University , Montpellier , France
| | - Marie-Paule Lefranc
- IMGT®, The international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University , Montpellier , France
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Kerzel S, Rogosch T, Struecker B, Maier RF, Kabesch M, Zemlin M. Unlike in Children with Allergic Asthma, IgE Transcripts from Preschool Children with Atopic Dermatitis Display Signs of Superantigen-Driven Activation. THE JOURNAL OF IMMUNOLOGY 2016; 196:4885-92. [PMID: 27183570 DOI: 10.4049/jimmunol.1402889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/11/2016] [Indexed: 01/11/2023]
Abstract
The IgE repertoire in children with asthma reflects an adaptive B cell response, indicative of Ag-driven selection. However, the same might not apply to atopic dermatitis, which is often the first manifestation of atopy. The objective of our present study was to characterize the IgE repertoire of preschool children with atopic dermatitis with regard to signs of superantigen-like activation, clonal relationship, and indications of Ag selection. Total RNA was isolated from PBMCs of five children with atopic dermatitis. IgE transcripts were amplified, cloned, and sequenced using RT-PCR. We obtained 200 functional IgE sequences, which were compared with 1140 sequences from 11 children with asthma. Whereas variable gene segment of the H Ig chain (VH) gene usage in asthma reflected germline distribution, IgE transcripts from children with atopic dermatitis displayed a dominance of the otherwise scarcely expressed VH2 and VH4 family. Whereas IgE transcripts from children with asthma were highly mutated (7.2%), somatic mutation rate in atopic dermatitis was less than half as high (3.4%). Moreover, the proportion of transcripts that were indicative of Ag selection was reduced to 11% in atopic dermatitis (24% in asthma). In summary, IgE repertoires vary significantly between children with different atopic diseases. Compared with children with asthma, IgE transcripts from preschool children with atopic dermatitis are significantly less mutated, clonally less focused, and less indicative of Ag selection. We consider our data reconcilable with the hypothesis that a superantigen-like activation contributes to the maturation and selection of the IgE repertoire in atopic dermatitis.
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Affiliation(s)
- Sebastian Kerzel
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg, St. Hedwig Campus, D-93049 Regensburg, Germany; and Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Tobias Rogosch
- Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Benjamin Struecker
- Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Rolf F Maier
- Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg, St. Hedwig Campus, D-93049 Regensburg, Germany; and
| | - Michael Zemlin
- Department of Pediatrics, Philipps-University Marburg, D-35043 Marburg, Germany
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Ligase-4 Deficiency Causes Distinctive Immune Abnormalities in Asymptomatic Individuals. J Clin Immunol 2016; 36:341-53. [PMID: 27063650 DOI: 10.1007/s10875-016-0266-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/07/2016] [Indexed: 01/01/2023]
Abstract
PURPOSE DNA Ligase 4 (LIG4) is a key factor in the non-homologous end-joining (NHEJ) DNA double-strand break repair pathway needed for V(D)J recombination and the generation of the T cell receptor and immunoglobulin molecules. Defects in LIG4 result in a variable syndrome of growth retardation, pancytopenia, combined immunodeficiency, cellular radiosensitivity, and developmental delay. METHODS We diagnosed a patient with LIG4 syndrome by radiosensitivity testing on peripheral blood cells, and established that two of her four healthy siblings carried the same compound heterozygous LIG4 mutations. An extensive analysis of the immune phenotype, cellular radiosensitivity, telomere length, and T and B cell antigen receptor repertoire was performed in all siblings. RESULTS In the three genotypically affected individuals, variable severities of radiosensitivity, alterations of T and B cell counts with an increased percentage of memory cells, and hypogammaglobulinemia, were noticed. Analysis of T and B cell antigen receptor repertoires demonstrated increased usage of alternative microhomology-mediated end-joining (MHMEJ) repair, leading to diminished N nucleotide addition and shorter CDR3 length. However, overall repertoire diversity was preserved. CONCLUSIONS We demonstrate that LIG4 syndrome presents with high clinical variability even within the same family, and that distinctive immunologic abnormalities may be observed also in yet asymptomatic individuals.
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Cortina-Ceballos B, Godoy-Lozano EE, Sámano-Sánchez H, Aguilar-Salgado A, Velasco-Herrera MDC, Vargas-Chávez C, Velázquez-Ramírez D, Romero G, Moreno J, Téllez-Sosa J, Martínez-Barnetche J. Reconstructing and mining the B cell repertoire with ImmunediveRsity. MAbs 2016; 7:516-24. [PMID: 25875140 PMCID: PMC4622655 DOI: 10.1080/19420862.2015.1026502] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The B cell antigen receptor repertoire is highly diverse and constantly modified by clonal selection. High-throughput DNA sequencing (HTS) of the lymphocyte repertoire (Rep-Seq) represents a promising technology to explore such diversity ex-vivo and assist in the identification of antigen-specific antibodies based on molecular signatures of clonal selection. Therefore, integrative tools for repertoire reconstruction and analysis from antibody sequences are needed. We developed ImmunediveRity, a stand-alone pipeline primarily based in R programming for the integral analysis of B cell repertoire data generated by HTS. The pipeline integrates GNU software and in house scripts to perform quality filtering, sequencing noise correction and repertoire reconstruction based on V, D and J segment assignment, clonal origin and unique heavy chain identification. Post-analysis scripts generate a wealth of repertoire metrics that in conjunction with a rich graphical output facilitates sample comparison and repertoire mining. Its performance was tested with raw and curated human and mouse 454-Roche sequencing benchmarks providing good approximations of repertoire structure. Furthermore, ImmunediveRsity was used to mine the B cell repertoire of immunized mice with a model antigen, allowing the identification of previously validated antigen-specific antibodies, and revealing different and unexpected clonal diversity patterns in the post-immunization IgM and IgG compartments. Although ImmunediveRsity is similar to other recently developed tools, it offers significant advantages that facilitate repertoire analysis and repertoire mining. ImmunediveRsity is open source and free for academic purposes and it runs on 64 bit GNU/Linux and MacOS. Available at: https://bitbucket.org/ImmunediveRsity/immunediversity/
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Affiliation(s)
- Bernardo Cortina-Ceballos
- a Centro de Investigación Sobre Enfermedades Infecciosas; Instituto Nacional de Salud Pública (CISEI-INSP); Cuernavaca , Morelos , México
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33
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B cell development in chromosome 22q11.2 deletion syndrome. Clin Immunol 2016; 163:1-9. [DOI: 10.1016/j.clim.2015.12.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 12/08/2015] [Indexed: 12/24/2022]
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Corsiero E, Bombardieri M, Carlotti E, Pratesi F, Robinson W, Migliorini P, Pitzalis C. Single cell cloning and recombinant monoclonal antibodies generation from RA synovial B cells reveal frequent targeting of citrullinated histones of NETs. Ann Rheum Dis 2015; 75:1866-75. [PMID: 26659717 PMCID: PMC5036240 DOI: 10.1136/annrheumdis-2015-208356] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/01/2015] [Indexed: 12/24/2022]
Abstract
Objectives Rheumatoid arthritis (RA) is characterised by breach of self-tolerance towards citrullinated antigens with generation of anti-citrullinated peptide/proteins antibodies (ACPA). Currently, the nature and source of citrullinated antigens driving the humoral autoimmune response within synovial ectopic lymphoid structures (ELS) is a crucial unknown aspect of RA pathogenesis. Here we characterised the autoreactive B-cell response of lesional B cells isolated from ELS+RA synovium. Methods Single synovial tissue CD19+cells were Fluorescence Activated Cell Sorting (FACS)-sorted and VH/VL Ig genes cloned to generate recombinant monoclonal antibodies (rmAbs) from patients with ELS+/ACPA+RA. Results RA-rmAbs immunoreactivity analysis provided the following key findings: (1) in a chIP-based array containing 300 autoantigens and in a ‘citrullinome’ multiplex assay, a strong reactivity against citrullinated histones H2A/H2B (citH2A/H2B) was observed in ∼40% of RA-rmAbs, followed by cit-fibrinogen and cit-vimentin; (2) anti-citH2A/H2B-reactive RA-rmAbs (but not anti-citH2A/H2B negative) selectively recognised neutrophil extracellular traps (NETs) from peripheral blood and/or RA joint neutrophils; (3) anti-citH2A/citH2B and anti-NET immunobinding was dependent on affinity maturation and was completely abrogated following reversion of hypermutated IgVH/VL genes to germline sequences; (4) ELS+ (not ELS−) RA synovial tissues engrafted into Severe Combined ImmunoDeficiency (SCID) mice released human anti-citH2A/citH2B and anti-NET antibodies in association with the intra-graft expression of CXCL13 and lymphotoxin (LT)-β, two master regulators of ELS. Conclusion We provided novel evidence that B cells differentiated within synovial ELS in the RA joints frequent target deiminated proteins which could be generated during NETosis of RA synovial neutrophils including histones. Thus, NETs could represent a source of citrullinated antigens fuelling the ACPA autoimmune response within the RA synovium.
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Affiliation(s)
- Elisa Corsiero
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Michele Bombardieri
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Emanuela Carlotti
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
| | - Federico Pratesi
- Clinical Immunology and Allergy Unit, Department of Clinical & Experimental Medicine, University of Pisa, Pisa, Italy
| | | | - Paola Migliorini
- Clinical Immunology and Allergy Unit, Department of Clinical & Experimental Medicine, University of Pisa, Pisa, Italy
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, London, UK
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35
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Schaller S, Weinberger J, Jimenez-Heredia R, Danzer M, Oberbauer R, Gabriel C, Winkler SM. ImmunExplorer (IMEX): a software framework for diversity and clonality analyses of immunoglobulins and T cell receptors on the basis of IMGT/HighV-QUEST preprocessed NGS data. BMC Bioinformatics 2015; 16:252. [PMID: 26264428 PMCID: PMC4531494 DOI: 10.1186/s12859-015-0687-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
Background Today’s modern research of B and T cell antigen receptors (the immunoglobulins (IG) or antibodies and T cell receptors (TR)) forms the basis for detailed analyses of the human adaptive immune system. For instance, insights in the state of the adaptive immune system provide information that is essentially important in monitoring transplantation processes and the regulation of immune suppressiva. In this context, algorithms and tools are necessary for analyzing the IG and TR diversity on nucleotide as well as on amino acid sequence level, identifying highly proliferated clonotypes, determining the diversity of the cell repertoire found in a sample, comparing different states of the human immune system, and visualizing all relevant information. Results We here present IMEX, a software framework for the detailed characterization and visualization of the state of human IG and TR repertoires. IMEX offers a broad range of algorithms for statistical analysis of IG and TR data, CDR and V-(D)-J analysis, diversity analysis by calculating the distribution of IG and TR, calculating primer efficiency, and comparing multiple data sets. We use a mathematical model that is able to describe the number of unique clonotypes in a sample taking into account the true number of unique sequences and read errors; we heuristically optimize the parameters of this model. IMEX uses IMGT/HighV-QUEST analysis outputs and includes methods for splitting and merging to enable the submission to this portal and to combine the outputs results, respectively. All calculation results can be visualized and exported. Conclusion IMEX is an user-friendly and flexible framework for performing clonality experiments based on CDR and V-(D)-J rearranged regions, diversity analysis, primer efficiency, and various different visualization experiments. Using IMEX, various immunological reactions and alterations can be investigated in detail. IMEX is freely available for Windows and Unix platforms at http://bioinformatics.fh-hagenberg.at/immunexplorer/. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0687-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susanne Schaller
- University of Applied Sciences Upper Austria, Hagenberg Campus, Bioinformatics Research Group, Softwarepark 13, Hagenberg, 4232, Austria.
| | - Johannes Weinberger
- Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria. .,Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Donaueschingenstrasse 13, Vienna, 1200, Austria.
| | - Raul Jimenez-Heredia
- Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria. .,Ludwig Boltzmann Institute for Experimental and Clinical Traumatology, Donaueschingenstrasse 13, Vienna, 1200, Austria.
| | - Martin Danzer
- Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria.
| | - Rainer Oberbauer
- Elisabethinen Hospital, Fadingerstrasse 1, Linz, 4020, Austria. .,Medical University of Vienna, Department of Nephrology, Spitalgasse 23, Vienna, 1090, Austria.
| | - Christian Gabriel
- Red Cross Transfusion Service of Upper Austria, Krankenhausstrasse 7, Linz, 4020, Austria.
| | - Stephan M Winkler
- University of Applied Sciences Upper Austria, Hagenberg Campus, Bioinformatics Research Group, Softwarepark 13, Hagenberg, 4232, Austria.
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Patil SU, Ogunniyi AO, Calatroni A, Tadigotla VR, Ruiter B, Ma A, Moon J, Love J, Shreffler WG. Peanut oral immunotherapy transiently expands circulating Ara h 2-specific B cells with a homologous repertoire in unrelated subjects. J Allergy Clin Immunol 2015; 136:125-134.e12. [PMID: 25985925 PMCID: PMC4494892 DOI: 10.1016/j.jaci.2015.03.026] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/16/2015] [Accepted: 03/12/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Peanut oral immunotherapy (PNOIT) induces persistent tolerance to peanut in a subset of patients and induces specific antibodies that might play a role in clinical protection. However, the contribution of induced antibody clones to clinical tolerance in PNOIT is unknown. OBJECTIVE We hypothesized that PNOIT induces a clonal, allergen-specific B-cell response that could serve as a surrogate for clinical outcomes. METHODS We used a fluorescent Ara h 2 multimer for affinity selection of Ara h 2-specific B cells and subsequent single-cell immunoglobulin amplification. The diversity of related clones was evaluated by means of next-generation sequencing of immunoglobulin heavy chains from circulating memory B cells with 2x250 paired-end sequencing on the Illumina MiSeq platform. RESULTS Expression of class-switched antibodies from Ara h 2-positive cells confirms enrichment for Ara h 2 specificity. PNOIT induces an early and transient expansion of circulating Ara h 2-specific memory B cells that peaks at week 7. Ara h 2-specific sequences from memory cells have rates of nonsilent mutations consistent with affinity maturation. The repertoire of Ara h 2-specific antibodies is oligoclonal. Next-generation sequencing-based repertoire analysis of circulating memory B cells reveals evidence for convergent selection of related sequences in 3 unrelated subjects, suggesting the presence of similar Ara h 2-specific B-cell clones. CONCLUSIONS Using a novel affinity selection approach to identify antigen-specific B cells, we demonstrate that the early PNOIT-induced Ara h 2-specific B-cell receptor repertoire is oligoclonal and somatically hypermutated and shares similar clonal groups among unrelated subjects consistent with convergent selection.
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Affiliation(s)
- Sarita U. Patil
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Food Allergy Center, Massachusetts General Hospital and MassGeneral Hospital for Children
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA
| | - Adebola O. Ogunniyi
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA
| | | | | | - Bert Ruiter
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Food Allergy Center, Massachusetts General Hospital and MassGeneral Hospital for Children
| | - Alex Ma
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - James Moon
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - J.Christopher Love
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard Medical School
| | - Wayne G. Shreffler
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Food Allergy Center, Massachusetts General Hospital and MassGeneral Hospital for Children
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Intrathecal BCR transcriptome in multiple sclerosis versus other neuroinflammation: Equally diverse and compartmentalized, but more mutated, biased and overlapping with the proteome. Clin Immunol 2015; 160:211-25. [PMID: 26055752 DOI: 10.1016/j.clim.2015.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 05/28/2015] [Accepted: 06/01/2015] [Indexed: 12/22/2022]
Abstract
The mechanisms driving the intrathecal synthesis of IgG in multiple sclerosis (MS) are unknown. We combined high-throughput sequencing of transcribed immunoglobulin heavy-chain variable (IGHV) genes and mass spectrometry to chart the diversity and compartmentalization of IgG-producing B cells in the cerebrospinal fluid (CSF) of MS patients and controls with other neuroinflammatory diseases. In both groups, a few clones dominated the intrathecal IGHV transcriptome. In most MS patients and some controls, dominant transcripts matched the CSF IgG. The IGHV transcripts in CSF of MS patients frequently carried IGHV4 genes and had more replacement mutations compared to controls. In both groups, dominant IGHV transcripts were identified within clusters of clonally related B cells that had identical or related IGHV transcripts in the blood. These findings suggest more pronounced affinity maturation, but an equal degree of diversity and compartmentalization of the intrathecal B-cell response in MS compared to other neuroinflammatory diseases.
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Absence of surrogate light chain results in spontaneous autoreactive germinal centres expanding V(H)81X-expressing B cells. Nat Commun 2015; 6:7077. [PMID: 25959489 DOI: 10.1038/ncomms8077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/31/2015] [Indexed: 02/01/2023] Open
Abstract
Random recombination of antibody heavy- and light-chain genes results in a diverse B-cell receptor (BCR) repertoire including self-reactive BCRs. However, tolerance mechanisms that prevent the development of self-reactive B cells remain incompletely understood. The absence of the surrogate light chain, which assembles with antibody heavy chain forming a pre-BCR, leads to production of antinuclear antibodies (ANAs). Here we show that the naive follicular B-cell pool is enriched for cells expressing prototypic ANA heavy chains in these mice in a non-autoimmune background with a broad antibody repertoire. This results in the spontaneous formation of T-cell-dependent germinal centres that are enriched with B cells expressing prototypic ANA heavy chains. However, peripheral tolerance appears maintained by selection thresholds on cells entering the memory B-cell and plasma cell pools, as exemplified by the exclusion of cells expressing the intrinsically self-reactive V(H)81X from both pools.
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Batoulis H, Wunsch M, Birkenheier J, Rottlaender A, Gorboulev V, Kuerten S. Central nervous system infiltrates are characterized by features of ongoing B cell-related immune activity in MP4-induced experimental autoimmune encephalomyelitis. Clin Immunol 2015; 158:47-58. [PMID: 25796192 DOI: 10.1016/j.clim.2015.03.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 12/25/2022]
Abstract
In multiple sclerosis (MS) lymphoid follicle-like aggregates have been reported in the meninges of patients. Here we investigated the functional relevance of B cell infiltration into the central nervous system (CNS) in MP4-induced experimental autoimmune encephalomyelitis (EAE), a B cell-dependent mouse model of MS. In chronic EAE, B cell aggregates were characterized by the presence of CXCL13(+) and germinal center CD10(+) B cells. Germline transcripts were expressed in the CNS and particularly related to TH17-associated isotypes. We also observed B cells with restricted VH gene usage that differed from clones found in the spleen. Finally, we detected CNS-restricted spreading of the antigen-specific B cell response towards a myelin and a neuronal autoantigen. These data imply the development of autonomous B cell-mediated autoimmunity in the CNS in EAE - a concept that might also apply to MS itself.
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Affiliation(s)
- Helena Batoulis
- Department of Anatomy I, University of Cologne, Joseph-Stelzmann-Str. 9, 50931 Cologne, Germany
| | - Marie Wunsch
- Department of Anatomy and Cell Biology, University of Wuerzburg, Koellikerstr. 6, 97070 Wuerzburg, Germany
| | - Johannes Birkenheier
- Department of Anatomy I, University of Cologne, Joseph-Stelzmann-Str. 9, 50931 Cologne, Germany
| | - Andrea Rottlaender
- Department of Anatomy and Cell Biology, University of Wuerzburg, Koellikerstr. 6, 97070 Wuerzburg, Germany
| | - Valentin Gorboulev
- Department of Anatomy and Cell Biology, University of Wuerzburg, Koellikerstr. 6, 97070 Wuerzburg, Germany
| | - Stefanie Kuerten
- Department of Anatomy and Cell Biology, University of Wuerzburg, Koellikerstr. 6, 97070 Wuerzburg, Germany.
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Rechavi E, Lev A, Lee YN, Simon AJ, Yinon Y, Lipitz S, Amariglio N, Weisz B, Notarangelo LD, Somech R. Timely and spatially regulated maturation of B and T cell repertoire during human fetal development. Sci Transl Med 2015; 7:276ra25. [DOI: 10.1126/scitranslmed.aaa0072] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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41
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Schroeder HW. The evolution and development of the antibody repertoire. Front Immunol 2015; 6:33. [PMID: 25699050 PMCID: PMC4318424 DOI: 10.3389/fimmu.2015.00033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 01/16/2015] [Indexed: 11/19/2022] Open
Affiliation(s)
- Harry W Schroeder
- Department of Medicine, Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham , Birmingham, AL , USA
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Zinöcker S, Schindler CE, Skinner J, Rogosch T, Waisberg M, Schickel JN, Meffre E, Kayentao K, Ongoïba A, Traoré B, Pierce SK. The V gene repertoires of classical and atypical memory B cells in malaria-susceptible West African children. THE JOURNAL OF IMMUNOLOGY 2015; 194:929-39. [PMID: 25556245 DOI: 10.4049/jimmunol.1402168] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Immunity to Plasmodium falciparum malaria is naturally acquired in individuals living in malaria-endemic areas of Africa. Abs play a key role in mediating this immunity; however, the acquisition of the components of Ab immunity, long-lived plasma cells and memory B cells (MBCs), is remarkably inefficient, requiring years of malaria exposure. Although long-lived classical MBCs (CD19(+)/CD20(+)/CD21(+)/CD27(+)/CD10(-)) are gradually acquired in response to natural infection, exposure to P. falciparum also results in a large expansion of what we have termed atypical MBCs (CD19(+)/CD20(+)/CD21(-)/CD27(-)/CD10(-)). At present, the function of atypical MBCs in malaria is not known, nor are the factors that drive their differentiation. To gain insight into the relationship between classical and atypical IgG(+) MBCs, we compared the Ab H and L chain V gene repertoires of children living in a malaria-endemic region in Mali. We found that these repertoires were remarkably similar by a variety of criteria, including V gene usage, rate of somatic hypermutation, and CDR-H3 length and composition. The similarity in these repertoires suggests that classical MBCs and atypical MBCs differentiate in response to similar Ag-dependent selective pressures in malaria-exposed children and that atypical MBCs do not express a unique V gene repertoire.
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Affiliation(s)
- Severin Zinöcker
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852;
| | - Christine E Schindler
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Jeff Skinner
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Tobias Rogosch
- Laboratory for Neonatology and Pediatric Immunology, Department of Pediatrics, Philipps-University, D-35032 Marburg, Germany
| | - Michael Waisberg
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852; Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908
| | - Jean-Nicolas Schickel
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510; and
| | - Eric Meffre
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06510; and
| | - Kassoum Kayentao
- Mali International Center for Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Aïssata Ongoïba
- Mali International Center for Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Boubacar Traoré
- Mali International Center for Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852;
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Corsiero E, Sutcliffe N, Pitzalis C, Bombardieri M. Accumulation of self-reactive naïve and memory B cell reveals sequential defects in B cell tolerance checkpoints in Sjögren's syndrome. PLoS One 2014; 9:e114575. [PMID: 25535746 PMCID: PMC4275206 DOI: 10.1371/journal.pone.0114575] [Citation(s) in RCA: 30] [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: 08/12/2014] [Accepted: 11/11/2014] [Indexed: 11/18/2022] Open
Abstract
Sjögren's syndrome (SS) is an autoimmune disease characterised by breach of self-tolerance towards nuclear antigens resulting in high affinity circulating autoantibodies. Although peripheral B cell disturbances have been described in SS, with predominance of naïve and reduction of memory B cells, the stage at which errors in B cell tolerance checkpoints accumulate in SS is unknown. Here we determined the frequency of self- and poly-reactive B cells in the circulating naïve and memory compartment of SS patients. Single CD27-IgD+ naïve, CD27+IgD+ memory unswitched and CD27+IgD- memory switched B cells were sorted by FACS from the peripheral blood of 7 SS patients. To detect the frequency of polyreactive and autoreactive clones, paired Ig VH and VL genes were amplified, cloned and expressed as recombinant monoclonal antibodies (rmAbs) displaying identical specificity of the original B cells. IgVH and VL gene usage and immunoreactivity of SS rmAbs were compared with those obtained from healthy donors (HD). From a total of 353 VH and 293 VL individual sequences, we obtained 114 rmAbs from circulating naïve (n = 66) and memory (n = 48) B cells of SS patients. Analysis of the Ig V gene repertoire did not show significant differences in SS vs. HD B cells. In SS patients, circulating naïve B cells (with germline VH and VL genes) displayed a significant accumulation of clones autoreactive against Hep-2 cells compared to HD (43.1% vs. 25%). Moreover, we demonstrated a progressive increase in the frequency of circulating anti-nuclear naïve (9.3%), memory unswitched (22.2%) and memory switched (27.3%) B cells in SS patients. Overall, these data provide novel evidence supporting the existence of both early and late defects in B cell tolerance checkpoints in patients with SS resulting in the accumulation of autoreactive naïve and memory B cells.
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Affiliation(s)
- Elisa Corsiero
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, United Kingdom
- * E-mail: (EC); (MB)
| | - Nurhan Sutcliffe
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, United Kingdom
| | - Michele Bombardieri
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine & Dentistry, Queen Mary University of London, John Vane Science Centre, Charterhouse Square, London EC1M 6BQ, United Kingdom
- * E-mail: (EC); (MB)
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Rogosch T, Kerzel S, Dey F, Wagner JJ, Zhang Z, Maier RF, Zemlin M. IgG4 and IgE transcripts in childhood allergic asthma reflect divergent antigen-driven selection. THE JOURNAL OF IMMUNOLOGY 2014; 193:5801-8. [PMID: 25385824 DOI: 10.4049/jimmunol.1401409] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The physiologic function of the "odd" Ab IgG4 remains enigmatic. IgG4 mediates immunotolerance, as, for example, during specific immunotherapy of allergies, but it mediates tissue damage in autoimmune pemphigus vulgaris and "IgG4-related disease." Approximately half of the circulating IgG4 molecules are bispecific owing to their unique ability to exchange half-molecules. Better understanding of the interrelation between IgG4 and IgE repertoires may yield insight into the pathogenesis of allergies and into potential novel therapies that modulate IgG4 responses. We aimed to compare the selective forces that forge the IgG4 and IgE repertoires in allergic asthma. Using an IgG4-specific RT-PCR, we amplified, cloned, and sequenced IgG4 H chain transcripts of PBMCs from 10 children with allergic asthma. We obtained 558 functional IgG4 sequences, of which 286 were unique. Compared with previously published unique IgE transcripts from the same blood samples, the somatic mutation rate was significantly enhanced in IgG4 transcripts (62 versus 83%; p < 0.001), whereas fewer IgG4 sequences displayed statistical evidence of Ag-driven selection (p < 0.001). On average, the hypervariable CDRH3 region was four nucleotides shorter in IgG4 than in IgE transcripts (p < 0.001). IgG4 transcripts in the circulation of children with allergic asthma reflect some characteristics of classical Ag-driven B2 immune responses but display less indication of Ag selection than do IgE transcripts. Although allergen-specific IgG4 can block IgE-mediated allergen presentation and degranulation of mast cells, key factors that influence the Ag-binding properties of the Ab differ between the overall repertoires of circulating IgG4- and IgE-expressing cells.
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Affiliation(s)
- Tobias Rogosch
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Sebastian Kerzel
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg, St. Hedwig Campus, 93053 Regensburg, Germany; and
| | - Friederike Dey
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | | | - Zhixin Zhang
- Department of Pathology and Microbiology, Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198
| | - Rolf F Maier
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany
| | - Michael Zemlin
- Department of Pediatrics, Philipps-University Marburg, D-35033 Marburg, Germany;
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The same self-peptide selects conventional and regulatory CD4⁺ T cells with identical antigen receptors. Nat Commun 2014; 5:5061. [PMID: 25270305 PMCID: PMC4183978 DOI: 10.1038/ncomms6061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 08/25/2014] [Indexed: 12/28/2022] Open
Abstract
The role of the T cell receptor (TCR) in commitment of thymocytes to regulatory CD4+Foxp3+ and conventional CD4−Foxp3− T cell lineages remains controversial. According to the prevailing view, commitment to the former lineage, in contrast to the latter, requires that high affinity TCRs bind rare class II MHC/peptide complexes presented in “thymic niches”, which could explain differences between their TCR repertoires. Here we challenge this view and show that the binding of identical TCRs to the same ubiquitously expressed MHC/peptide complex often directs thymocytes to both CD4+ lineages, indicating that the TCR affinity does not play the instructive role, and that restricted presentation of peptides in ”thymic niches” is not necessary for selection of CD4+Foxp3+ T cells. However, depending on whether immature thymocytes bound the ligand predominantly with low or high affinity, the repertoires of regulatory and conventional CD4+ T cells were correspondingly similar or mostly different, suggesting that negative rather than positive selection sets them apart.
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46
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Sorouri M, Fitzsimmons SP, Aydanian AG, Bennett S, Shapiro MA. Diversity of the antibody response to tetanus toxoid: comparison of hybridoma library to phage display library. PLoS One 2014; 9:e106699. [PMID: 25268771 PMCID: PMC4182348 DOI: 10.1371/journal.pone.0106699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 08/08/2014] [Indexed: 11/18/2022] Open
Abstract
Monoclonal antibodies are important tools in research and since the 1990s have been an important therapeutic class targeting a wide variety of diseases. Earlier methods of mAb production relied exclusively on the lengthy process of making hybridomas. The advent of phage display technology introduced an alternative approach for mAb production. A potential concern with this approach is its complete dependence on an in vitro selection process, which may result in selection of V(H)-V(L) pairs normally eliminated during the in vivo selection process. The diversity of V(H)-V(L) pairs selected from phage display libraries relative to an endogenous response is unknown. To address these questions, we constructed a panel of hybridomas and a phage display library using the spleen of a single tetanus toxoid-immunized mouse and compared the diversity of the immune response generated using each technique. Surprisingly, the tetanus toxoid-specific antibodies produced by the hybridoma library exhibited a higher degree of V(H)-V(L) genetic diversity than their phage display-derived counterparts. Furthermore, the overlap among the V-genes from each library was very limited. Consistent with the notion that accumulation of many small DNA changes lead to increased antigen specificity and affinity, the phage clones displayed substantial micro-heterogeneity. Contrary to previous reports, we found that antigen specificity against tetanus toxoid is encoded by both V(κ) and V(H) genes. Finally, the phage-derived tetanus-specific clones had a lower binding affinity than the hybridomas, a phenomenon thought to be the result of random pairing of the V-genes.
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Affiliation(s)
- Mahsa Sorouri
- Laboratory of Molecular and Developmental Immunology, Division of Monoclonal Antibodies, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Sean P. Fitzsimmons
- Laboratory of Molecular and Developmental Immunology, Division of Monoclonal Antibodies, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Antonina G. Aydanian
- Laboratory of Molecular and Developmental Immunology, Division of Monoclonal Antibodies, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Sonita Bennett
- Laboratory of Molecular and Developmental Immunology, Division of Monoclonal Antibodies, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
| | - Marjorie A. Shapiro
- Laboratory of Molecular and Developmental Immunology, Division of Monoclonal Antibodies, Center for Drug Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, United States of America
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Schwartz MA, Kolhatkar NS, Thouvenel C, Khim S, Rawlings DJ. CD4+ T cells and CD40 participate in selection and homeostasis of peripheral B cells. THE JOURNAL OF IMMUNOLOGY 2014; 193:3492-502. [PMID: 25172502 DOI: 10.4049/jimmunol.1400798] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Control of peripheral B cell development and homeostasis depends critically on coordinate signals received through the BAFFRs and BCRs. The extent to which other signals contribute to this process, however, remains undefined. We present data indicating that CD4(+) T cells directly influence naive B cell development via CD40 signaling. Loss of CD4(+) T cells or CD40-CD40L interaction leads to reduced B cell homeostatic proliferation and hindered B cell reconstitution posttransplantation. Furthermore, we demonstrate that in the absence of CD40 signals, these events are modulated by BCR self-reactivity. Strikingly, murine models lacking CD40 reveal a broadly altered BCR specificity and limited diversity by both single-cell cloning and high-throughput sequencing techniques. Collectively, our results imply that any setting of T cell lymphopenia or reduced CD40 function, including B cell recovery following transplantation, will impact the naive B cell repertoire.
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Affiliation(s)
- Marc A Schwartz
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
| | - Nikita S Kolhatkar
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195
| | - Chris Thouvenel
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195; and Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101
| | - Socheath Khim
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195; and Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101
| | - David J Rawlings
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98195; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195; and Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101
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48
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O'Connell AE, Volpi S, Dobbs K, Fiorini C, Tsitsikov E, de Boer H, Barlan IB, Despotovic JM, Espinosa-Rosales FJ, Hanson IC, Kanariou MG, Martínez-Beckerat R, Mayorga-Sirera A, Mejia-Carvajal C, Radwan N, Weiss AR, Pai SY, Lee YN, Notarangelo LD. Next generation sequencing reveals skewing of the T and B cell receptor repertoires in patients with wiskott-Aldrich syndrome. Front Immunol 2014; 5:340. [PMID: 25101082 PMCID: PMC4102881 DOI: 10.3389/fimmu.2014.00340] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/04/2014] [Indexed: 12/26/2022] Open
Abstract
The Wiskott–Aldrich syndrome (WAS) is due to mutations of the WAS gene encoding for the cytoskeletal WAS protein, leading to abnormal downstream signaling from the T cell and B cell antigen receptors (TCR and BCR). We hypothesized that the impaired signaling through the TCR and BCR in WAS would subsequently lead to aberrations in the immune repertoire of WAS patients. Using next generation sequencing (NGS), the T cell receptor β and B cell immunoglobulin heavy chain (IGH) repertoires of eight patients with WAS and six controls were sequenced. Clonal expansions were identified within memory CD4+ cells as well as in total, naïve and memory CD8+ cells from WAS patients. In the B cell compartment, WAS patient IGH repertoires were also clonally expanded and showed skewed usage of IGHV and IGHJ genes, and increased usage of IGHG constant genes, compared with controls. To our knowledge, this is the first study that demonstrates significant abnormalities of the immune repertoire in WAS patients using NGS.
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Affiliation(s)
- Amy E O'Connell
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA
| | - Stefano Volpi
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA
| | - Kerry Dobbs
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA
| | - Claudia Fiorini
- Department of Hematology/Oncology, Boston Children's Hospital , Boston, MA , USA
| | - Erdyni Tsitsikov
- Department of Laboratory Medicine, Boston Children's Hospital , Boston, MA , USA
| | - Helen de Boer
- Department of Hematology/Oncology, Boston Children's Hospital , Boston, MA , USA
| | - Isil B Barlan
- Marmara University Medical Center , Istanbul , Turkey
| | | | | | | | | | - Roxana Martínez-Beckerat
- Department of Pediatric Hemato-Oncology, Hospital Mario Catarino Rivas , San Pedro Sula , Honduras
| | | | | | | | | | - Sung-Yun Pai
- Department of Hematology/Oncology, Boston Children's Hospital , Boston, MA , USA
| | - Yu Nee Lee
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA
| | - Luigi D Notarangelo
- Department of Immunology, Boston Children's Hospital , Boston, MA , USA ; Manton Center for Orphan Disease Research, Boston Children's Hospital , Boston, MA , USA
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49
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Fundamental characteristics of the expressed immunoglobulin VH and VL repertoire in different canine breeds in comparison with those of humans and mice. Mol Immunol 2014; 59:71-8. [DOI: 10.1016/j.molimm.2014.01.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 01/12/2014] [Accepted: 01/13/2014] [Indexed: 11/19/2022]
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50
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Lee YN, Frugoni F, Dobbs K, Walter JE, Giliani S, Gennery AR, Al-Herz W, Haddad E, LeDeist F, Bleesing JH, Henderson LA, Pai SY, Nelson RP, El-Ghoneimy DH, El-Feky RA, Reda SM, Hossny E, Soler-Palacin P, Fuleihan RL, Patel NC, Massaad MJ, Geha RS, Puck JM, Palma P, Cancrini C, Chen K, Vihinen M, Alt FW, Notarangelo LD. A systematic analysis of recombination activity and genotype-phenotype correlation in human recombination-activating gene 1 deficiency. J Allergy Clin Immunol 2014; 133:1099-108. [PMID: 24290284 PMCID: PMC4005599 DOI: 10.1016/j.jaci.2013.10.007] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 10/03/2013] [Accepted: 10/04/2013] [Indexed: 11/17/2022]
Abstract
BACKGROUND The recombination-activating gene (RAG) 1/2 proteins play a critical role in the development of T and B cells by initiating the VDJ recombination process that leads to generation of a broad T-cell receptor (TCR) and B-cell receptor repertoire. Pathogenic mutations in the RAG1/2 genes result in various forms of primary immunodeficiency, ranging from T(-)B(-) severe combined immune deficiency to delayed-onset disease with granuloma formation, autoimmunity, or both. It is not clear what contributes to such heterogeneity of phenotypes. OBJECTIVE We sought to investigate the molecular basis for phenotypic diversity presented in patients with various RAG1 mutations. METHODS We have developed a flow cytometry-based assay that allows analysis of RAG recombination activity based on green fluorescent protein expression and have assessed the induction of the Ighc locus rearrangements in mouse Rag1(-/-) pro-B cells reconstituted with wild-type or mutant human RAG1 (hRAG1) using deep sequencing technology. RESULTS Here we demonstrate correlation between defective recombination activity of hRAG1 mutant proteins and severity of the clinical and immunologic phenotype and provide insights on the molecular mechanisms accounting for such phenotypic diversity. CONCLUSIONS Using a sensitive assay to measure the RAG1 activity level of 79 mutations in a physiologic setting, we demonstrate correlation between recombination activity of RAG1 mutants and the severity of clinical presentation and show that RAG1 mutants can induce specific abnormalities of the VDJ recombination process.
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Affiliation(s)
- Yu Nee Lee
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, Mass
| | - Francesco Frugoni
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, Mass
| | - Kerry Dobbs
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, Mass
| | - Jolan E Walter
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, Mass; Division of Pediatric Allergy/Immunology, Massachusetts General Hospital for Children, Boston, Mass
| | - Silvia Giliani
- A. Nocivelli Institute for Molecular Medicine, Pediatric Clinic, University of Brescia, and the Section of Genetics, Department of Pathology Spedali Civili, Brescia, Italy
| | - Andrew R Gennery
- Department of Paediatric Immunology, Newcastle Upon Tyne Hospital, NHS Foundation Trust, United Kingdom and Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Elie Haddad
- Department of Pediatrics and Department of Microbiology, Infectiology and Immunology, University of Montreal, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Francoise LeDeist
- Department of Pediatrics and Department of Microbiology, Infectiology and Immunology, University of Montreal, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Jack H Bleesing
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Lauren A Henderson
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, Mass
| | - Sung-Yun Pai
- Division of Hematology-Oncology, Boston Children's Hospital, Boston, Mass
| | - Robert P Nelson
- Divisions of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, Ind
| | - Dalia H El-Ghoneimy
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Reem A El-Feky
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Shereen M Reda
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Elham Hossny
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Pere Soler-Palacin
- Paediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Ramsay L Fuleihan
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Niraj C Patel
- Immunology Clinic, Levine Children's Hospital, Carolinas Medical Center, Charlotte, NC
| | - Michel J Massaad
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, Mass
| | - Raif S Geha
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, Mass
| | - Jennifer M Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children's Hospital, San Francisco, Calif
| | - Paolo Palma
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Caterina Cancrini
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Karin Chen
- Division of Allergy, Immunology & Rheumatology, Department of Pediatrics, University of Utah, Salt Lake City, Utah
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, and the Department of Genetics, Harvard Medical School, Boston, Mass.
| | - Luigi D Notarangelo
- Division of Immunology and Manton Center for Orphan Disease Research, Children's Hospital, Harvard Medical School, Boston, Mass.
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