1
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Sarafova SD. Accurate incorporation of somatic recombination in a hands-on activity that demonstrates the central dogma of molecular biology. J Microbiol Biol Educ 2024; 25:e0016923. [PMID: 38661398 PMCID: PMC11044637 DOI: 10.1128/jmbe.00169-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
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2
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Smirnova AO, Miroshnichenkova AM, Belyaeva LD, Kelmanson IV, Lebedev YB, Mamedov IZ, Chudakov DM, Komkov AY. Novel bimodal TRBD1-TRBD2 rearrangements with dual or absent D-region contribute to TRB V-(D)-J combinatorial diversity. Front Immunol 2023; 14:1245175. [PMID: 37744336 PMCID: PMC10513440 DOI: 10.3389/fimmu.2023.1245175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023] Open
Abstract
T-cell receptor (TR) diversity of the variable domains is generated by recombination of both the alpha (TRA) and beta (TRB) chains. The textbook process of TRB chain production starts with TRBD and TRBJ gene rearrangement, followed by the rearrangement of a TRBV gene to the partially rearranged D-J gene. Unsuccessful V-D-J TRB rearrangements lead to apoptosis of the cell. Here, we performed deep sequencing of the poorly explored pool of partial TRBD1-TRBD2 rearrangements in T-cell genomic DNA. We reconstructed full repertoires of human partial TRBD1-TRBD2 rearrangements using novel sequencing and validated them by detecting V-D-J recombination-specific byproducts: excision circles containing the recombination signal (RS) joint 5'D2-RS - 3'D1-RS. Identified rearrangements were in compliance with the classical 12/23 rule, common for humans, rats, and mice and contained typical V-D-J recombination footprints. Interestingly, we detected a bimodal distribution of D-D junctions indicating two active recombination sites producing long and short D-D rearrangements. Long TRB D-D rearrangements with two D-regions are coding joints D1-D2 remaining classically on the chromosome. The short TRB D-D rearrangements with no D-region are signal joints, the coding joint D1-D2 being excised from the chromosome. They both contribute to the TRB V-(D)-J combinatorial diversity. Indeed, short D-D rearrangements may be followed by direct V-J2 recombination. Long D-D rearrangements may recombine further with J2 and V genes forming partial D1-D2-J2 and then complete V-D1-D2-J2 rearrangement. Productive TRB V-D1-D2-J2 chains are present and expressed in thousands of clones of human antigen-experienced memory T cells proving their capacity for antigen recognition and actual participation in the immune response.
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Affiliation(s)
- Anastasia O. Smirnova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Laima D. Belyaeva
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ilya V. Kelmanson
- Department of Biomolecular Sciences and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yuri B. Lebedev
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ilgar Z. Mamedov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Dmitriy M. Chudakov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Alexander Y. Komkov
- Genomics of Adaptive Immunity Department, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Abu Dhabi Stem Cells Center (ADSCC), Abu Dhabi, United Arab Emirates
- Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology, and Immunology, Moscow, Russia
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3
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Hu Z, Cohen S, Swanson SJ. The immunogenicity of human-origin therapeutic antibodies are associated with V gene usage. Front Immunol 2023; 14:1237754. [PMID: 37720227 PMCID: PMC10502710 DOI: 10.3389/fimmu.2023.1237754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/18/2023] [Indexed: 09/19/2023] Open
Abstract
Therapeutic antibodies can elicit unwanted immune responses in a subset of patients, which leads to the production of anti-drug antibodies (ADA). Some of these ADAs have been reported to effect the pharmacokinetics, efficacy and/or safety of the therapeutic antibodies. The sequence diversity of antibodies are generated by VDJ recombination and mutagenesis. While the antibody generation process can create a large candidate pool for identifying high-affinity antibodies, it also could produce sequences that are foreign to the human immune system. However, it is not clear how VDJ recombination and mutagenesis impact the clinical ADA rate of therapeutic antibodies. In this study, we identified a positive correlation between the clinical ADA rate and the number of introduced mutations in the antibody sequences. We also found that the use of rare V alleles in human-origin antibody therapeutics is associated with higher risk of immunogenicity. The results suggest that antibody engineering projects should start with frameworks that contain commonly used V alleles and prioritize antibody candidates with low number of mutations to reduce the risk of immunogenicity.
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Dauphars DJ, Wu G, Bassing CH, Krangel MS. Methods for Study of Mouse T Cell Receptor α and β Gene Rearrangements. Methods Mol Biol 2023; 2580:261-282. [PMID: 36374463 DOI: 10.1007/978-1-0716-2740-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Quantitative real-time PCR and next-generation sequencing (NGS) are invaluable techniques to analyze T cell receptor (Tcr) gene rearrangements in mouse lymphocyte populations. Although these approaches are powerful, they also have limitations that must be accounted for in experimental design and data interpretation. Here, we provide relevant background required for understanding these limitations and then outline established quantitative real-time PCR and NGS methods that can be used for analysis of mouse Tcra and Tcrb gene rearrangements in mice.
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Affiliation(s)
- Danielle J Dauphars
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA
| | - Glendon Wu
- Immunology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Craig H Bassing
- Immunology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael S Krangel
- Department of Immunology, Duke University School of Medicine, Durham, NC, USA.
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5
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Aubrey M, Warburg ZJ, Murre C. Helix-Loop-Helix Proteins in Adaptive Immune Development. Front Immunol 2022; 13:881656. [PMID: 35634342 PMCID: PMC9134016 DOI: 10.3389/fimmu.2022.881656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
The E/ID protein axis is instrumental for defining the developmental progression and functions of hematopoietic cells. The E proteins are dimeric transcription factors that activate gene expression programs and coordinate changes in chromatin organization. Id proteins are antagonists of E protein activity. Relative levels of E/Id proteins are modulated throughout hematopoietic development to enable the progression of hematopoietic stem cells into multiple adaptive and innate immune lineages including natural killer cells, B cells and T cells. In early progenitors, the E proteins promote commitment to the T and B cell lineages by orchestrating lineage specific programs of gene expression and regulating VDJ recombination of antigen receptor loci. In mature B cells, the E/Id protein axis functions to promote class switch recombination and somatic hypermutation. E protein activity further regulates differentiation into distinct CD4+ and CD8+ T cells subsets and instructs mature T cell immune responses. In this review, we discuss how the E/Id proteins define the adaptive immune system lineages, focusing on their role in directing developmental gene programs.
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Affiliation(s)
- Megan Aubrey
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Zachary J Warburg
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Cornelis Murre
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, CA, United States
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6
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Yadav M, Jalan M, Srivastava M. Enhancer dependent repositioning of TCRb locus with respect to the chromosome territory. J Mol Biol 2022; 434:167509. [PMID: 35202629 DOI: 10.1016/j.jmb.2022.167509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/11/2022] [Accepted: 02/16/2022] [Indexed: 11/19/2022]
Abstract
Intranuclear position of several genes is dynamically altered during development concordant with their activation. To understand this dynamic, but non-random, nuclear organization, it is important to identify the relevant regulatory elements and trans acting factors. Murine TCRb locus gets activated during thymic development. Enhancer Eb is important for VDJ recombination at TCRb locus as it is critically required establishment of recombination center. Our analysis revealed that TCRb locus gets located out of the chromosome territory specifically in developing thymocytes. Further, CRISPR/Cas9 based deletion mutagenesis established an unambiguous role of enhancer Eb in defining TCRb location relative to chromosome territory. The ability to reposition the target locus relative to chromosome territory highlights a novel aspect pertaining to activity of enhancers which may contribute to their ability to regulate gene expression. Additionally, our observations have implications for understanding the role of enhancers in three-dimensional genome organization and function.
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Affiliation(s)
- Monika Yadav
- National Institute of Immunology, Aruna Asaf Ali Road, New Delhi 110067, India
| | - Manisha Jalan
- National Institute of Immunology, Aruna Asaf Ali Road, New Delhi 110067, India
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7
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Aizik L, Dror Y, Taussig D, Barzel A, Carmi Y, Wine Y. Antibody Repertoire Analysis of Tumor-Infiltrating B Cells Reveals Distinct Signatures and Distributions Across Tissues. Front Immunol 2021; 12:705381. [PMID: 34349765 PMCID: PMC8327180 DOI: 10.3389/fimmu.2021.705381] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
The role of B cells in the tumor microenvironment (TME) has largely been under investigated, and data regarding the antibody repertoire encoded by B cells in the TME and the adjacent lymphoid organs are scarce. Here, we utilized B cell receptor high-throughput sequencing (BCR-Seq) to profile the antibody repertoire signature of tumor-infiltrating lymphocyte B cells (TIL−Bs) in comparison to B cells from three anatomic compartments in a mouse model of triple-negative breast cancer. We found that TIL-Bs exhibit distinct antibody repertoire measures, including high clonal polarization and elevated somatic hypermutation rates, suggesting a local antigen-driven B-cell response. Importantly, TIL-Bs were highly mutated but non-class switched, suggesting that class-switch recombination may be inhibited in the TME. Tracing the distribution of TIL-B clones across various compartments indicated that they migrate to and from the TME. The data thus suggests that antibody repertoire signatures can serve as indicators for identifying tumor-reactive B cells.
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Affiliation(s)
- Ligal Aizik
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Dror
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - David Taussig
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Adi Barzel
- The School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yaron Carmi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yariv Wine
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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8
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Akiyama T, Yamamoto T. Regulation of Early Lymphocyte Development via mRNA Decay Catalyzed by the CCR4-NOT Complex. Front Immunol 2021; 12:715675. [PMID: 34349771 PMCID: PMC8326961 DOI: 10.3389/fimmu.2021.715675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
Development of lymphocytes is precisely regulated by various mechanisms. In addition to transcriptional rates, post-transcriptional regulation of mRNA abundance contributes to differentiation of lymphocytes. mRNA decay is a post-transcriptional mechanism controlling mRNA abundance. The carbon catabolite repression 4 (CCR4)-negative on TATA-less (NOT) complex controls mRNA longevity by catalyzing mRNA deadenylation, which is the rate-limiting step in the mRNA decay pathway. mRNA decay, regulated by the CCR4-NOT complex, is required for differentiation of pro-B to pre-B cells and V(D)J recombination in pro-B cells. In this process, it is likely that the RNA-binding proteins, ZFP36 ring finger protein like 1 and 2, recruit the CCR4-NOT complex to specific target mRNAs, thereby inducing cell quiescence of pro-B cells. A recent study showed that the CCR4-NOT complex participates in positive selection of thymocytes. Mechanistically, the CCR4-NOT deadenylase complex inhibits abnormal apoptosis by reducing the expression level of mRNAs encoding pro-apoptotic proteins, which are otherwise up-regulated during positive selection. We discuss mechanisms regulating CCR4-NOT complex-dependent mRNA decay in lymphocyte development and selection.
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Affiliation(s)
- Taishin Akiyama
- Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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9
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Kenter AL, Watson CT, Spille JH. Igh Locus Polymorphism May Dictate Topological Chromatin Conformation and V Gene Usage in the Ig Repertoire. Front Immunol 2021; 12:682589. [PMID: 34084176 PMCID: PMC8167033 DOI: 10.3389/fimmu.2021.682589] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/26/2021] [Indexed: 01/08/2023] Open
Abstract
Vast repertoires of unique antigen receptors are created in developing B and T lymphocytes. The antigen receptor loci contain many variable (V), diversity (D) and joining (J) gene segments that are arrayed across very large genomic expanses and are joined to form variable-region exons of expressed immunoglobulins and T cell receptors. This process creates the potential for an organism to respond to large numbers of different pathogens. Here, we consider the possibility that genetic polymorphisms with alterations in a vast array of regulatory elements in the immunoglobulin heavy chain (IgH) locus lead to changes in locus topology and impact immune-repertoire formation.
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Affiliation(s)
- Amy L. Kenter
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, United States
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Jan-Hendrik Spille
- Department of Physics, University of Illinois at Chicago, Chicago, IL, United States
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10
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Bosticardo M, Pala F, Notarangelo LD. RAG deficiencies: Recent advances in disease pathogenesis and novel therapeutic approaches. Eur J Immunol 2021; 51:1028-1038. [PMID: 33682138 PMCID: PMC8325549 DOI: 10.1002/eji.202048880] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 01/13/2021] [Accepted: 03/03/2021] [Indexed: 12/26/2022]
Abstract
The RAG1 and RAG2 proteins initiate the process of V(D)J recombination and therefore play an essential role in adaptive immunity. While null mutations in the RAG genes cause severe combined immune deficiency with lack of T and B cells (T- B- SCID) and susceptibility to life-threatening, early-onset infections, studies in humans and mice have demonstrated that hypomorphic RAG mutations are associated with defects of central and peripheral tolerance resulting in immune dysregulation. In this review, we provide an overview of the extended spectrum of RAG deficiencies and their associated clinical and immunological phenotypes in humans. We discuss recent advances in the mechanisms that control RAG expression and function, the effects of perturbed RAG activity on lymphoid development and immune homeostasis, and propose novel approaches to correct this group of disorders.
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Affiliation(s)
- Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Pala
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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11
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Shinoda K, Maman Y, Canela A, Schatz DG, Livak F, Nussenzweig A. Intra-Vκ Cluster Recombination Shapes the Ig Kappa Locus Repertoire. Cell Rep 2020; 29:4471-4481.e6. [PMID: 31875554 DOI: 10.1016/j.celrep.2019.11.088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/04/2019] [Accepted: 11/21/2019] [Indexed: 10/25/2022] Open
Abstract
During V(D)J recombination, RAG proteins introduce DNA double-strand breaks (DSBs) at recombination signal sequences (RSSs) that contain either 12- or 23-nt spacer regions. Coordinated 12/23 cleavage predicts that DSBs at variable (V) gene segments should equal the level of breakage at joining (J) segments. Contrary to this, here we report abundant RAG-dependent DSBs at multiple Vκ gene segments independent of V-J rearrangement. We find that a large fraction of Vκ gene segments are flanked not only by a bone-fide 12 spacer but also an overlapping, 23-spacer flipped RSS. These compatible pairs of RSSs mediate recombination and deletion inside the Vκ cluster even in the complete absence of Jκ gene segments and support a V(D)J recombination center (RC) independent of the conventional Jκ-centered RC. We propose an improved model of Vκ-Jκ repertoire formation by incorporating these surprisingly frequent, evolutionarily conserved intra-Vκ cluster recombination events.
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Affiliation(s)
- Kenta Shinoda
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yaakov Maman
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA; The Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Andres Canela
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA; The Hakubi Center for Advanced Research and Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - David G Schatz
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ferenc Livak
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD, USA.
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12
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Abstract
A new form of somatic gene recombination (SGR) has been identified in the human brain that affects the Alzheimer's disease gene, amyloid precursor protein (APP). SGR occurs when a gene sequence is cut and recombined within a single cell's genomic DNA, generally independent of DNA replication and the cell cycle. The newly identified brain SGR produces genomic complementary DNAs (gencDNAs) lacking introns, which integrate into locations distinct from germline loci. This brief review will present an overview of likely related recombination mechanisms and genomic cDNA-like sequences that implicate evolutionary origins for brain SGR. Similarities and differences exist between brain SGR and VDJ recombination in the immune system, the first identified SGR form that now has a well-defined enzymatic machinery. Both require gene transcription, but brain SGR uses an RNA intermediate and reverse transcriptase (RT) activity, which are characteristics shared with endogenous retrotransposons. The identified gencDNAs have similarities to other cDNA-like sequences existing throughout phylogeny, including intron-less genes and inactive germline processed pseudogenes, with likely overlapping biosynthetic processes. gencDNAs arise somatically in an individual to produce multiple copies; can be functional; appear most frequently within postmitotic cells; have diverse sequences; change with age; and can change with disease state. Normally occurring brain SGR may represent a mechanism for gene optimization and long-term cellular memory, whereas its dysregulation could underlie multiple brain disorders and, potentially, other diseases like cancer. The involvement of RT activity implicates already Food and Drug Administration-approved RT inhibitors as possible near-term interventions for managing SGR-associated diseases and suggest next-generation therapeutics targeting SGR elements.
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Affiliation(s)
- Gwendolyn Kaeser
- Degenerative Disease Program at the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Jerold Chun
- Degenerative Disease Program at the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
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13
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Cantor DJ, King B, Blumenberg L, DiMauro T, Aifantis I, Koralov SB, Skok JA, David G. Impaired Expression of Rearranged Immunoglobulin Genes and Premature p53 Activation Block B Cell Development in BMI1 Null Mice. Cell Rep 2019; 26:108-118.e4. [PMID: 30605667 DOI: 10.1016/j.celrep.2018.12.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/01/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
Abstract
B cell development is a highly regulated process that requires stepwise rearrangement of immunoglobulin genes to generate a functional B cell receptor (BCR). The polycomb group protein BMI1 is required for B cell development, but its function in developing B cells remains poorly defined. We demonstrate that BMI1 functions in a cell-autonomous manner at two stages during early B cell development. First, loss of BMI1 results in a differentiation block at the pro-B cell to pre-B cell transition due to the inability of BMI1-deficient cells to transcribe newly rearranged Igh genes. Accordingly, introduction of a pre-rearranged Igh allele partially restored B cell development in Bmi1−/− mice. In addition, BMI1 is required to prevent premature p53 signaling, and as a consequence, Bmi1−/− large pre-B cells fail to properly proliferate. Altogether, our results clarify the role of BMI1 in early B cell development and uncover an unexpected function of BMI1 during VDJ recombination. Cantor et al. identify a cell-autonomous role for the polycomb group protein BMI1 in early B cell development. At the pro-B cell to pre-B cell transition, BMI1 promotes the expression of newly rearranged Igh genes in pro-B cells and subsequently prevents premature p53 activation and enables large pre-B cell proliferation.
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14
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Mondot S, Lantz O, Lefranc MP, Boudinot P. The T cell receptor (TRA) locus in the rabbit (Oryctolagus cuniculus): Genomic features and consequences for invariant T cells. Eur J Immunol 2019; 49:2146-2158. [PMID: 31355919 DOI: 10.1002/eji.201948228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 06/14/2019] [Indexed: 11/07/2022]
Abstract
The rabbit has been widely used in immunology and infectiology. Rabbit immunoglobulins have been extensively studied, leading to the discovery of their idiotypes, allotypic diversity, and of the diversification of the primary repertoire by hyperconversion. Much less is known about rabbit T cell receptors (TR), especially TRA. This isotype is particularly important for innate-like T cells, which typically express invariant TRA (iTRA). The presence of such cells in the rabbit remains an enigma. Rabbit NKT cells seem to be very rare, and lagomorphs lack MAIT cells. TRAV1, the variable gene expressed in the iTRA of these cells across most mammals, and MR1, the MH1-like receptor that present riboflavin derivatives to MAIT cells, are missing in rabbit. An alternative iTRA has been identified, that may be expressed by new innate-like T cells. To facilitate TRA repertoire analyses in rabbit, we report here a full description of TRA and TRD loci and a subgroup definition based on IMGT® classification. Rabbit TRA rearrangements follow the same temporal pattern that is observed in mouse and human. Rare transcripts expressing TRDV/TRDD/TRDJ rearrangements spliced to TRAC were detected. TRA and TRD genes have been made available in IMGT and IMGT/HighV-QUEST, allowing easy analysis of TRA/TRD RepSeq.
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Affiliation(s)
- Stanislas Mondot
- MICALIS, Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
| | - Olivier Lantz
- INSERM U932, Institut Curie, Paris Sciences et Lettres Research University, Paris, France.,Center of Clinical Investigation in Biotherapy 1428, Gustave-Roussy/Curie, Paris, France.,Laboratoire d'Immunologie Clinique, Institut Curie, Paris, France
| | - Marie-Paule Lefranc
- IMGT®, the International ImMunoGeneTics Information System® (IMGT), Institut de Génétique Humaine, CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Pierre Boudinot
- Virologie et Immunologie Moléculaires (VIM), Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Jouy-en-Josas, France
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15
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Safonova Y, Pevzner PA. De novo Inference of Diversity Genes and Analysis of Non-canonical V(DD)J Recombination in Immunoglobulins. Front Immunol 2019; 10:987. [PMID: 31134072 PMCID: PMC6516046 DOI: 10.3389/fimmu.2019.00987] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 04/16/2019] [Indexed: 12/03/2022] Open
Abstract
The V(D)J recombination forms the immunoglobulin genes by joining the variable (V), diversity (D), and joining (J) germline genes. Since variations in germline genes have been linked to various diseases, personalized immunogenomics aims at finding alleles of germline genes across various patients. Although recent studies described algorithms for de novo inference of V and J genes from immunosequencing data, they stopped short of solving a more difficult problem of reconstructing D genes that form the highly divergent CDR3 regions and provide the most important contribution to the antigen binding. We present the IgScout algorithm for de novo D gene reconstruction and apply it to reveal new alleles of human D genes and previously unknown D genes in camel, an important model organism in immunology. We further analyze non-canonical V(DD)J recombination that results in unusually long CDR3s with tandem fused IGHD genes and thus expands the diversity of the antibody repertoires. We demonstrate that tandem CDR3s represent a consistent and functional feature of all analyzed immunosequencing datasets, reveal ultra-long CDR3s, and shed light on the mechanism responsible for their formation.
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Affiliation(s)
- Yana Safonova
- Center for Information Theory and Applications, University of California, San Diego, San Diego, CA, United States
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, San Diego, CA, United States
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16
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Abstract
Functional antigen receptor genes are assembled by somatic rearrangements that are largely lymphocyte lineage specific. The immunoglobulin heavy chain (IgH) gene locus is unique amongst the seven antigen receptor loci in undergoing partial gene rearrangements in the wrong lineage. Here we demonstrate that breakdown of lineage-specificity is associated with inappropriate activation of the Eμ enhancer during T cell development by a different constellation of transcription factors than those used in developing B cells. This is reflected in reduced enhancer-induced epigenetic changes, eRNAs, formation of the RAG1/2-rich recombination center, attenuated chromatin looping and markedly different utilization of DH gene segments in CD4+CD8+ (DP) thymocytes. Additionally, CTCF-dependent VH locus compaction is disrupted in DP cells despite comparable transcription factor binding in both lineages. These observations identify multiple mechanisms that contribute to lineage-specific antigen receptor gene assembly.
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Affiliation(s)
- Gita Kumari
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, United States
| | - Tatiana Gerasimova
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, United States
| | - Hansen Du
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, United States
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - William H Wood
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - Kevin G Becker
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, United States
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, MD, United States
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17
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Tirosh I, Yamazaki Y, Frugoni F, Ververs FA, Allenspach EJ, Zhang Y, Burns S, Al-Herz W, Noroski L, Walter JE, Gennery AR, van der Burg M, Notarangelo LD, Lee YN. Recombination activity of human recombination-activating gene 2 (RAG2) mutations and correlation with clinical phenotype. J Allergy Clin Immunol 2018; 143:726-735. [PMID: 29772310 DOI: 10.1016/j.jaci.2018.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Mutations in recombination-activating gene (RAG) 1 and RAG2 are associated with a broad range of clinical and immunologic phenotypes in human subjects. OBJECTIVE Using a flow cytometry-based assay, we aimed to measure the recombinase activity of naturally occurring RAG2 mutant proteins and to correlate our results with the severity of the clinical and immunologic phenotype. METHODS Abelson virus-transformed Rag2-/- pro-B cells engineered to contain an inverted green fluorescent protein (GFP) cassette flanked by recombination signal sequences were transduced with retroviruses encoding either wild-type or 41 naturally occurring RAG2 variants. Bicistronic vectors were used to introduce compound heterozygous RAG2 variants. The percentage of GFP-expressing cells was evaluated by using flow cytometry, and high-throughput sequencing was used to analyze rearrangements at the endogenous immunoglobulin heavy chain (Igh) locus. RESULTS The RAG2 variants showed a wide range of recombination activity. Mutations associated with severe combined immunodeficiency and Omenn syndrome had significantly lower activity than those detected in patients with less severe clinical presentations. Four variants (P253R, F386L, N474S, and M502V) previously thought to be pathogenic were found to have wild-type levels of activity. Use of bicistronic vectors permitted us to assess more carefully the effect of compound heterozygous mutations, with good correlation between GFP expression and the number and diversity of Igh rearrangements. CONCLUSIONS Our data support genotype-phenotype correlation in the setting of RAG2 deficiency. The assay described can be used to define the possible disease-causing role of novel RAG2 variants and might help predict the severity of the clinical phenotype.
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Affiliation(s)
- Irit Tirosh
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Yasuhiro Yamazaki
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Francesco Frugoni
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Francesca A Ververs
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Eric J Allenspach
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Siobhan Burns
- Institute for Immunity and Transplantation, University College London, London, United Kingdom; Department of Immunology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Lenora Noroski
- Division of Allergy and Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Tex
| | - Jolan E Walter
- Division of Pediatric Allergy/Immunology, University of South Florida and Johns Hopkins All Children's Hospital, St Petersburg, Fla
| | - Andrew R Gennery
- Department of Pediatric Immunology, Newcastle Upon Tyne Hospital, NHS Foundation Trust, United Kingdom and Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| | - Yu Nee Lee
- Pediatric Department A and the Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel Hashomer, Ramat-Gan and Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
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18
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Wirasinha RC, Singh M, Archer SK, Chan A, Harrison PF, Goodnow CC, Daley SR. αβ T-cell receptors with a central CDR3 cysteine are enriched in CD8αα intraepithelial lymphocytes and their thymic precursors. Immunol Cell Biol 2018; 96:553-561. [PMID: 29726044 DOI: 10.1111/imcb.12047] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/09/2018] [Accepted: 03/23/2018] [Indexed: 01/04/2023]
Abstract
The thymus plays a crucial role in immune tolerance by exposing developing T cells (thymocytes) to a myriad of self-antigens. Strong T-cell receptor (TCR) engagement induces tolerance in self-reactive thymocytes by stimulating apoptosis or selection into specialized T-cell lineages, including intestinal TCRαβ+ CD8αα+ intraepithelial lymphocytes (IEL). TCR-intrinsic amino acid motifs that can be used to predict whether a TCR will be strongly self-reactive remain elusive. Here, a novel TCR sequence alignment approach revealed that T-cell lineages in C57BL/6 mice had divergent usage of cysteine within two positions of the amino acid at the apex of the complementarity-determining region 3 (CDR3) of the TCRα or TCRβ chain. Compared to pre-selection thymocytes, central CDR3 cysteine usage was increased in IEL and Type A IEL precursors (IELp) and markedly decreased in Foxp3+ regulatory T cells (T-reg) and naïve T cells. These findings reveal a TCR-intrinsic motif that distinguishes Type A IELp and IEL from T-reg and naïve T cells.
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Affiliation(s)
- Rushika C Wirasinha
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Mandeep Singh
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Stuart K Archer
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, 3800, Australia
| | - Anna Chan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
| | - Paul F Harrison
- Monash Bioinformatics Platform, Monash University, Melbourne, VIC, 3800, Australia
| | - Christopher C Goodnow
- Immunology Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Stephen R Daley
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia
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19
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Blum LK, Cao RRL, Sweatt AJ, Bill M, Lahey LJ, Hsi AC, Lee CS, Kongpachith S, Ju CH, Mao R, Wong HH, Nicolls MR, Zamanian RT, Robinson WH. Circulating plasmablasts are elevated and produce pathogenic anti-endothelial cell autoantibodies in idiopathic pulmonary arterial hypertension. Eur J Immunol 2018; 48:874-884. [PMID: 29369345 DOI: 10.1002/eji.201747460] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 12/18/2017] [Accepted: 01/17/2018] [Indexed: 01/05/2023]
Abstract
Idiopathic pulmonary arterial hypertension (IPAH) is a devastating pulmonary vascular disease in which autoimmune and inflammatory phenomena are implicated. B cells and autoantibodies have been associated with IPAH and identified as potential therapeutic targets. However, the specific populations of B cells involved and their roles in disease pathogenesis are not clearly defined. We aimed to assess the levels of activated B cells (plasmablasts) in IPAH, and to characterize recombinant antibodies derived from these plasmablasts. Blood plasmablasts are elevated in IPAH, remain elevated over time, and produce IgA autoantibodies. Single-cell sequencing of plasmablasts in IPAH revealed repertoires of affinity-matured antibodies with small clonal expansions, consistent with an ongoing autoimmune response. Recombinant antibodies representative of these clonal lineages bound known autoantigen targets and displayed an unexpectedly high degree of polyreactivity. Representative IPAH plasmablast recombinant antibodies stimulated human umbilical vein endothelial cells to produce cytokines and overexpress the adhesion molecule ICAM-1. Together, our results demonstrate an ongoing adaptive autoimmune response involving IgA plasmablasts that produce anti-endothelial cell autoantibodies in IPAH. These antibodies stimulate endothelial cell production of cytokines and adhesion molecules, which may contribute to disease pathogenesis. These findings suggest a role for mucosally-driven autoimmunity and autoimmune injury in the pathogenesis of IPAH.
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Affiliation(s)
- Lisa K Blum
- Stanford University School of Medicine, Division of Immunology and Rheumatology, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Richard R L Cao
- Stanford University School of Medicine, Division of Immunology and Rheumatology, Stanford, CA, USA
| | - Andrew J Sweatt
- Stanford University Medical Center, Division of Pulmonary and Critical Care Medicine, Stanford, CA, USA
| | - Matthew Bill
- Stanford University Medical Center, Division of Pulmonary and Critical Care Medicine, Stanford, CA, USA
| | - Lauren J Lahey
- Stanford University School of Medicine, Division of Immunology and Rheumatology, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Andrew C Hsi
- Stanford University Medical Center, Division of Pulmonary and Critical Care Medicine, Stanford, CA, USA
| | - Casey S Lee
- Stanford University School of Medicine, Division of Immunology and Rheumatology, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Sarah Kongpachith
- Stanford University School of Medicine, Division of Immunology and Rheumatology, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Chia-Hsin Ju
- Stanford University School of Medicine, Division of Immunology and Rheumatology, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Rong Mao
- Stanford University School of Medicine, Division of Immunology and Rheumatology, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Heidi H Wong
- Stanford University School of Medicine, Division of Immunology and Rheumatology, Stanford, CA, USA
| | - Mark R Nicolls
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Stanford University Medical Center, Division of Pulmonary and Critical Care Medicine, Stanford, CA, USA
| | - Roham T Zamanian
- Stanford University Medical Center, Division of Pulmonary and Critical Care Medicine, Stanford, CA, USA
| | - William H Robinson
- Stanford University School of Medicine, Division of Immunology and Rheumatology, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
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20
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Abstract
Mutations in the RAG1/RAG2 genes are associated with a broad spectrum of clinical phenotypes, ranging from severe combined immunodeficiency to various autoimmune diseases. The diversity of the clinical symptoms is determined not only by the residual RAG recombinase enzyme activity as determined by the mutations, but also by multiple environmental factors and, in rare cases, by second site mutations within the RAG1/RAG2 genes. The residual recombinase activity is responsible for the oligoclonal expansion of autoreactive T cells. Omenn syndrome is the result of intense Th2 type inflammation involving the skin and multiple other organs triggered by these T cells. In this review, the molecular pathology of diseases caused by RAG1/RAG2 mutations, in particular Omenn syndrome, will be discussed. Furthermore, abnormalities in other molecules involved in V(D)J recombination will be discussed in relation to Omenn-like syndrome.
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Affiliation(s)
- Akihiro Yachie
- Department of Pediatrics, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University
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21
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Stengel KR, Barnett KR, Wang J, Liu Q, Hodges E, Hiebert SW, Bhaskara S. Deacetylase activity of histone deacetylase 3 is required for productive VDJ recombination and B-cell development. Proc Natl Acad Sci U S A 2017; 114:8608-13. [PMID: 28739911 DOI: 10.1073/pnas.1701610114] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Histone deacetylase 3 (HDAC3) is the catalytic component of NCoR/SMRT corepressor complexes that mediate the actions of transcription factors implicated in the regulation of B-cell development and function. We crossed Hdac3 conditional knockout mice with Mb1-Cre knockin animals to delete Hdac3 in early progenitor B cells. The spleens of Hdac3F/-Mb1-Cre+/- mice were virtually devoid of mature B cells, and B220+CD43+ B-cell progenitors accumulated within the bone marrow. Quantitative deep sequencing of the Ig heavy chain locus from B220+CD43+ populations identified a defect in VHDJH recombination with a severe reduction in productive rearrangements, which directly corresponded to the loss of pre-B cells from Hdac3Δ/- bone marrow. For Hdac3Δ/- B cells that did show productive VDJ rearrangement, there was significant skewing toward the incorporation of proximal VH gene segments and a corresponding reduction in distal VH gene segment use. Although transcriptional effects within these loci were modest, Hdac3Δ/- progenitor cells displayed global changes in chromatin structure that likely hindered effective distal V-DJ recombination. Reintroduction of wild-type Hdac3 restored normal B-cell development, whereas an Hdac3 point mutant lacking deacetylase activity failed to complement this defect. Thus, the deacetylase activity of Hdac3 is required for the generation of mature B cells.
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22
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Rawat P, Jalan M, Sadhu A, Kanaujia A, Srivastava M. Chromatin Domain Organization of the TCRb Locus and Its Perturbation by Ectopic CTCF Binding. Mol Cell Biol 2017; 37:e00557-16. [PMID: 28137913 DOI: 10.1128/MCB.00557-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/25/2017] [Indexed: 01/23/2023] Open
Abstract
CTCF-mediated chromatin interactions influence organization and function of mammalian genome in diverse ways. We analyzed the interactions among CTCF binding sites (CBS) at the murine TCRb locus to discern the role of CTCF-mediated interactions in the regulation of transcription and VDJ recombination. Chromosome conformation capture analysis revealed thymocyte-specific long-range intrachromosomal interactions among various CBS across the locus that were relevant for defining the limit of the enhancer Eb-regulated recombination center (RC) and for facilitating the spatial proximity of TCRb variable (V) gene segments to the RC. Ectopic CTCF binding in the RC region, effected via genetic manipulation, altered CBS-directed chromatin loops, interfered with RC establishment, and reduced the spatial proximity of the RC with Trbv segments. Changes in chromatin loop organization by ectopic CTCF binding were relatively modest but influenced transcription and VDJ recombination dramatically. Besides revealing the importance of CTCF-mediated chromatin organization for TCRb regulation, the observed chromatin loops were consistent with the emerging idea that CBS orientations influence chromatin loop organization and underscored the importance of CBS orientations for defining chromatin architecture that supports VDJ recombination. Further, our study suggests that in addition to mediating long-range chromatin interactions, CTCF influences intricate configuration of chromatin loops that govern functional interactions between elements.
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23
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Sethna Z, Elhanati Y, Dudgeon CS, Callan CG Jr, Levine AJ, Mora T, Walczak AM. Insights into immune system development and function from mouse T-cell repertoires. Proc Natl Acad Sci U S A 2017; 114:2253-8. [PMID: 28196891 DOI: 10.1073/pnas.1700241114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors. This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts on the surface receptor gene each time a new immune cell is created from a stem cell. By analyzing T-cell receptor (TCR) sequence repertoires taken from the blood and thymus of mice of different ages, we quantify the changes in the VDJ recombination process that occur from embryo to young adult. We find a rapid increase with age in the number of random insertions and a dramatic increase in diversity. Because the blood accumulates thymic output over time, blood repertoires are mixtures of different statistical recombination processes, and we unravel the mixture statistics to obtain a picture of the time evolution of the early immune system. Sequence repertoire analysis also allows us to detect the statistical impact of selection on the output of the VDJ recombination process. The effects we find are nearly identical between thymus and blood, suggesting that our analysis mainly detects selection for proper folding of the TCR receptor protein. We further find that selection is weaker in laboratory mice than in humans and it does not affect the diversity of the repertoire.
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24
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Hung SJ, Chen YL, Chu CH, Lee CC, Chen WL, Lin YL, Lin MC, Ho CL, Liu T. TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences. BMC Bioinformatics 2016; 17:433. [PMID: 27782801 PMCID: PMC5080739 DOI: 10.1186/s12859-016-1304-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 10/21/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND T cells and B cells are essential in the adaptive immunity via expressing T cell receptors and immunoglogulins respectively for recognizing antigens. To recognize a wide variety of antigens, a highly diverse repertoire of receptors is generated via complex recombination of the receptor genes. Reasonably, frequencies of the recombination events have been shown to predict immune diseases and provide insights into the development of immunity. The field is further boosted by high-throughput sequencing and several computational tools have been released to analyze the recombined sequences. However, all current tools assume regular recombination of the receptor genes, which is not always valid in data prepared using a RACE approach. Compared to the traditional multiplex PCR approach, RACE is free of primer bias, therefore can provide accurate estimation of recombination frequencies. To handle the non-regular recombination events, a new computational program is needed. RESULTS We propose TRIg to handle non-regular T cell receptor and immunoglobulin sequences. Unlike all current programs, TRIg does alignments to the whole receptor gene instead of only to the coding regions. This brings new computational challenges, e.g., ambiguous alignments due to multiple hits to repetitive regions. To reduce ambiguity, TRIg applies a heuristic strategy and incorporates gene annotation to identify authentic alignments. On our own and public RACE datasets, TRIg correctly identified non-regularly recombined sequences, which could not be achieved by current programs. TRIg also works well for regularly recombined sequences. CONCLUSIONS TRIg takes into account non-regular recombination of T cell receptor and immunoglobulin genes, therefore is suitable for analyzing RACE data. Such analysis will provide accurate estimation of recombination events, which will benefit various immune studies directly. In addition, TRIg is suitable for studying aberrant recombination in immune diseases. TRIg is freely available at https://github.com/TLlab/trig .
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Affiliation(s)
- Sheng-Jou Hung
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yi-Lin Chen
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Chia-Hung Chu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Chuan-Chun Lee
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Wan-Li Chen
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Ya-Lan Lin
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Ming-Ching Lin
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Chung-Liang Ho
- Molecular Diagnostic Laboratory, Department of Pathology, National Cheng Kung University Hospital, Tainan City, Taiwan.,Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, Tainan City, Taiwan
| | - Tsunglin Liu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan City, Taiwan.
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25
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Li S, Liu W, Li Y, Zhao S, Liu C, Hu M, Yue W, Liu Y, Wang Y, Yang R, Xiang R, Liu F. Contribution of secondary Igkappa rearrangement to primary immunoglobulin repertoire diversification. Mol Immunol 2016; 78:193-206. [PMID: 27665270 DOI: 10.1016/j.molimm.2016.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 09/01/2016] [Accepted: 09/06/2016] [Indexed: 10/21/2022]
Abstract
Abs reactive to DNA and DNA/histone complexes are a distinguished characteristic of primary immunoglobulin repertoires in autoimmune B6.MRL-Faslpr and MRL/MpJ-Faslpr mice. These mice are defective in Fas receptor, which is critical for the apoptosis of autoreactive B cells by an extrinsic pathway. In the present study, we explored the possibility that bone marrow small pre-B and immature B cells from adult B6.MRL-Faslpr mice and MRL/MpJ-Faslpr mice respectively, which contain autoreactive B-cell antigen receptors (BCR) and manifest autoimmune syndromes, exhibit enhanced receptor editing patterns. Indeed, FASlpr pre B and immature B cells were shown to possess more ongoing replacements of non-productive (nP) than productive (P) primary VκJκ rearrangements. Significantly, the P vs nP ratios of these replaced primary rearrangements were 1:2, thus indicating that κ light-chain production appears not to inhibit secondary rearrangements. In addition, we identified multiple atypical rearrangements, such as Vκ cRS (cryptic recombination signals) cleavages. These results suggest that the onset of light chain secondary rearrangements persists similarly as a non-selected mode and independent of BCR autoreactivity during certain developmental windows of bone marrow B cells in lupus-prone mice and control, and leads us to propose the function of secondary, de novo Igκ rearrangements to increase BCR diversity.
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Affiliation(s)
- Shufang Li
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Wei Liu
- Tianjin Entry-Exit Inspection and Quarantine Bureau, Tianjin 300308, China
| | - Yinghui Li
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Shaorong Zhao
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Can Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Mengyun Hu
- Collage of Life Science, Nankai University, Tianjin, 300071, China
| | - Wei Yue
- Department of Neurology, Huanhu Hospital, Tianjin 300060, China
| | - Yanhua Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Yue Wang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Rongcun Yang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Rong Xiang
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China.
| | - Feifei Liu
- Department of Immunology, School of Medicine, Nankai University, Tianjin 300071, China.
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26
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Abstract
We quantify the VDJ recombination and somatic hypermutation processes in human B cells using probabilistic inference methods on high-throughput DNA sequence repertoires of human B-cell receptor heavy chains. Our analysis captures the statistical properties of the naive repertoire, first after its initial generation via VDJ recombination and then after selection for functionality. We also infer statistical properties of the somatic hypermutation machinery (exclusive of subsequent effects of selection). Our main results are the following: the B-cell repertoire is substantially more diverse than T-cell repertoires, owing to longer junctional insertions; sequences that pass initial selection are distinguished by having a higher probability of being generated in a VDJ recombination event; somatic hypermutations have a non-uniform distribution along the V gene that is well explained by an independent site model for the sequence context around the hypermutation site.
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Affiliation(s)
- Yuval Elhanati
- Laboratoire de physique théorique, UMR8549, CNRS and École normale supérieure, 24, rue Lhomond, 75005 Paris, France
| | - Zachary Sethna
- Joseph Henry Laboratories, Princeton University, Princeton, NJ 08544, USA
| | - Quentin Marcou
- Laboratoire de physique théorique, UMR8549, CNRS and École normale supérieure, 24, rue Lhomond, 75005 Paris, France
| | - Curtis G Callan
- Joseph Henry Laboratories, Princeton University, Princeton, NJ 08544, USA
| | - Thierry Mora
- Laboratoire de physique statistique, UMR8550, CNRS and École normale supérieure, 24, rue Lhomond, 75005 Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique théorique, UMR8549, CNRS and École normale supérieure, 24, rue Lhomond, 75005 Paris, France
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Galson JD, Trück J, Fowler A, Münz M, Cerundolo V, Pollard AJ, Lunter G, Kelly DF. In-Depth Assessment of Within-Individual and Inter-Individual Variation in the B Cell Receptor Repertoire. Front Immunol 2015; 6:531. [PMID: 26528292 PMCID: PMC4601265 DOI: 10.3389/fimmu.2015.00531] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/28/2015] [Indexed: 11/24/2022] Open
Abstract
High-throughput sequencing of the B cell receptor (BCR) repertoire can provide rapid characterization of the B cell response in a wide variety of applications in health, after vaccination and in infectious, inflammatory and immune-driven disease, and is starting to yield clinical applications. However, the interpretation of repertoire data is compromised by a lack of studies to assess the intra and inter-individual variation in the BCR repertoire over time in healthy individuals. We applied a standardized isotype-specific BCR repertoire deep sequencing protocol to a single highly sampled participant, and then evaluated the method in 9 further participants to comprehensively describe such variation. We assessed total repertoire metrics of mutation, diversity, VJ gene usage and isotype subclass usage as well as tracking specific BCR sequence clusters. There was good assay reproducibility (both in PCR amplification and biological replicates), but we detected striking fluctuations in the repertoire over time that we hypothesize may be due to subclinical immune activation. Repertoire properties were unique for each individual, which could partly be explained by a decrease in IgG2 with age, and genetic differences at the immunoglobulin locus. There was a small repertoire of public clusters (0.5, 0.3, and 1.4% of total IgA, IgG, and IgM clusters, respectively), which was enriched for expanded clusters containing sequences with suspected specificity toward antigens that should have been historically encountered by all participants through prior immunization or infection. We thus provide baseline BCR repertoire information that can be used to inform future study design, and aid in interpretation of results from these studies. Furthermore, our results indicate that BCR repertoire studies could be used to track changes in the public repertoire in and between populations that might relate to population immunity against infectious diseases, and identify the characteristics of inflammatory and immunological diseases.
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Affiliation(s)
- Jacob D. Galson
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
- Paediatric Immunology, University Children’s Hospital, Zürich, Switzerland
| | - Anna Fowler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Márton Münz
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vincenzo Cerundolo
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, UK
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dominic F. Kelly
- Oxford Vaccine Group, Department of Paediatrics, The NIHR Oxford Biomedical Research Center, University of Oxford, Oxford, UK
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Mathieu AL, Verronese E, Rice GI, Fouyssac F, Bertrand Y, Picard C, Chansel M, Walter JE, Notarangelo LD, Butte MJ, Nadeau KC, Csomos K, Chen DJ, Chen K, Delgado A, Rigal C, Bardin C, Schuetz C, Moshous D, Reumaux H, Plenat F, Phan A, Zabot MT, Balme B, Viel S, Bienvenu J, Cochat P, van der Burg M, Caux C, Kemp EH, Rouvet I, Malcus C, Méritet JF, Lim A, Crow YJ, Fabien N, Ménétrier-Caux C, De Villartay JP, Walzer T, Belot A. PRKDC mutations associated with immunodeficiency, granuloma, and autoimmune regulator-dependent autoimmunity. J Allergy Clin Immunol 2015; 135:1578-88.e5. [PMID: 25842288 PMCID: PMC4487867 DOI: 10.1016/j.jaci.2015.01.040] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 12/28/2014] [Accepted: 01/06/2015] [Indexed: 02/05/2023]
Abstract
BACKGROUND PRKDC encodes for DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a kinase that forms part of a complex (DNA-dependent protein kinase [DNA-PK]) crucial for DNA double-strand break repair and V(D)J recombination. In mice DNA-PK also interacts with the transcription factor autoimmune regulator (AIRE) to promote central T-cell tolerance. OBJECTIVE We sought to understand the causes of an inflammatory disease with granuloma and autoimmunity associated with decreasing T- and B-cell counts over time that had been diagnosed in 2 unrelated patients. METHODS Genetic, molecular, and functional analyses were performed to characterize an inflammatory disease evocative of a combined immunodeficiency. RESULTS We identified PRKDC mutations in both patients. These patients exhibited a defect in DNA double-strand break repair and V(D)J recombination. Whole-blood mRNA analysis revealed a strong interferon signature. On activation, memory T cells displayed a skewed cytokine response typical of TH2 and TH1 but not TH17. Moreover, mutated DNA-PKcs did not promote AIRE-dependent transcription of peripheral tissue antigens in vitro. The latter defect correlated in vivo with production of anti-calcium-sensing receptor autoantibodies, which are typically found in AIRE-deficient patients. In addition, 9 months after bone marrow transplantation, patient 1 had Hashimoto thyroiditis, suggesting that organ-specific autoimmunity might be linked to nonhematopoietic cells, such as AIRE-expressing thymic epithelial cells. CONCLUSION Deficiency of DNA-PKcs, a key AIRE partner, can present as an inflammatory disease with organ-specific autoimmunity, suggesting a role for DNA-PKcs in regulating autoimmune responses and maintaining AIRE-dependent tolerance in human subjects.
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Affiliation(s)
- Anne-Laure Mathieu
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France
| | - Estelle Verronese
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Gillian I Rice
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Centre, Manchester, United Kingdom
| | - Fanny Fouyssac
- Pediatric Haematology and Oncology Department, Children Hospital-CHU NANCY Vandoeuvre les Nancy, Nancy, France
| | - Yves Bertrand
- Institut d'Hématologie et d'Oncologie Pédiatrique (Hospices Civils de Lyon), Université Claude Bernard Lyon I, Lyon, France
| | - Capucine Picard
- Study Center for Primary Immunodeficiencies, Assistance Publique-Hôpitaux de Paris, Necker Hospital, Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Sorbonne Paris Cité, Paris Descartes University, Imagine Institute, Paris Descartes University, Paris, France
| | - Marie Chansel
- INSERM UMR 1163, Laboratoire Dynamique du Génome et Système Immunitaire Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Jolan E Walter
- Pediatric Allergy & Immunology and the Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - Luigi D Notarangelo
- Division of Immunology, Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Manish J Butte
- Department of Pediatrics, Division of Immunology, Allergy and Rheumatology, Stanford University, Stanford, Calif
| | - Kari Christine Nadeau
- Department of Pediatrics, Division of Immunology, Allergy and Rheumatology, Stanford University, Stanford, Calif
| | - Krisztian Csomos
- Pediatric Allergy & Immunology and the Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, Mass
| | - David J Chen
- Division of Molecular Radiation Biology Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Karin Chen
- Department of Pediatrics, Division of Allergy, Immunology & Rheumatology, University of Utah School of Medicine, Salt Lake City, Utah
| | - Ana Delgado
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Chantal Rigal
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Christine Bardin
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Catharina Schuetz
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Despina Moshous
- INSERM UMR 1163, Laboratoire Dynamique du Génome et Système Immunitaire Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Héloïse Reumaux
- Pediatric Rheumatology and Emergency Unit, Jeanne de Flandre Hospital, Lille, France
| | - François Plenat
- Pathology Department, Hémato-Oncologie Pédiatrique, CHU Nancy, Nancy, France
| | - Alice Phan
- Pediatric Rheumatology, Nephrology and Dermatology Department and EPICIME Hospices Civils de Lyon and Université Claude-Bernard Lyon 1, Lyon, France
| | | | - Brigitte Balme
- Pathology Department, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Lyon, France
| | - Sébastien Viel
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France; Immunobiology Department, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Jacques Bienvenu
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France; Immunobiology Department, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Pierre Cochat
- Pediatric Rheumatology, Nephrology and Dermatology Department and EPICIME Hospices Civils de Lyon and Université Claude-Bernard Lyon 1, Lyon, France
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Christophe Caux
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - E Helen Kemp
- Department of Human Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Isabelle Rouvet
- Biotechnology Department, Hospices Civils de Lyon, Lyon, France
| | - Christophe Malcus
- Cell Immunology Department, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France
| | | | - Annick Lim
- Immunoscope Group, Immunology Department, Institut Pasteur, Paris, France
| | - Yanick J Crow
- Manchester Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Centre, Manchester, United Kingdom
| | - Nicole Fabien
- Immunobiology Department, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Lyon, France
| | - Christine Ménétrier-Caux
- Université de Lyon, INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Plateforme d'Innovation en Immuno-monitoring et Immunothérapie, Centre Léon Bérard, and in the framework of the LABEX DevWeCan (ANR-10-LABX-0061) of University de Lyon, within the program "Investissements d'Avenir" (ANR-11-IDEX-0007) operated by the French National Research Agency (ANR), Lyon, France
| | - Jean-Pierre De Villartay
- INSERM UMR 1163, Laboratoire Dynamique du Génome et Système Immunitaire Université Paris Descartes-Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Thierry Walzer
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France
| | - Alexandre Belot
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France; Inserm U1111, Lyon, France; Ecole Normale Supérieure de Lyon, Lyon, France; CNRS, UMR5308, Lyon, France; Pediatric Rheumatology, Nephrology and Dermatology Department and EPICIME Hospices Civils de Lyon and Université Claude-Bernard Lyon 1, Lyon, France.
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Ramesh M, Hamm D, Simchoni N, Cunningham-Rundles C. Clonal and constricted T cell repertoire in Common Variable Immune Deficiency. Clin Immunol 2015; 178:1-9. [PMID: 25596453 DOI: 10.1016/j.clim.2015.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 12/22/2014] [Accepted: 01/04/2015] [Indexed: 01/08/2023]
Abstract
We used high throughput sequencing to examine the structure and composition of the T cell receptor β chain in Common Variable Immune Deficiency (CVID). TCRβ CDR3 regions were amplified and sequenced from genomic DNA of 44 adult CVID subjects and 22 healthy adults, using a high-throughput multiplex PCR. CVID TCRs had significantly less junctional diversity, fewer n-nucleotide insertions and deletions, and completely lacked a population of highly modified TCRs, with 13 or more V-gene nucleotide deletions, seen in healthy controls. The CVID CDR3 sequences were significantly more clonal than control DNA, and displayed unique V gene usage. Despite reduced junctional diversity, increased clonality and similar infectious exposures, DNA of CVID subjects shared fewer TCR sequences as compared to controls. These abnormalities are pervasive, found in out-of-frame sequences and thus independent of selection and were not associated with specific clinical complications. These data support an inherent T cell defect in CVID.
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Affiliation(s)
| | | | - Noa Simchoni
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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30
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Ciubotaru M, Surleac M, Musat MG, Rusu AM, Ionita E, Albu PCC. DNA bending in the synaptic complex in V(D)J recombination: turning an ancestral transpososome upside down. Discoveries (Craiova) 2014; 2:e13. [PMID: 32309545 PMCID: PMC6941560 DOI: 10.15190/d.2014.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In all jawed vertebrates RAG (recombination activating gene) recombinase orchestrates V(D)J recombination in B and T lymphocyte precursors, assembling the V, D and J germline gene segments into continuous functional entities which encode the variable regions of their immune receptors. V(D)J recombination is the process by which most of the diversity of our specific immune receptors is acquired and is thought to have originated by domestication of a transposon in the genome of a vertebrate. RAG acts similarly to the cut and paste transposases, by first binding two recombination signal DNA sequences (RSSs), which flank the two coding genes to be adjoined, in a process called synaptic or paired complex (PC) formation. At these RSS-coding borders, RAG first nicks one DNA strand, then creates hairpins, thus cleaving the duplex DNA at both RSSs. Although RAG reaction mechanism resembles that of insect mobile element transposases and RAG itself can inefficiently perform intramolecular and intermolecular integration into the target DNA, inside the nuclei of the developing lymphocytes transposition is extremely rare and is kept under proper surveillance. Our review may help understand how RAG synaptic complex organization prevents deleterious transposition. The phosphoryl transfer reaction mechanism of RNAseH-like fold DDE motif enzymes, including RAG, is discussed accentuating the peculiarities described for various transposases from the light of their available high resolution structures (Tn5, Mu, Mos1 and Hermes). Contrasting the structural 3D organization of DNA in these transpososomes with that of the RSSs-DNA in RAG PC allows us to propose several clues for how evolutionarily RAG may have become “specialized” in recombination versus transposition.
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Affiliation(s)
- Mihai Ciubotaru
- Department of Immunobiology, Yale University School of Medicine, 300 Cedar St., TAC S620, New Haven, CT 06511, USA.,National Institute for Physics and Nuclear Engineering Horia Hulubei, Department of Life and Environmental Physics, Atomistilor Str., 077125, Bucharest-Magurele, Romania
| | - Marius Surleac
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031, Bucharest, Romania
| | - Mihaela G Musat
- National Institute for Physics and Nuclear Engineering Horia Hulubei, Department of Life and Environmental Physics, Atomistilor Str., 077125, Bucharest-Magurele, Romania
| | - Andreea M Rusu
- National Institute for Physics and Nuclear Engineering Horia Hulubei, Department of Life and Environmental Physics, Atomistilor Str., 077125, Bucharest-Magurele, Romania
| | - Elena Ionita
- National Institute for Physics and Nuclear Engineering Horia Hulubei, Department of Life and Environmental Physics, Atomistilor Str., 077125, Bucharest-Magurele, Romania
| | - Paul C C Albu
- National Institute for Physics and Nuclear Engineering Horia Hulubei, Department of Life and Environmental Physics, Atomistilor Str., 077125, Bucharest-Magurele, Romania
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31
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Niklas N, Pröll J, Weinberger J, Zopf A, Wiesinger K, Krismer K, Bettelheim P, Gabriel C. Qualifying high-throughput immune repertoire sequencing. Cell Immunol 2014; 288:31-8. [PMID: 24607567 DOI: 10.1016/j.cellimm.2014.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 11/06/2013] [Accepted: 02/12/2014] [Indexed: 10/25/2022]
Abstract
Diversity of B and T cell receptors, achieved by gene recombination and somatic hypermutation, allows the immune system for recognition and targeted reaction against various threats. Next-generation sequencing for assessment of a cell's gene composition and variation makes deep analysis of one individual's immune spectrum feasible. An easy to apply but detailed analysis and visualization strategy is necessary to process all sequences generated. We performed sequencing utilizing the 454 system for CLL and control samples, utilized the IMGT database and applied the presented analysis tools. With the applied protocol, malignant clones are found and characterized, mutational status compared to germline identity is elaborated in detail showing that the CLL mutation status is not as monoclonal as generally thought. On the other hand, this strategy is not solely applicable to the 454 sequencing system but can easily be transferred to any other next-generation sequencing platform.
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Affiliation(s)
- Norbert Niklas
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Johannes Pröll
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Johannes Weinberger
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Agnes Zopf
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Karin Wiesinger
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
| | - Konstantin Krismer
- University of Applied Sciences Upper Austria, Softwarepark 11, 4232 Hagenberg, Austria.
| | - Peter Bettelheim
- Division of Hematology/Oncology, Elisabethinen Hospital Linz, Fadingerstraße 1, 4020 Linz, Austria.
| | - Christian Gabriel
- Red Cross Transfusion Service for Upper Austria, Krankenhausstraße 7, 4020 Linz, Austria.
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Burmeister T, Molkentin M, Schwartz S, Gökbuget N, Hoelzer D, Thiel E, Reinhardt R. Erroneous class switching and false VDJ recombination: molecular dissection of t(8;14)/MYC-IGH translocations in Burkitt-type lymphoblastic leukemia/B-cell lymphoma. Mol Oncol 2013; 7:850-8. [PMID: 23673335 DOI: 10.1016/j.molonc.2013.04.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 04/04/2013] [Accepted: 04/16/2013] [Indexed: 12/30/2022] Open
Abstract
The chromosomal translocation t(8;14)(q24;q32) with juxtaposition of MYC to enhancer elements in the immunoglobulin heavy chain (IGH) gene locus is the genetic hallmark of the majority of Burkitt lymphoma and a subset of Diffuse large B-cell lymphoma patients. Around 3% of adult B-lineage acute lymphoblastic leukemia (ALL) patients show this aberration. Flow cytometry mostly reveals a "mature B-ALL" or "Burkitt-type" ALL immunophenotype. Using long-distance PCR for t(8;14)/MYC-IGH fusion, we investigated bone marrow, peripheral blood and a few other samples with suspected Burkitt-ALL or mature B-ALL and identified 133 MYC-IGH-positive cases. The location of the chromosomal breaks in the IGH joining and the 8 different switch regions was determined using a set of long-distance PCRs. The chromosomal breakpoints with the adjacent MYC regions on 8q24 were characterized by direct sequencing in 49 cases. The distribution of chromosomal breaks among the IGH joining and switch regions was the following: JH 23.3%, M 21.8%, G1 15.0%, G2 7.5%, G3 3.8%, G4 4.5%, A1 12.8%, A2 3.8%, E 7.5%. Two breakpoint clusters near MYC were delineated. There was no clear correlation between the degree of somatic hypermutation and the chromosomal break locations. Epstein Barr virus was detected in 5 cases (4%). This detailed and extensive molecular analysis illustrates the molecular complexity of the MYC-IGH translocations and the detected distribution of breakpoints provides additional evidence that this translocation results from failed switch and VDJ recombinations. This study may serve as a model for the analysis of other IGH translocations in B-cell lymphoma.
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Affiliation(s)
- Thomas Burmeister
- Charité, Med. Klinik für Hämatologie, Onkologie und Tumorimmunologie, Berlin, Germany.
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