1
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Xu M, Ito-Kureha T, Kang HS, Chernev A, Raj T, Hoefig KP, Hohn C, Giesert F, Wang Y, Pan W, Ziętara N, Straub T, Feederle R, Daniel C, Adler B, König J, Feske S, Tsokos GC, Wurst W, Urlaub H, Sattler M, Kisielow J, Wulczyn FG, Łyszkiewicz M, Heissmeyer V. The thymocyte-specific RNA-binding protein Arpp21 provides TCR repertoire diversity by binding to the 3'-UTR and promoting Rag1 mRNA expression. Nat Commun 2024; 15:2194. [PMID: 38467629 PMCID: PMC10928157 DOI: 10.1038/s41467-024-46371-z] [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] [Received: 04/20/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
The regulation of thymocyte development by RNA-binding proteins (RBPs) is largely unexplored. We identify 642 RBPs in the thymus and focus on Arpp21, which shows selective and dynamic expression in early thymocytes. Arpp21 is downregulated in response to T cell receptor (TCR) and Ca2+ signals. Downregulation requires Stim1/Stim2 and CaMK4 expression and involves Arpp21 protein phosphorylation, polyubiquitination and proteasomal degradation. Arpp21 directly binds RNA through its R3H domain, with a preference for uridine-rich motifs, promoting the expression of target mRNAs. Analysis of the Arpp21-bound transcriptome reveals strong interactions with the Rag1 3'-UTR. Arpp21-deficient thymocytes show reduced Rag1 expression, delayed TCR rearrangement and a less diverse TCR repertoire. This phenotype is recapitulated in Rag1 3'-UTR mutant mice harboring a deletion of the Arpp21 response region. These findings show how thymocyte-specific Arpp21 promotes Rag1 expression to enable TCR repertoire diversity until signals from the TCR terminate Arpp21 and Rag1 activities.
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Affiliation(s)
- Meng Xu
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Taku Ito-Kureha
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center (BNMRZ), Garching, Germany
| | - Aleksandar Chernev
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Göttingen, Germany
| | - Timsse Raj
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Kai P Hoefig
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany
| | - Christine Hohn
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Yinhu Wang
- Department of Pathology, New York University, Grossman School of Medicine, New York, NY, USA
| | - Wenliang Pan
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Natalia Ziętara
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Tobias Straub
- Institute for Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, German Research Center for Environmental Health, Neuherberg, Germany
| | - Carolin Daniel
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Barbara Adler
- Max von Pettenkofer Institute, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Stefan Feske
- Department of Pathology, New York University, Grossman School of Medicine, New York, NY, USA
| | - George C Tsokos
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Developmental Genetics, Munich School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) site Munich, Munich, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Göttingen, Germany
- University Medical Center Göttingen, Department of Clinical Chemistry, Bioanalytics Group, Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center (BNMRZ), Garching, Germany
| | - Jan Kisielow
- Institute for Molecular Health Sciences, ETH Zürich, Zürich, Switzerland.
- Repertoire Immune Medicines (Switzerland) AG, Schlieren, Switzerland.
| | - F Gregory Wulczyn
- Institute for Integrative Neuroanatomie, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Marcin Łyszkiewicz
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany.
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany.
| | - Vigo Heissmeyer
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany.
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany.
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2
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Heimli M, Tennebø Flåm S, Sagsveen Hjorthaug H, Bjørnstad PM, Chernigovskaya M, Le QK, Tekpli X, Greiff V, Lie BA. Human thymic putative CD8αα precursors exhibit a biased TCR repertoire in single cell AIRR-seq. Sci Rep 2023; 13:17714. [PMID: 37853083 PMCID: PMC10584817 DOI: 10.1038/s41598-023-44693-4] [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] [Received: 03/30/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023] Open
Abstract
Thymic T cell development comprises T cell receptor (TCR) recombination and assessment of TCR avidity towards self-peptide-MHC complexes presented by antigen-presenting cells. Self-reactivity may lead to negative selection, or to agonist selection and differentiation into unconventional lineages such as regulatory T cells and CD8[Formula: see text] T cells. To explore the effect of the adaptive immune receptor repertoire on thymocyte developmental decisions, we performed single cell adaptive immune receptor repertoire sequencing (scAIRR-seq) of thymocytes from human young paediatric thymi and blood. Thymic PDCD1+ cells, a putative CD8[Formula: see text] T cell precursor population, exhibited several TCR features previously associated with thymic and peripheral ZNF683+ CD8[Formula: see text] T cells, including enrichment of large and positively charged complementarity-determining region 3 (CDR3) amino acids. Thus, the TCR repertoire may partially explain the decision between conventional vs. agonist selected thymocyte differentiation, an aspect of importance for the development of therapies for patients with immune-mediated diseases.
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Affiliation(s)
- Marte Heimli
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0424, Oslo, Norway
| | - Siri Tennebø Flåm
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0424, Oslo, Norway
| | - Hanne Sagsveen Hjorthaug
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0424, Oslo, Norway
| | - Pål Marius Bjørnstad
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0424, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway
| | - Quy Khang Le
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway
| | - Xavier Tekpli
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0424, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway
| | - Benedicte Alexandra Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0424, Oslo, Norway.
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3
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Botta C, Perez C, Larrayoz M, Puig N, Cedena MT, Termini R, Goicoechea I, Rodriguez S, Zabaleta A, Lopez A, Sarvide S, Blanco L, Papetti DM, Nobile MS, Besozzi D, Gentile M, Correale P, Siragusa S, Oriol A, González-Garcia ME, Sureda A, de Arriba F, Rios Tamayo R, Moraleda JM, Gironella M, Hernandez MT, Bargay J, Palomera L, Pérez-Montaña A, Goldschmidt H, Avet-Loiseau H, Roccaro A, Orfao A, Martinez-Lopez J, Rosiñol L, Lahuerta JJ, Blade J, Mateos MV, San-Miguel JF, Martinez Climent JA, Paiva B. Large T cell clones expressing immune checkpoints increase during multiple myeloma evolution and predict treatment resistance. Nat Commun 2023; 14:5825. [PMID: 37730678 PMCID: PMC10511411 DOI: 10.1038/s41467-023-41562-6] [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] [Received: 11/25/2022] [Accepted: 09/07/2023] [Indexed: 09/22/2023] Open
Abstract
Tumor recognition by T cells is essential for antitumor immunity. A comprehensive characterization of T cell diversity may be key to understanding the success of immunomodulatory drugs and failure of PD-1 blockade in tumors such as multiple myeloma (MM). Here, we use single-cell RNA and T cell receptor sequencing to characterize bone marrow T cells from healthy adults (n = 4) and patients with precursor (n = 8) and full-blown MM (n = 10). Large T cell clones from patients with MM expressed multiple immune checkpoints, suggesting a potentially dysfunctional phenotype. Dual targeting of PD-1 + LAG3 or PD-1 + TIGIT partially restored their function in mice with MM. We identify phenotypic hallmarks of large intratumoral T cell clones, and demonstrate that the CD27- and CD27+ T cell ratio, measured by flow cytometry, may serve as a surrogate of clonal T cell expansions and an independent prognostic factor in 543 patients with MM treated with lenalidomide-based treatment combinations.
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Grants
- This work was supported by grants from the Instituto de Salud Carlos III/Subdireccion General de Investigacion Sanitaria and co-financed by FEDER funds (CB16/12/00233, CB16/12/00369, PI17/01243, PI19/00818 and PI20/00048), and together with Fundación Científica de la Asociación Española Contra el Cáncer (FCAECC) for iMMunocell Transcan-2 (AC17/00101), FCAECC Predoctoral Grant Junta Provincial Navarra, the Cancer Research UK (C355/A26819), FCAECC and Italian Association for Cancer Research (AIRC) under the Accelerator Award Program (EDITOR), 2017 Multiple Myeloma Research Foundation Immunotherapy Networks of Excellence, Black Swan Research Initiative of the International Myeloma Foundation, European Hematology Association nonclinical advanced research grant (3680644), European Research Council 2015 Starting Grant (MYELOMANEXT grant 680200), the Cancer Research Innovation in Science Cancer Foundation (PR_EX_2020-02), the Leukemia Lymphoma Society, unrestricted grants from Bristol-Myers Squibb/Celgene and Takeda, Roche imCORE program (NAV-4 and NAV-15), Fondazione Regionale per la Ricerca Biomedica (Regione Lombardia) (Project ID 065 JTC 2016), ERA-NET TRANSCAN-2, and by My First AIRC Grant 2020 (n. 24534, 2021/2026), and by the Riney Family Multiple Myeloma Research Program Fund.
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Affiliation(s)
- Cirino Botta
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy.
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain.
| | - Cristina Perez
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Marta Larrayoz
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Noemi Puig
- Hospital Universitario de Salamanca, Instituto de Investigacion Biomedica de Salamanca (IBSAL), Centro de Investigación del Cancer (IBMCC-USAL, CSIC), CIBER-ONC number CB16/12/00233, Salamanca, Spain
| | - Maria-Teresa Cedena
- Hospital Universitario 12 de Octubre, CIBER-ONC number CB16/12/00369, Madrid, Spain
| | - Rosalinda Termini
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Ibai Goicoechea
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Sara Rodriguez
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Aintzane Zabaleta
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Aitziber Lopez
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Sarai Sarvide
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Laura Blanco
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Daniele M Papetti
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
| | - Marco S Nobile
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Venice, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre-B4, Milan, Italy
| | - Daniela Besozzi
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Milan, Italy
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre-B4, Milan, Italy
| | - Massimo Gentile
- Department of Oncohematology, "Annunziata" Hospital, Cosenza, Italy
| | - Pierpaolo Correale
- Medical Oncology Unit, Great Metropolitan Hospital "Riuniti" of Reggio Calabria, Reggio Calabria, Italy
| | - Sergio Siragusa
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Albert Oriol
- Institut Català d'Oncologia i Institut Josep Carreras, Badalona, Spain
| | | | - Anna Sureda
- Institut Català d'Oncologia-Hospitalet, Instituto de Investigación Biomédica de Bellvitge (IDIBELL), Barcelona, Spain
| | - Felipe de Arriba
- Hospital Morales Meseguer, IMIB-Arrixaca, Universidad de Murcia, Murcia, Spain
| | | | - Jose-Maria Moraleda
- Hospital Morales Meseguer, IMIB-Arrixaca, Universidad de Murcia, Murcia, Spain
| | | | | | - Joan Bargay
- Hospital Son Llatzer, Palma de Mallorca, Spain
| | | | | | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, Heidelberg, Germany
| | | | - Aldo Roccaro
- Department of Hematology, ASST Spedali Civili di Brescia, Brescia, BS, Italy
| | - Alberto Orfao
- Cancer Research Center (IBMCC-CSIC/USAL-IBSAL), CIBER-ONC number CB16/12/00400, Salamanca, Spain
- Cytometry Service (NUCLEUS) and Department of Medicine, University of Salamanca, Salamanca, Spain
| | | | | | - Juan-José Lahuerta
- Hospital Universitario 12 de Octubre, CIBER-ONC number CB16/12/00369, Madrid, Spain
| | - Joan Blade
- Hospital Clínic IDIBAPS, Barcelona, Spain
| | - Maria-Victoria Mateos
- Hospital Universitario de Salamanca, Instituto de Investigacion Biomedica de Salamanca (IBSAL), Centro de Investigación del Cancer (IBMCC-USAL, CSIC), CIBER-ONC number CB16/12/00233, Salamanca, Spain
| | - Jesús F San-Miguel
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Jose-Angel Martinez Climent
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain
| | - Bruno Paiva
- Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), CCUN, Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC numbers CB16/12/00369, CB16/12/00489, Pamplona, Spain.
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4
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Bhat KH, Priyadarshi S, Naiyer S, Qu X, Farooq H, Kleiman E, Xu J, Lei X, Cantillo JF, Wuerffel R, Baumgarth N, Liang J, Feeney AJ, Kenter AL. An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation. Nat Commun 2023; 14:1225. [PMID: 36869028 DOI: 10.1038/s41467-023-36414-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/31/2023] [Indexed: 03/05/2023] Open
Abstract
The mouse Igh locus is organized into a developmentally regulated topologically associated domain (TAD) that is divided into subTADs. Here we identify a series of distal VH enhancers (EVHs) that collaborate to configure the locus. EVHs engage in a network of long-range interactions that interconnect the subTADs and the recombination center at the DHJH gene cluster. Deletion of EVH1 reduces V gene rearrangement in its vicinity and alters discrete chromatin loops and higher order locus conformation. Reduction in the rearrangement of the VH11 gene used in anti-PtC responses is a likely cause of the observed reduced splenic B1 B cell compartment. EVH1 appears to block long-range loop extrusion that in turn contributes to locus contraction and determines the proximity of distant VH genes to the recombination center. EVH1 is a critical architectural and regulatory element that coordinates chromatin conformational states that favor V(D)J rearrangement.
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5
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Snir T, Philip H, Gordin M, Zilberberg A, Efroni S. The temporal behavior of the murine T cell receptor repertoire following Immunotherapy. Sci Data 2023; 10:108. [PMID: 36823176 PMCID: PMC9950060 DOI: 10.1038/s41597-023-01982-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 01/24/2023] [Indexed: 02/25/2023] Open
Abstract
Immunotherapy is now an essential tool for cancer treatment, and the unique features of an individual's T cell receptor repertoire are known to play a key role in its effectiveness. The repertoire, famously vast due to a cascade of cellular mechanisms, can be quantified using repertoire sequencing. In this study, we sampled the repertoire over several time points following treatment with anti-CTLA-4, in a syngeniec mouse model for colorectal cancer, generating a longitudinal dataset of T cell clones and their abundance. The dynamics of the repertoire can be observed in response to treatment over a period of four weeks, as clonal expansion of specific clones ascends and descends. The data made available here can be used to determine treatment and predict its effect, while also providing a unique look at the behavior of the immune system over time.
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Affiliation(s)
- Tom Snir
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Hagit Philip
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Miri Gordin
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Alona Zilberberg
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sol Efroni
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.
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6
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Jaffe DB, Shahi P, Adams BA, Chrisman AM, Finnegan PM, Raman N, Royall AE, Tsai F, Vollbrecht T, Reyes DS, Hepler NL, McDonnell WJ. Functional antibodies exhibit light chain coherence. Nature 2022; 611:352-357. [PMID: 36289331 PMCID: PMC9607724 DOI: 10.1038/s41586-022-05371-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/21/2022] [Indexed: 11/08/2022]
Abstract
The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies that bind particular antigens1. In most mammals, antibodies are composed of heavy and light chains that are generated sequentially by recombination of V, D (for heavy chains), J and C gene segments. Each chain contains three complementarity-determining regions (CDR1-CDR3), which contribute to antigen specificity. Certain heavy and light chains are preferred for particular antigens2-22. Here we consider pairs of B cells that share the same heavy chain V gene and CDRH3 amino acid sequence and were isolated from different donors, also known as public clonotypes23,24. We show that for naive antibodies (those not yet adapted to antigens), the probability that they use the same light chain V gene is around 10%, whereas for memory (functional) antibodies, it is around 80%, even if only one cell per clonotype is used. This property of functional antibodies is a phenomenon that we call light chain coherence. We also observe this phenomenon when similar heavy chains recur within a donor. Thus, although naive antibodies seem to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
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7
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Vincendeau E, Wei W, Zhang X, Planchais C, Yu W, Lenden-Hasse H, Cokelaer T, Pipoli da Fonseca J, Mouquet H, Adams DJ, Alt FW, Jackson SP, Balmus G, Lescale C, Deriano L. SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination. Nat Commun 2022; 13:3707. [PMID: 35764636 PMCID: PMC9240092 DOI: 10.1038/s41467-022-31287-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 07/27/2021] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
SHLD1 is part of the Shieldin (SHLD) complex, which acts downstream of 53BP1 to counteract DNA double-strand break (DSB) end resection and promote DNA repair via non-homologous end-joining (NHEJ). While 53BP1 is essential for immunoglobulin heavy chain class switch recombination (CSR), long-range V(D)J recombination and repair of RAG-induced DSBs in XLF-deficient cells, the function of SHLD during these processes remains elusive. Here we report that SHLD1 is dispensable for lymphocyte development and RAG-mediated V(D)J recombination, even in the absence of XLF. By contrast, SHLD1 is essential for restricting resection at AID-induced DSB ends in both NHEJ-proficient and NHEJ-deficient B cells, providing an end-protection mechanism that permits productive CSR by NHEJ and alternative end-joining. Finally, we show that this SHLD1 function is required for orientation-specific joining of AID-initiated DSBs. Our data thus suggest that 53BP1 promotes V(D)J recombination and CSR through two distinct mechanisms: SHLD-independent synapsis of V(D)J segments and switch regions within chromatin, and SHLD-dependent protection of AID-DSB ends against resection.
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Affiliation(s)
- Estelle Vincendeau
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Wenming Wei
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Xuefei Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China
| | - Cyril Planchais
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - Wei Yu
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Hélène Lenden-Hasse
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
- Institut Pasteur, Hub de Bioinformatique et Biostatistique, Département de Biologie Computationnelle, 75015, Paris, France
| | - Juliana Pipoli da Fonseca
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Gabriel Balmus
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Chloé Lescale
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
| | - Ludovic Deriano
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
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8
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Andreano E, Paciello I, Marchese S, Donnici L, Pierleoni G, Piccini G, Manganaro N, Pantano E, Abbiento V, Pileri P, Benincasa L, Giglioli G, Leonardi M, Maes P, De Santi C, Sala C, Montomoli E, De Francesco R, Rappuoli R. Anatomy of Omicron BA.1 and BA.2 neutralizing antibodies in COVID-19 mRNA vaccinees. Nat Commun 2022; 13:3375. [PMID: 35697673 PMCID: PMC9189263 DOI: 10.1038/s41467-022-31115-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 05/04/2022] [Accepted: 06/05/2022] [Indexed: 12/15/2022] Open
Abstract
SARS-CoV-2 vaccines, administered to billions of people worldwide, mitigate the effects of the COVID-19 pandemic, however little is known about the molecular basis of antibody cross-protection to emerging variants, such as Omicron BA.1, its sublineage BA.2, and other coronaviruses. To answer this question, 276 neutralizing monoclonal antibodies (nAbs), previously isolated from seronegative and seropositive donors vaccinated with BNT162b2 mRNA vaccine, were tested for neutralization against the Omicron BA.1 and BA.2 variants, and SARS-CoV-1 virus. Only 14.2, 19.9 and 4.0% of tested antibodies neutralize BA.1, BA.2, and SARS-CoV-1 respectively. These nAbs recognize mainly the SARS-CoV-2 receptor binding domain (RBD) and target Class 3 and Class 4 epitope regions on the SARS-CoV-2 spike protein. Interestingly, around 50% of BA.2 nAbs did not neutralize BA.1 and among these, several targeted the NTD. Cross-protective antibodies derive from a variety of germlines, the most frequents of which were the IGHV1-58;IGHJ3-1, IGHV2-5;IGHJ4-1 and IGHV1-69;IGHV4-1. Only 15.6, 20.3 and 7.8% of predominant gene-derived nAbs elicited against the original Wuhan virus cross-neutralize Omicron BA.1, BA.2 and SARS-CoV-1 respectively. Our data provide evidence, at molecular level, of the presence of cross-neutralizing antibodies induced by vaccination and map conserved epitopes on the S protein that can inform vaccine design.
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Affiliation(s)
- Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Ida Paciello
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Silvia Marchese
- Department of Pharmacological and Biomolecular Sciences DiSFeB, University of Milan, Milan, Italy
| | - Lorena Donnici
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Giulio Pierleoni
- VisMederi S.r.l, Siena, Italy
- VisMederi Research S.r.l., Siena, Italy
| | | | - Noemi Manganaro
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Elisa Pantano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Valentina Abbiento
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Piero Pileri
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | | | | | | | - Piet Maes
- KU Leuven, Rega Institute, Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Leuven, Belgium
| | - Concetta De Santi
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Claudia Sala
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Emanuele Montomoli
- VisMederi S.r.l, Siena, Italy
- VisMederi Research S.r.l., Siena, Italy
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Raffaele De Francesco
- Department of Pharmacological and Biomolecular Sciences DiSFeB, University of Milan, Milan, Italy
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Rino Rappuoli
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy.
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena, Italy.
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9
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Lin D, Wang D, Li P, Yang X, Liu W, Huang L, Zhang Z, Zhang Y, Zhang W, Zhang N, Zhang M, Huang X. Dynamic analysis of peripheral blood TCR β-chain CDR3 repertoire in occupational medicamentosa-like dermatitis due to trichloroethylene. Sci Rep 2021; 11:9971. [PMID: 33976265 PMCID: PMC8113444 DOI: 10.1038/s41598-021-89431-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/11/2020] [Accepted: 04/27/2021] [Indexed: 11/23/2022] Open
Abstract
Previously, we had cross-sectionally explored the characteristics of T cell receptor (TCR) repertoires from occupational medicamentosa-like dermatitis due to trichloroethylene (OMDT) patients, now we further analyzed the dynamic features of OMDT TCR repertoires. Peripheral blood TCR β-chain complementarity-determining region 3 (CDR3) genes were detected with the high throughput sequencing in 24 OMDT cases in their acute, chronic and recovery stages, respectively, and in 24 trichloroethylene-exposed healthy controls. The TCR repertoire diversity, TRBV/TRBD/TRBJ gene usage and combination, frequencies of CDR3 nucleotide (nt) and amino acid (aa) sequences in the cases in different stages and in the controls were analyzed. TRBV6-4 and TRBV7-9 frequencies significantly differed between the cases and controls (both P < 6.1 × 10-4). TRBV6-4 combination with TRBJ2-1, TRBJ2-2, TRBJ2-3, and TRBJ2-6, and TRBV7-9 combination with TRBJ2-1 were associated with the stage by OMDT severity (all P < 0.001). Ten CDR3-nt and 7 CDR3-aa sequences in TRBV7-9-TRBJ2-1 combination and 1 CDR3-nt and 1 CDR3-aa sequences in TRBV6-4-TRBJ2-1 combination were identified as associated with the severity of OMDT (all P < 0.001). We revealed further how TCR repertoires vary with the severity in the development of OMDT, and severity-related TCRs may provide important therapeutic targets for OMDT in clinical practice.
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Affiliation(s)
- Dafeng Lin
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China.
| | - Dianpeng Wang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China
| | - Peimao Li
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China
| | - Xiangli Yang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China
| | - Wei Liu
- Key Laboratory of Modern Toxicology of Shenzhen, Medical Key Laboratory of Guangdong Province, Medical Key Laboratory of Health Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Lu Huang
- Fuyong Prevention and Health Care Center, Bao'an District, Shenzhen, 518103, China
| | - Zhimin Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China
| | - Yanfang Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China
| | - Wen Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China
| | - Naixing Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China.
| | - Ming Zhang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China
| | - Xianqing Huang
- Medical Laboratory, Shenzhen Prevention and Treatment Center for Occupational Diseases, 2019 Buxin Rd., Luohu district, Shenzhen, 518020, China
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10
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Liu S, Yuan S, Gao X, Tao X, Yu W, Li X, Chen S, Xu A. Functional regulation of an ancestral RAG transposon ProtoRAG by a trans-acting factor YY1 in lancelet. Nat Commun 2020; 11:4515. [PMID: 32908127 PMCID: PMC7481187 DOI: 10.1038/s41467-020-18261-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 09/30/2019] [Accepted: 08/09/2020] [Indexed: 01/04/2023] Open
Abstract
The discovery of ancestral RAG transposons in early deuterostomia reveals the origin of vertebrate V(D)J recombination. Here, we analyze the functional regulation of a RAG transposon, ProtoRAG, in lancelet. We find that a specific interaction between the cis-acting element within the TIR sequences of ProtoRAG and a trans-acting factor, lancelet YY1-like (bbYY1), is important for the transcriptional regulation of lancelet RAG-like genes (bbRAG1L and bbRAG2L). Mechanistically, bbYY1 suppresses the transposition of ProtoRAG; meanwhile, bbYY1 promotes host DNA rejoins (HDJ) and TIR-TIR joints (TTJ) after TIR-dependent excision by facilitating the binding of bbRAG1L/2 L to TIR-containing DNA, and by interacting with the bbRAG1L/2 L complex. Our data thus suggest that bbYY1 has dual functions in fine-tuning the activity of ProtoRAG and maintaining the genome stability of the host.
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Affiliation(s)
- Song Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Shaochun Yuan
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, People's Republic of China.
| | - Xiaoman Gao
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Xin Tao
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Wenjuan Yu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Xu Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China.
- School of Life Sciences, Beijing University of Chinese Medicine, 100029, Beijing, People's Republic of China.
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11
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Watson CT, Steinberg KM, Graves TA, Warren RL, Malig M, Schein J, Wilson RK, Holt RA, Eichler EE, Breden F. Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity. Genes Immun 2015; 16:24-34. [PMID: 25338678 PMCID: PMC4304971 DOI: 10.1038/gene.2014.56] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [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: 07/02/2014] [Revised: 09/03/2014] [Accepted: 09/03/2014] [Indexed: 12/24/2022]
Abstract
Germline variation at immunoglobulin (IG) loci is critical for pathogen-mediated immunity, but establishing complete haplotype sequences in these regions has been problematic because of complex sequence architecture and diploid source DNA. We sequenced BAC clones from the effectively haploid human hydatidiform mole cell line, CHM1htert, across the light chain IG loci, kappa (IGK) and lambda (IGL), creating single haplotype representations of these regions. The IGL haplotype generated here is 1.25 Mb of contiguous sequence, including four novel IGLV alleles, one novel IGLC allele, and an 11.9-kb insertion. The CH17 IGK haplotype consists of two 644 kb proximal and 466 kb distal contigs separated by a large gap of unknown size; these assemblies added 49 kb of unique sequence extending into this gap. Our analysis also resulted in the characterization of seven novel IGKV alleles and a 16.7-kb region exhibiting signatures of interlocus sequence exchange between distal and proximal IGKV gene clusters. Genetic diversity in IGK/IGL was compared with that of the IG heavy chain (IGH) locus within the same haploid genome, revealing threefold (IGK) and sixfold (IGL) higher diversity in the IGH locus, potentially associated with increased levels of segmental duplication and the telomeric location of IGH.
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Affiliation(s)
- C T Watson
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - K M Steinberg
- Department of Genome Sciences, University of Washington, Seattle, WA USA
- The Genome Institute, Washington University, St Louis, MO USA
| | - T A Graves
- The Genome Institute, Washington University, St Louis, MO USA
| | - R L Warren
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia Canada
| | - M Malig
- Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - J Schein
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia Canada
| | - R K Wilson
- The Genome Institute, Washington University, St Louis, MO USA
| | - R A Holt
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia Canada
| | - E E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA USA
- Howard Hughes Medical Institute, Seattle, WA USA
| | - F Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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12
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Ndifon W, Gal H, Shifrut E, Aharoni R, Yissachar N, Waysbort N, Reich-Zeliger S, Arnon R, Friedman N. Chromatin conformation governs T-cell receptor Jβ gene segment usage. Proc Natl Acad Sci U S A 2012; 109:15865-70. [PMID: 22984176 PMCID: PMC3465372 DOI: 10.1073/pnas.1203916109] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [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] [Indexed: 11/18/2022] Open
Abstract
T cells play fundamental roles in adaptive immunity, relying on a diverse repertoire of T-cell receptor (TCR) α and β chains. Diversity of the TCR β chain is generated in part by a random yet intrinsically biased combinatorial rearrangement of variable (Vβ), diversity (Dβ), and joining (Jβ) gene segments. The mechanisms that determine biases in gene segment use remain unclear. Here we show, using a high-throughput TCR sequencing approach, that a physical model of chromatin conformation at the DJβ genomic locus explains more than 80% of the biases in Jβ use that we measured in murine T cells. This model also predicts correctly how differences in intersegment genomic distances between humans and mice translate into differences in Jβ bias between TCR repertoires of these two species. As a consequence of these structural and other biases, TCR sequences are produced with different a priori frequencies, thus affecting their probability of becoming public TCRs that are shared among individuals. Surprisingly, we find that many more TCR sequences are shared among all five mice we studied than among only subgroups of three or four mice. We derive a necessary mathematical condition explaining this finding, which indicates that the TCR repertoire contains a core set of receptor sequences that are highly abundant among individuals, if their a priori probability of being produced by the recombination process is higher than a defined threshold. Our results provide evidence for an expanded role of chromatin conformation in VDJ rearrangement, from control of gene accessibility to precise determination of gene segment use.
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Affiliation(s)
| | | | - Eric Shifrut
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Rina Aharoni
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Nissan Yissachar
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Nir Waysbort
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | | | - Ruth Arnon
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
| | - Nir Friedman
- Department of Immunology, Weizmann Institute of Science, Rehovot, 76100 Israel
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13
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Lee YN, Alt FW, Reyes J, Gleason M, Zarrin AA, Jung D. Differential utilization of T cell receptor TCR alpha/TCR delta locus variable region gene segments is mediated by accessibility. Proc Natl Acad Sci U S A 2009; 106:17487-92. [PMID: 19805067 PMCID: PMC2765100 DOI: 10.1073/pnas.0909723106] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [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: 08/03/2009] [Indexed: 01/15/2023] Open
Abstract
T cell receptor (TCR) variable region exons are assembled from germline V, (D), and J gene segments, each of which is flanked by recombination signal (RS) sequences that are composed of a conserved heptamer, a spacer of 12 or 23 bp, and a characteristic nonamer. V(D)J recombination only occurs between V, D, and J segments flanked by RS sequences that contain, respectively, 12(12-RS)- and 23(23-RS)-bp spacers (12/23 rule). Additional mechanisms can restrict joining of 12/23 RS matched segments beyond the 12/23 rule (B12/23). The TCRdelta locus is contained within the TCRalpha locus; TCRalpha variable region exons are encoded by TRAV and TRAJ segments and those of TCRdelta by TRDV, TRDD, and TRDJ segments. On the basis of the 12/23 rule, both TRAV and TRDV gene segments are compatible to rearrange with TRDD gene segments; however, TRAV-to-TRDD joins are not observed in vivo. Absence of TRAV-to-TRDD rearrangement might be explained either by B12/23 restriction or by differential accessibility of the TRDV versus TRAV gene segments for rearrangement to TRDD. We used in vitro substrate analysis to reveal that both TRAV and TRDV 23-RSs mediate rearrangements to the 5'TRDD1 12-RS, demonstrating that B12/23 restriction does not explain these rearrangement biases. However, targeted replacement of TRDD1 and its 12-RSs with TRAJ38 and its 12-RS showed that TRDV gene segments rearrange with the ectopic TRAJ38, whereas TRAV segments do not. Our results demonstrate that sorting of TRAV and TRDV gene segments is determined by differential locus accessibility during T cell development.
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Affiliation(s)
- Yu Nee Lee
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - Frederick W. Alt
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - Julia Reyes
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - Megan Gleason
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - Ali A. Zarrin
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
| | - David Jung
- Howard Hughes Medical Institute, Children's Hospital Boston, Immune Disease Institute, Harvard Medical School, Boston, MA 02115
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14
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Cui X, Meek K. Linking double-stranded DNA breaks to the recombination activating gene complex directs repair to the nonhomologous end-joining pathway. Proc Natl Acad Sci U S A 2007; 104:17046-51. [PMID: 17939999 PMCID: PMC2040436 DOI: 10.1073/pnas.0610928104] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Indexed: 01/13/2023] Open
Abstract
Two major DNA repair pathways, nonhomologous end-joining (NHEJ) and homologous recombination (HR), repair double-stranded DNA breaks (DSBs) in all eukaryotes. Additionally, several alternative end-joining pathways (or subpathways) have been reported that characteristically use short-sequence homologies at the DNA ends to facilitate joining. How a cell chooses which DNA repair pathway to use (at any particular DSB) is a central and largely unanswered question. For one type of DSB, there is apparently no choice. DSBs mediated by the lymphocyte-specific recombination activating gene (RAG) endonuclease are repaired virtually exclusively by NHEJ. Here we demonstrate that non-RAG-mediated DSBs can be similarly forced into the NHEJ pathway by physical association with the RAG endonuclease.
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Affiliation(s)
- Xiaoping Cui
- College of Veterinary Medicine and Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI 48824
| | - Katheryn Meek
- College of Veterinary Medicine and Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, MI 48824
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15
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Abstract
DNA polymerases are involved in different cellular events, including genome replication and DNA repair. In the last few years, a large number of novel DNA polymerases have been discovered, and the biochemical analysis of their properties has revealed a long list of intriguing features. Some of these polymerases have a very low fidelity and have been suggested to play mutator roles in different processes, like translesion synthesis or somatic hypermutation. The current view of these processes is reviewed, and the current understanding of DNA polymerases and their role as mutator enzymes is discussed.
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Affiliation(s)
- Miguel García-Díaz
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM). Universidad Autónoma, 28049 Madrid, Spain.
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16
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Rooney S, Alt FW, Lombard D, Whitlow S, Eckersdorff M, Fleming J, Fugmann S, Ferguson DO, Schatz DG, Sekiguchi J. Defective DNA repair and increased genomic instability in Artemis-deficient murine cells. J Exp Med 2003; 197:553-65. [PMID: 12615897 PMCID: PMC2193825 DOI: 10.1084/jem.20021891] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.5] [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] [Indexed: 01/03/2023] Open
Abstract
In developing lymphocytes, the recombination activating gene endonuclease cleaves DNA between V, D, or J coding and recombination signal (RS) sequences to form hairpin coding and blunt RS ends, which are fused to form coding and RS joins. Nonhomologous end joining (NHEJ) factors repair DNA double strand breaks including those induced during VDJ recombination. Human radiosensitive severe combined immunodeficiency results from lack of Artemis function, an NHEJ factor with in vitro endonuclease/exonuclease activities. We inactivated Artemis in murine embryonic stem (ES) cells by targeted mutation. Artemis deficiency results in impaired VDJ coding, but not RS, end joining. In addition, Artemis-deficient ES cells are sensitive to a radiomimetic drug, but less sensitive to ionizing radiation. VDJ coding joins from Artemis-deficient ES cells, which surprisingly are distinct from the highly deleted joins consistently obtained from DNA-dependent protein kinase catalytic subunit-deficient ES cells, frequently lack deletions and often display large junctional palindromes, consistent with a hairpin coding end opening defect. Strikingly, Artemis-deficient ES cells have increased chromosomal instability including telomeric fusions. Thus, Artemis appears to be required for a subset of NHEJ reactions that require end processing. Moreover, Artemis functions as a genomic caretaker, most notably in prevention of translocations and telomeric fusions. As Artemis deficiency is compatible with human life, Artemis may also suppress genomic instability in humans.
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Affiliation(s)
- Sean Rooney
- Howard Hughes Medical Institute, The Children's Hospital, The Center for Blood Research, Harvard Medical School, Boston, MA 02115, USA
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17
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Abstract
Lymphocyte antigen receptors are not encoded by germline genes, but rather are produced by combinatorial joining between clusters of gene segments in somatic cells. Within a given cluster, gene segment usage during recombination is thought to be largely random, with biased representation in mature T lymphocytes resulting from protein-mediated selection of a subset of the total repertoire. Here we show that T cell receptor D beta and J beta gene segment usage is not random, but is patterned at the time of recombination. The hierarchy of gene segment usage is independent of gene segment proximity, but rather is influenced by the ability of the flanking recombination signal sequences (RSS) to bind the recombinase and/or to form a paired synaptic complex. Importantly, the relative frequency of gene segment usage established during recombination is very similar to that found after protein-mediated selection, suggesting that in addition to targeting recombinase activity, the RSS may have evolved to bias the naive repertoire in favor of useful gene products.
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Affiliation(s)
- F Livak
- Section of Immunobiology, Yale University School of Medicine, New Haven, Connecticut 08360, USA
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Mahajan KN, Gangi-Peterson L, Sorscher DH, Wang J, Gathy KN, Mahajan NP, Reeves WH, Mitchell BS. Association of terminal deoxynucleotidyl transferase with Ku. Proc Natl Acad Sci U S A 1999; 96:13926-31. [PMID: 10570175 PMCID: PMC24167 DOI: 10.1073/pnas.96.24.13926] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [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: 11/18/2022] Open
Abstract
Terminal deoxynucleotidyl transferase (TdT) catalyzes the addition of nucleotides at the junctions of rearranging Ig and T cell receptor gene segments, thereby generating antigen receptor diversity. Ku is a heterodimeric protein composed of 70- and 86-kDa subunits that binds DNA ends and is required for V(D)J recombination and DNA double-strand break (DSB) repair. We provide evidence for a direct interaction between TdT and Ku proteins. Studies with a baculovirus expression system show that TdT can interact specifically with each of the Ku subunits and with the heterodimer. The interaction between Ku and TdT is also observed in pre-T cells with endogenously expressed proteins. The protein-protein interaction is DNA independent and occurs at physiological salt concentrations. Deletion mutagenesis experiments reveal that the N-terminal region of TdT (131 amino acids) is essential for interaction with the Ku heterodimer. This region, although not important for TdT polymerization activity, contains a BRCA1 C-terminal domain that has been shown to mediate interactions of proteins involved in DNA repair. The induction of DSBs in Cos-7 cells transfected with a human TdT expression construct resulted in the appearance of discrete nuclear foci in which TdT and Ku colocalize. The physical association of TdT with Ku suggests a possible mechanism by which TdT is recruited to the sites of DSBs such as V(D)J recombination intermediates.
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Affiliation(s)
- K N Mahajan
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
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Durum SK, Candèias S, Nakajima H, Leonard WJ, Baird AM, Berg LJ, Muegge K. Interleukin 7 receptor control of T cell receptor gamma gene rearrangement: role of receptor-associated chains and locus accessibility. J Exp Med 1998; 188:2233-41. [PMID: 9858510 PMCID: PMC2212428 DOI: 10.1084/jem.188.12.2233] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.8] [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] [Indexed: 12/16/2022] Open
Abstract
VDJ recombination of T cell receptor and immunoglobulin loci occurs in immature lymphoid cells. Although the molecular mechanisms of DNA cleavage and ligation have become more clear, it is not understood what controls which target loci undergo rearrangement. In interleukin 7 receptor (IL-7R)alpha-/- murine thymocytes, it has been shown that rearrangement of the T cell receptor (TCR)-gamma locus is virtually abrogated, whereas other rearranging loci are less severely affected. By examining different strains of mice with targeted mutations, we now observe that the signaling pathway leading from IL-7Ralpha to rearrangement of the TCR-gamma locus requires the gammac receptor chain and the gammac-associated Janus kinase Jak3. Production of sterile transcripts from the TCR-gamma locus, a process that generally precedes rearrangement of a locus, was greatly repressed in IL-7Ralpha-/- thymocytes. The repressed transcription was not due to a lack in transcription factors since the three transcription factors known to regulate this locus were readily detected in IL-7Ralpha-/- thymocytes. Instead, the TCR-gamma locus was shown to be methylated in IL-7Ralpha-/- thymocytes. Treatment of IL-7Ralpha-/- precursor T cells with the specific histone deacetylase inhibitor trichostatin A released the block of TCR-gamma gene rearrangement. This data supports the model that IL-7R promotes TCR-gamma gene rearrangement by regulating accessibility of the locus via demethylation and histone acetylation of the locus.
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MESH Headings
- Animals
- Bone Marrow Cells
- Chromatin/metabolism
- DNA/metabolism
- DNA Methylation
- Enhancer Elements, Genetic/genetics
- Enzyme Inhibitors/pharmacology
- Gene Rearrangement, gamma-Chain T-Cell Antigen Receptor/drug effects
- Gene Rearrangement, gamma-Chain T-Cell Antigen Receptor/genetics
- Genes, RAG-1/genetics
- Genes, RAG-1/physiology
- Hematopoietic Stem Cells/immunology
- Hematopoietic Stem Cells/metabolism
- Histone Deacetylase Inhibitors
- Histone Deacetylases/metabolism
- Hydroxamic Acids/pharmacology
- Janus Kinase 3
- Mice
- Mice, Inbred C57BL
- Protein-Tyrosine Kinases/genetics
- Protein-Tyrosine Kinases/metabolism
- RNA/biosynthesis
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Receptors, Interleukin-7/genetics
- Receptors, Interleukin-7/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Thymus Gland/drug effects
- Thymus Gland/embryology
- Transcription Factors/metabolism
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Affiliation(s)
- S K Durum
- Laboratory of Molecular Immunoregulation, National Cancer Institute, Frederick, Maryland 21702, USA
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Abstract
In mammalian cells, double-strand break repair and V(D)J recombination require DNA-dependent protein kinase (DNA-PK), a serine/threonine kinase that is activated by DNA. DNA-PK consists of a 460-kDa subunit (p460) that contains a putative kinase domain and a heterodimeric subunit (Ku) that binds to double-stranded DNA ends. Previous reports suggested that the activation of DNA-PK requires the binding of Ku to DNA. To investigate this further, p460 and Ku were purified separately to homogeneity. Surprisingly, p460 was capable of binding to DNA in the absence of Ku. The binding of p460 to double-stranded DNA ends was salt-labile and could be disrupted by single-stranded or supercoiled DNA, properties distinct from the binding of Ku to DNA. Under low salt conditions, which permitted the binding of p460 to DNA ends, the kinase was activated. Under higher salt conditions, which inhibited the binding of p460, activation of the kinase required the addition of Ku. Significantly, when the length of DNA decreased to 22 bp, Ku competed with p460 for DNA binding and inhibited kinase activity. These data demonstrate that p460 is a self-contained kinase that is activated by direct interaction with double-stranded DNA and that the role of Ku is to stabilize the binding of p460 to DNA ends.
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Affiliation(s)
- O Hammarsten
- Department of Medicine, Stanford University Medical Center, CA 94305-5115, USA
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