1
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Uhlemann H, Epp K, Klesse C, Link-Rachner CS, Surendranath V, Günther UP, Schetelig J, Heidenreich F. Shape of the art: TCR-repertoire after allogeneic hematopoietic cell transplantation. Best Pract Res Clin Haematol 2024; 37:101558. [PMID: 39098804 DOI: 10.1016/j.beha.2024.101558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 05/03/2024] [Accepted: 06/27/2024] [Indexed: 08/06/2024]
Abstract
The human adaptive immune repertoire is characterized by specificity and diversity to provide immunity against past and future tasks. Such tasks are mainly infections but also malignant transformations of cells. With its multiple lines of defense, the human immune system contains both, rapid reaction forces and the potential to capture, disassemble and analyze strange structures in order to teach the adaptive immune system and mount a specific immune response. Prevention and mitigation of autoimmunity is of equal importance. In the context of allogeneic hematopoietic cell transplantation (HCT) specific challenges exist with the transfer of cells from the adapted donor immune system to the immunosuppressed recipient. Those challenges are immunogenetic disparity between donor and host, reconstitution of immunity early after HCT by expansion of mature immune effector cells, and impaired thymic function, if the recipient is an adult (as it is the case in most HCTs). The possibility to characterize the adaptive immune repertoire by massively parallel sequencing of T-cell receptor gene rearrangements allows for a much more detailed characterization of the T-cell repertoire. In addition, high-dimensional characterization of immune effector cells based on their immunophenotype and single cell RNA sequencing allow for much deeper insights in adaptive immune responses. We here review, existing - still incomplete - information on immune reconstitution after allogeneic HCT. Building on the technological advances much deeper insights into immune recovery after HCT and adaptive immune responses and can be expected in the coming years.
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Affiliation(s)
- Heike Uhlemann
- University Hospital Carl Gustav Carus, Dresden, Germany; DKMS Group gGmbH, Clinical Trials Unit, Dresden, Germany.
| | - Katharina Epp
- University Hospital Carl Gustav Carus, Dresden, Germany
| | | | | | | | | | - Johannes Schetelig
- University Hospital Carl Gustav Carus, Dresden, Germany; DKMS Group gGmbH, Clinical Trials Unit, Dresden, Germany
| | - Falk Heidenreich
- University Hospital Carl Gustav Carus, Dresden, Germany; DKMS Group gGmbH, Clinical Trials Unit, Dresden, Germany
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2
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Naik AK, Dauphars DJ, Corbett E, Simpson L, Schatz DG, Krangel MS. RORγt up-regulates RAG gene expression in DP thymocytes to expand the Tcra repertoire. Sci Immunol 2024; 9:eadh5318. [PMID: 38489350 PMCID: PMC11005092 DOI: 10.1126/sciimmunol.adh5318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 02/21/2024] [Indexed: 03/17/2024]
Abstract
Recombination activating gene (RAG) expression increases as thymocytes transition from the CD4-CD8- double-negative (DN) to the CD4+CD8+ double-positive (DP) stage, but the physiological importance and mechanism of transcriptional up-regulation are unknown. Here, we show that a DP-specific component of the recombination activating genes antisilencer (DPASE) provokes elevated RAG expression in DP thymocytes. Mouse DP thymocytes lacking the DPASE display RAG expression equivalent to that in DN thymocytes, but this supports only a partial Tcra repertoire due to inefficient secondary Vα-Jα rearrangement. These data indicate that RAG up-regulation is required for a replete Tcra repertoire and that RAG expression is fine-tuned during lymphocyte development to meet the requirements of distinct antigen receptor loci. We further show that transcription factor RORγt directs RAG up-regulation in DP thymocytes by binding to the DPASE and that RORγt influences the Tcra repertoire by binding to the Tcra enhancer. These data, together with prior work showing RORγt to control Tcra rearrangement by regulating DP thymocyte proliferation and survival, reveal RORγt to orchestrate multiple pathways that support formation of the Tcra repertoire.
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Affiliation(s)
- Abani Kanta Naik
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - Danielle J Dauphars
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - Elizabeth Corbett
- Department of Immunobiology and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Lunden Simpson
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
| | - David G Schatz
- Department of Immunobiology and Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Michael S Krangel
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, USA
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3
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Suo C, Polanski K, Dann E, Lindeboom RGH, Vilarrasa-Blasi R, Vento-Tormo R, Haniffa M, Meyer KB, Dratva LM, Tuong ZK, Clatworthy MR, Teichmann SA. Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins. Nat Biotechnol 2024; 42:40-51. [PMID: 37055623 PMCID: PMC10791579 DOI: 10.1038/s41587-023-01734-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/07/2023] [Indexed: 04/15/2023]
Abstract
Assessment of single-cell gene expression (single-cell RNA sequencing) and adaptive immune receptor (AIR) sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of nonproductive and partially spliced contigs. We devised a strategy to create an AIR feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double-positive T cells to mature single-positive CD4/CD8 T cells, generating predictions of factors regulating lineage commitment. Dandelion analysis of other cell compartments provided insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach. Dandelion is available at https://www.github.com/zktuong/dandelion .
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Affiliation(s)
- Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Paediatrics, Cambridge University Hospitals, Cambridge, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | | | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Lisa M Dratva
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Zewen Kelvin Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
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4
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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] [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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5
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Dai R, Zhu Y, Li Z, Qin L, Liu N, Liao S, Hao B. Three-way contact analysis characterizes the higher order organization of the Tcra locus. Nucleic Acids Res 2023; 51:8987-9000. [PMID: 37534534 PMCID: PMC10516640 DOI: 10.1093/nar/gkad641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 07/07/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
The generation of highly diverse antigen receptors in T and B lymphocytes relies on V(D)J recombination. The enhancer Eα has been implicated in regulating the accessibility of Vα and Jα genes through long-range interactions during rearrangements of the T-cell antigen receptor gene Tcra. However, direct evidence for Eα physically mediating the interaction of Vα and Jα genes is still lacking. In this study, we utilized the 3C-HTGTS assay, a chromatin interaction technique based on 3C, to analyze the higher order chromatin structure of the Tcra locus. Our analysis revealed the presence of sufficient information in the 3C-HTGTS data to detect multiway contacts. Three-way contact analysis of the Tcra locus demonstrated the co-occurrence of the proximal Jα genes, Vα genes and Eα in CD4+CD8+ double-positive thymocytes. Notably, the INT2-TEAp loop emerged as a prominent structure likely to be responsible for bringing the proximal Jα genes and the Vα genes into proximity. Moreover, the enhancer Eα utilizes this loop to establish physical proximity with the proximal Vα gene region. This study provides insights into the higher order chromatin structure of the Tcra locus, shedding light on the spatial organization of chromatin and its impact on V(D)J recombination.
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Affiliation(s)
- Ranran Dai
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Yongchang Zhu
- Department of Immunology, School of Basic Medical, Zhengzhou University, Zhengzhou 450001, China
- Medical Genetic Institute of Henan Province, Henan Key Laboratory of Genetic Diseases and Functional Genomics, National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province 450003, China
| | - Zhaoqiang Li
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Litao Qin
- Medical Genetic Institute of Henan Province, Henan Key Laboratory of Genetic Diseases and Functional Genomics, National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province 450003, China
| | - Nan Liu
- Division of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province 510515, China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Henan Key Laboratory of Genetic Diseases and Functional Genomics, National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan Province 450003, China
| | - Bingtao Hao
- Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong Province 510515, China
- Department of Immunology, School of Basic Medical, Zhengzhou University, Zhengzhou 450001, China
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6
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Xu C, Li S, Fulford TS, Christo SN, Mackay LK, Gray DH, Uldrich AP, Pellicci DG, I Godfrey D, Koay HF. Expansion of MAIT cells in the combined absence of NKT and γδ-T cells. Mucosal Immunol 2023; 16:446-461. [PMID: 37182737 DOI: 10.1016/j.mucimm.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/11/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
Mucosal-associated invariant T (MAIT) cells, natural killer T (NKT) cells, and γδT cells are collectively referred to as 'unconventional T cells' due to their recognition of non-peptide antigens and restriction to MHC-I-like molecules. However, the factors controlling their widely variable frequencies between individuals and organs are poorly understood. We demonstrated that MAIT cells are increased in NKT or γδT cell-deficient mice and highly expand in mice lacking both cell types. TCRα repertoire analysis of γδT cell-deficient thymocytes revealed altered Trav segment usage relative to wild-type thymocytes, highlighting retention of the Tcra-Tcrd locus from the 129 mouse strain used to generate Tcrd-/- mice. This resulted in a moderate increase in distal Trav segment usage, including Trav1, potentially contributing to increased generation of Trav1-Traj33+ MAIT cells in the Tcrd-/- thymus. Importantly, adoptively transferred MAIT cells underwent increased homeostatic proliferation within NKT/gdT cell-deficient tissues, with MAIT cell subsets exhibiting tissue-specific homing patterns. Our data reveal a shared niche for unconventional T cells, where competition for common factors may be exploited to collectively modulate these cells in the immune response. Lastly, our findings emphasise careful assessment of studies using NKT or γδT cell-deficient mice when investigating the role of unconventional T cells in disease.
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Affiliation(s)
- Calvin Xu
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Shihan Li
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Thomas S Fulford
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Susan N Christo
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Daniel Hd Gray
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Department of Medical Biology, University of Melbourne, Parkville, Australia
| | - Adam P Uldrich
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia
| | - Daniel G Pellicci
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia; Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Parkville, Australia.
| | - Dale I Godfrey
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.
| | - Hui-Fern Koay
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Australia.
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7
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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] [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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8
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Hoolehan W, Harris JC, Byrum JN, Simpson DA, Rodgers K. An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays. Nucleic Acids Res 2022; 50:11696-11711. [PMID: 36370096 PMCID: PMC9723617 DOI: 10.1093/nar/gkac1038] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 11/13/2022] Open
Abstract
In the adaptive immune system, V(D)J recombination initiates the production of a diverse antigen receptor repertoire in developing B and T cells. Recombination activating proteins, RAG1 and RAG2 (RAG1/2), catalyze V(D)J recombination by cleaving adjacent to recombination signal sequences (RSSs) that flank antigen receptor gene segments. Previous studies defined the consensus RSS as containing conserved heptamer and nonamer sequences separated by a less conserved 12 or 23 base-pair spacer sequence. However, many RSSs deviate from the consensus sequence. Here, we developed a cell-based, massively parallel assay to evaluate V(D)J recombination activity on thousands of RSSs where the 12-RSS heptamer and adjoining spacer region contained randomized sequences. While the consensus heptamer sequence (CACAGTG) was marginally preferred, V(D)J recombination was highly active on a wide range of non-consensus sequences. Select purine/pyrimidine motifs that may accommodate heptamer unwinding in the RAG1/2 active site were generally preferred. In addition, while different coding flanks and nonamer sequences affected recombination efficiency, the relative dependency on the purine/pyrimidine motifs in the RSS heptamer remained unchanged. Our results suggest RAG1/2 specificity for RSS heptamers is primarily dictated by DNA structural features dependent on purine/pyrimidine pattern, and to a lesser extent, RAG:RSS base-specific interactions.
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Affiliation(s)
- Walker Hoolehan
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Justin C Harris
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jennifer N Byrum
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Destiny A Simpson
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Karla K Rodgers
- To whom correspondence should be addressed. Tel: +1 405 271 2227 (Ext 61248);
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9
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Ratiu JJ, Barclay WE, Lin E, Wang Q, Wellford S, Mehta N, Harnois MJ, DiPalma D, Roy S, Contreras AV, Shinohara ML, Wiest D, Zhuang Y. Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection thymocytes. Nat Commun 2022; 13:5901. [PMID: 36202870 PMCID: PMC9537144 DOI: 10.1038/s41467-022-33610-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 09/22/2022] [Indexed: 01/05/2023] Open
Abstract
Production of a functional peripheral T cell compartment typically involves massive expansion of the bone marrow progenitors that seed the thymus. There are two main phases of expansion during T cell development, following T lineage commitment of double-negative (DN) 2 cells and after successful rearrangement and selection for functional TCRβ chains in DN3 thymocytes, which promotes the transition of DN4 cells to the DP stage. The signals driving the expansion of DN2 thymocytes are well studied. However, factors regulating the proliferation and survival of DN4 cells remain poorly understood. Here, we uncover an unexpected link between the transcription factor Zfp335 and control of cGAS/STING-dependent cell death in post-β-selection DN4 thymocytes. Zfp335 controls survival by sustaining expression of Ankle2, which suppresses cGAS/STING-dependent cell death. Together, this study identifies Zfp335 as a key transcription factor regulating the survival of proliferating post-β-selection thymocytes and demonstrates a key role for the cGAS/STING pathway in driving apoptosis of developing T cells.
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Affiliation(s)
- Jeremy J Ratiu
- Duke University, Department of Immunology, Durham, NC, 27710, USA.
| | | | - Elliot Lin
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Qun Wang
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | | | - Naren Mehta
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | | | - Devon DiPalma
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Sumedha Roy
- Duke University, Department of Immunology, Durham, NC, 27710, USA
| | - Alejandra V Contreras
- Fox Chase Cancer Center, Blood Cell Development and Function Program, Philadelphia, PA, 19111, USA
| | - Mari L Shinohara
- Duke University, Department of Immunology, Durham, NC, 27710, USA
- Duke University, Department of Molecular Genetics and Microbiology, Durham, NC, 27710, USA
| | - David Wiest
- Fox Chase Cancer Center, Blood Cell Development and Function Program, Philadelphia, PA, 19111, USA
| | - Yuan Zhuang
- Duke University, Department of Immunology, Durham, NC, 27710, USA
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10
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The immune landscape of human thymic epithelial tumors. Nat Commun 2022; 13:5463. [PMID: 36115836 PMCID: PMC9482639 DOI: 10.1038/s41467-022-33170-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
Human thymic epithelial tumors (TET) are common malignancies in the anterior mediastinum with limited biological understanding. Here we show, by single cell analysis of the immune landscape, that the developmental pattern of intra-tumoral T-cells identify three types within TETs. We characterize the developmental alterations and TCR repertoires of tumor-infiltrating T cells in the context of the distinguishing epithelial tumor cell types. We demonstrate that a subset of tumor cells, featuring medullary thymic epithelial cell (TEC) phenotype and marked by KRT14/GNB3 expression, accumulate in type 1 TETs, while T-cell positive selection is inhibited. Type 2 TETs are dominated by CCL25+ cortical TEC-like cells that appear to promote T-cell positive selection. Interestingly, the CHI3L1+ medullary TEC-like cells that are the characteristic feature of type 3 TETs don’t seem to support T-cell development, however, they may induce a tissue-resident CD8+ T cell response. In summary, our work suggests that the molecular subtype of epithelial tumour cells in TETs determine their tumour immune microenvironment, thus GNB3 and CHI3L1 might predict the immunological behavior and hence prognosis of these tumours. Thymic epithelial tumours represent a heterogenous group of malignancies with varied immune cell infiltration and prognosis. Here authors systematically analyze the phenotypes of both epithelial and immune cells that form these tumours, and identify three major subtypes with different T cell involvement that might affect prognosis.
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11
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Suo C, Dann E, Goh I, Jardine L, Kleshchevnikov V, Park JE, Botting RA, Stephenson E, Engelbert J, Tuong ZK, Polanski K, Yayon N, Xu C, Suchanek O, Elmentaite R, Domínguez Conde C, He P, Pritchard S, Miah M, Moldovan C, Steemers AS, Mazin P, Prete M, Horsfall D, Marioni JC, Clatworthy MR, Haniffa M, Teichmann SA. Mapping the developing human immune system across organs. Science 2022; 376:eabo0510. [PMID: 35549310 PMCID: PMC7612819 DOI: 10.1126/science.abo0510] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-cell genomics studies have decoded the immune-cell composition of several human prenatal organs but were limited in understanding the developing immune system as a distributed network across tissues. We profiled nine prenatal tissues combining single-cell RNA sequencing, antigen-receptor sequencing, and spatial transcriptomics to reconstruct the developing human immune system. This revealed the late acquisition of immune effector functions by myeloid and lymphoid cell subsets and the maturation of monocytes and T cells prior to peripheral tissue seeding. Moreover, we uncovered system-wide blood and immune cell development beyond primary hematopoietic organs, characterized human prenatal B1 cells, and shed light on the origin of unconventional T cells. Our atlas provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine, and disease understanding.
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Affiliation(s)
- Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Department of Paediatrics, Cambridge University Hospitals, Hills Road, Cambridge, UK
| | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Haematology Department, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Zewen Kelvin Tuong
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nadav Yayon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mohi Miah
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Corina Moldovan
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - John C Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,European Molecular Biology Laboratory European Bioinformatics Institute, Hinxton, Cambridge, UK.,Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Molecular Immunity Unit, University of Cambridge Department of Medicine, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
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12
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Krovi SH, Loh L, Spengler A, Brunetti T, Gapin L. Current insights in mouse iNKT and MAIT cell development using single cell transcriptomics data. Semin Immunol 2022; 60:101658. [PMID: 36182863 DOI: 10.1016/j.smim.2022.101658] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/17/2022] [Accepted: 09/21/2022] [Indexed: 01/15/2023]
Abstract
Innate T (Tinn) cells are a collection of T cells with important regulatory functions that have a crucial role in immunity towards tumors, bacteria, viruses, and in cell-mediated autoimmunity. In mice, the two main αβ Tinn cell subsets include the invariant NKT (iNKT) cells that recognize glycolipid antigens presented by non-polymorphic CD1d molecules and the mucosal associated invariant T (MAIT) cells that recognize vitamin B metabolites presented by the non-polymorphic MR1 molecules. Due to their ability to promptly secrete large quantities of cytokines either after T cell antigen receptor (TCR) activation or upon exposure to tissue- and antigen-presenting cell-derived cytokines, Tinn cells are thought to act as a bridge between the innate and adaptive immune systems and have the ability to shape the overall immune response. Their swift response reflects the early acquisition of helper effector programs during their development in the thymus, independently of pathogen exposure and prior to taking up residence in peripheral tissues. Several studies recently profiled, in an unbiased manner, the transcriptomes of mouse thymic iNKT and MAIT cells at the single cell level. Based on these data, we re-examine in this review how Tinn cells develop in the mouse thymus and undergo effector differentiation.
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Affiliation(s)
| | - Liyen Loh
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | | | - Tonya Brunetti
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Laurent Gapin
- University of Colorado Anschutz Medical Campus, Aurora, USA.
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13
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Rodríguez-Caparrós A, Álvarez-Santiago J, López-Castellanos L, Ruiz-Rodríguez C, Valle-Pastor MJ, López-Ros J, Angulo Ú, Andrés-León E, Suñé C, Hernández-Munain C. Differently Regulated Gene-Specific Activity of Enhancers Located at the Boundary of Subtopologically Associated Domains: TCRα Enhancer. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:910-928. [PMID: 35082160 DOI: 10.4049/jimmunol.2000864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/05/2021] [Indexed: 11/19/2022]
Abstract
Enhancers activate transcription through long-distance interactions with their cognate promoters within a particular subtopologically associated domain (sub-TAD). The TCRα enhancer (Eα) is located at the sub-TAD boundary between the TCRα and DAD1 genes and regulates transcription toward both sides in an ∼1-Mb region. Analysis of Eα activity in transcribing the unrearranged TCRα gene at the 5'-sub-TAD has defined Eα as inactive in CD4-CD8- thymocytes, active in CD4+CD8+ thymocytes, and strongly downregulated in CD4+ and CD8+ thymocytes and αβ T lymphocytes. Despite its strongly reduced activity, Eα is still required for high TCRα transcription and expression of TCRαβ in mouse and human T lymphocytes, requiring collaboration with distant sequences for such functions. Because VαJα rearrangements in T lymphocytes do not induce novel long-range interactions between Eα and other genomic regions that remain in cis after recombination, strong Eα connectivity with the 3'-sub-TAD might prevent reduced transcription of the rearranged TCRα gene. Our analyses of transcriptional enhancer dependence during T cell development and non-T lineage tissues at the 3'-sub-TAD revealed that Eα can activate the transcription of specific genes, even when it is inactive to transcribe the TCRα gene at the 5'-sub-TAD. Hence distinct requirements for Eα function are necessary at specific genes at both sub-TADs, implying that enhancers do not merely function as chromatin loop anchors that nucleate the formation of factor condensates to increase gene transcription initiated at their cognate promoters. The observed different regulated Eα activity for activating specific genes at its flanking sub-TADs may be a general feature for enhancers located at sub-TAD boundaries.
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Affiliation(s)
- Alonso Rodríguez-Caparrós
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Jesús Álvarez-Santiago
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Laura López-Castellanos
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Candela Ruiz-Rodríguez
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - María Jesús Valle-Pastor
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Jennifer López-Ros
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Úrsula Angulo
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Eduardo Andrés-León
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Carlos Suñé
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
| | - Cristina Hernández-Munain
- Institute of Parasitology and Biomedicine López-Neyra-Spanish National Research Council and Health Science Technology Park, Granada, Spain
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14
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Dauphars DJ, Mihai A, Wang L, Zhuang Y, Krangel MS. Trav15-dv6 family Tcrd rearrangements diversify the Tcra repertoire. J Exp Med 2022; 219:212913. [PMID: 34910107 PMCID: PMC8679779 DOI: 10.1084/jem.20211581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/04/2021] [Accepted: 12/02/2021] [Indexed: 11/20/2022] Open
Abstract
The Tcra repertoire is generated by multiple rounds of Vα-Jα rearrangement. However, Tcrd recombination precedes Tcra recombination within the complex Tcra-Tcrd locus. Here, by ablating Tcrd recombination, we report that Tcrd rearrangement broadens primary Vα use to diversify the Tcra repertoire in mice. We reveal that use of Trav15-dv6 family V gene segments in Tcrd recombination imparts diversity in the Tcra repertoire by instigating use of central and distal Vα segments. Moreover, disruption of the regions containing these genes and their cis-regulatory elements identifies the Trav15-dv6 family as being responsible for driving central and distal Vα recombinations beyond their roles as substrates for Tcrd recombination. Our study demonstrates an indispensable role for Tcrd recombination in general, and the Trav15-dv6 family in particular, in the generation of a combinatorially diverse Tcra repertoire.
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Affiliation(s)
| | - Ariana Mihai
- Department of Immunology, Duke University Medical Center, Durham, NC
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC
| | - Yuan Zhuang
- Department of Immunology, Duke University Medical Center, Durham, NC
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC
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15
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Shiozawa S, Tsumiyama K, Miyazaki Y, Uto K, Sakurai K, Nakashima T, Matsuyama H, Doi A, Tarui M, Izumikawa M, Kimura M, Fujita Y, Satonaka C, Horiuchi T, Matsubara T, Oribe M, Yamane T, Kagawa H, Li QZ, Mizuno K, Mukai Y, Murakami K, Enya T, Tsukimoto S, Hakata Y, Miyazawa M, Shiozawa K. DOCK8-expressing T follicular helper cells newly generated beyond self-organized criticality cause systemic lupus erythematosus. iScience 2022; 25:103537. [PMID: 34977502 PMCID: PMC8689056 DOI: 10.1016/j.isci.2021.103537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/01/2021] [Accepted: 11/24/2021] [Indexed: 11/24/2022] Open
Abstract
Pathogens including autoantigens all failed to induce systemic lupus erythematosus (SLE). We, instead, studied the integrity of host's immune response that recognized pathogen. By stimulating TCR with an antigen repeatedly to levels that surpass host's steady-state response, self-organized criticality, SLE was induced in mice normally not prone to autoimmunity, wherein T follicular helper (Tfh) cells expressing the guanine nucleotide exchange factor DOCK8 on the cell surface were newly generated. DOCK8+Tfh cells passed through TCR re-revision and induced varieties of autoantibody and lupus lesions. They existed in splenic red pulp and peripheral blood of active lupus patients, which subsequently declined after therapy. Autoantibodies and disease were healed by anti-DOCK8 antibody in the mice including SLE-model (NZBxNZW) F1 mice. Thus, DOCK8+Tfh cells generated after repeated TCR stimulation by immunogenic form of pathogen, either exogenous or endogenous, in combination with HLA to levels that surpass system's self-organized criticality, cause SLE. Autoimmunity seldom takes place under integrated steady-state immune response Repeated invasion by pathogen, such as measles virus, is not exceptional but routine in life DOCK8+Tfh is generated upon TCR overstimulation by pathogen beyond self-organized criticality Newly generated DOCK8+Tfh induces autoantibodies and SLE, i.e., autoimmunity
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Affiliation(s)
- Shunichi Shiozawa
- Institute for Rheumatic Diseases, 944-25 Fujita, Katoshi 673-1462, Japan.,Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan.,Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan.,Department of Medicine, Rheumatology and Orthopedic Surgery, Matsubara Mayflower Hospital, 944-25 Fujita, Katoshi 673-1462, Japan
| | - Ken Tsumiyama
- Institute for Rheumatic Diseases, 944-25 Fujita, Katoshi 673-1462, Japan.,Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan.,Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan.,Department of Medicine, Rheumatology and Orthopedic Surgery, Matsubara Mayflower Hospital, 944-25 Fujita, Katoshi 673-1462, Japan
| | - Yumi Miyazaki
- Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan.,Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Kenichi Uto
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Keiichi Sakurai
- Institute for Rheumatic Diseases, 944-25 Fujita, Katoshi 673-1462, Japan.,Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan
| | - Toshie Nakashima
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Hiroko Matsuyama
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Ai Doi
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Miho Tarui
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Manabu Izumikawa
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Mai Kimura
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Yuko Fujita
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Chisako Satonaka
- Division of Bioregulation, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Sumaku, Kobe 654-0142, Japan
| | - Takahiko Horiuchi
- Department of Medicine, Kyushu University Beppu Hospital, 4546 Tsurumihara, Beppu 874-0838, Japan
| | - Tsukasa Matsubara
- Department of Medicine, Rheumatology and Orthopedic Surgery, Matsubara Mayflower Hospital, 944-25 Fujita, Katoshi 673-1462, Japan
| | - Motohiro Oribe
- Oribe Clinic, 1-8-15 Higashi-Odori, Oita 870-0823, Japan
| | - Takashi Yamane
- Department of Rheumatology, Kakogawa City Hospital, 439 Honmachi, Kakogawa 675-8611, Japan
| | - Hidetoshi Kagawa
- Department of Medicine, Red Cross Society Himeji Hospital, 1-12-1 Shimoteno, Himeji 670-8540, Japan
| | - Quan-Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, 6001 Forest Park Road/ND 6.504, Dallas, TX 75390-8814, USA
| | - Keiko Mizuno
- Drug Discovery Platform, KAN Research Institute, Inc., 6-8-2 Minatojimaminamicho, Kobe 650-0047, Japan
| | - Yohei Mukai
- Drug Discovery Platform, KAN Research Institute, Inc., 6-8-2 Minatojimaminamicho, Kobe 650-0047, Japan
| | - Kazuhiro Murakami
- Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsujima, Aobaku 981-8558, Japan
| | - Takuji Enya
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan.,Department of Pediatrics, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Shota Tsukimoto
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan.,Department of Anesthesiology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Yoshiyuki Hakata
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan
| | - Masaaki Miyazawa
- Department of Immunology, Kindai University Faculty of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan.,Kindai University Anti-Aging Center, 3-4-1 Kowakae, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazuko Shiozawa
- Department of Medicine, Rheumatology and Orthopedic Surgery, Matsubara Mayflower Hospital, 944-25 Fujita, Katoshi 673-1462, Japan.,Rheumatology and Collagen Disease Center, Hyogo Prefectural Kakogawa Medical Center, 203 Kanno, Kakogawa 675-8555, Japan
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16
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Liu S, Zhao K. The Toolbox for Untangling Chromosome Architecture in Immune Cells. Front Immunol 2021; 12:670884. [PMID: 33995409 PMCID: PMC8120992 DOI: 10.3389/fimmu.2021.670884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
The code of life is not only encrypted in the sequence of DNA but also in the way it is organized into chromosomes. Chromosome architecture is gradually being recognized as an important player in regulating cell activities (e.g., controlling spatiotemporal gene expression). In the past decade, the toolbox for elucidating genome structure has been expanding, providing an opportunity to explore this under charted territory. In this review, we will introduce the recent advancements in approaches for mapping spatial organization of the genome, emphasizing applications of these techniques to immune cells, and trying to bridge chromosome structure with immune cell activities.
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Affiliation(s)
- Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, United States
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17
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Feng D, Li Z, Qin L, Hao B. The role of chromatin organizer Satb1 in shaping TCR repertoire in adult thymus. Genome 2021; 64:821-832. [PMID: 33617384 DOI: 10.1139/gen-2020-0139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
T cells recognize the universe of foreign antigens with a diverse repertoire of T cell receptors generated by V(D)J recombination. Special AT-rich binding protein 1 (Satb1) is a chromatin organizer that plays an essential role in T cell development. Previous study has shown that Satb1 regulates the re-induction of recombinase Rag1 and Rag2 in CD4+CD8+ thymocytes, affecting the secondary rearrangement of the Tcra gene. Here, we detected the repertoires of four TCR genes, Tcrd, Tcrg, Tcrb, and Tcra, in the adult thymus, and explored the role of the Satb1 in shaping the TCR repertoires. We observed a strong bias in the V and J gene usages of the Tcrd and Tcrg repertoires in WT and Satb1-deleted thymocytes. Satb1 deletion had few effects on the V(D)J rearrangement and repertoire of the Tcrg, Tcrd, and Tcrb genes. The Tcra repertoire was severely impaired in Satb1-deleted thymocytes, while the primary rearrangement was relatively normal. We also found the CDR3 length of TCRα chain was significantly longer in Satb1-deleted thymocytes, which can be explained by the strong bias of the proximal Jα usage. Our results showed that Satb1 plays an essential role in shaping TCR repertoires in αβ T cells.
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Affiliation(s)
- Delong Feng
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Zhaoqiang Li
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Litao Qin
- Medical Genetic Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 450003, P.R. China.,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, Henan 450003, P.R. China
| | - Bingtao Hao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Medical Genetic Institute of Henan Province, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan 450003, P.R. China.,National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, Henan 450003, P.R. China
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18
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Rodríguez-Caparrós A, Álvarez-Santiago J, del Valle-Pastor MJ, Suñé C, López-Ros J, Hernández-Munain C. Regulation of T-cell Receptor Gene Expression by Three-Dimensional Locus Conformation and Enhancer Function. Int J Mol Sci 2020; 21:E8478. [PMID: 33187197 PMCID: PMC7696796 DOI: 10.3390/ijms21228478] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/04/2020] [Indexed: 11/16/2022] Open
Abstract
The adaptive immune response in vertebrates depends on the expression of antigen-specific receptors in lymphocytes. T-cell receptor (TCR) gene expression is exquisitely regulated during thymocyte development to drive the generation of αβ and γδ T lymphocytes. The TCRα, TCRβ, TCRγ, and TCRδ genes exist in two different configurations, unrearranged and rearranged. A correctly rearranged configuration is required for expression of a functional TCR chain. TCRs can take the form of one of three possible heterodimers, pre-TCR, TCRαβ, or TCRγδ which drive thymocyte maturation into αβ or γδ T lymphocytes. To pass from an unrearranged to a rearranged configuration, global and local three dimensional (3D) chromatin changes must occur during thymocyte development to regulate gene segment accessibility for V(D)J recombination. During this process, enhancers play a critical role by modifying the chromatin conformation and triggering noncoding germline transcription that promotes the recruitment of the recombination machinery. The different signaling that thymocytes receive during their development controls enhancer activity. Here, we summarize the dynamics of long-distance interactions established through chromatin regulatory elements that drive transcription and V(D)J recombination and how different signaling pathways are orchestrated to regulate the activity of enhancers to precisely control TCR gene expression during T-cell maturation.
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Affiliation(s)
| | | | | | | | | | - Cristina Hernández-Munain
- Institute of Parasitology and Biomedicine “López-Neyra”—Spanish Scientific Research Council (IPBLN-CSIC), Parque Tecnológico de Ciencias de la Salud (PTS), 18016 Granada, Spain; (A.R.-C.); (J.Á.-S.); (M.J.d.V.-P.); (C.S.); (J.L.-R.)
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19
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Zhao H, Li Z, Zhu Y, Bian S, Zhang Y, Qin L, Naik AK, He J, Zhang Z, Krangel MS, Hao B. A role of the CTCF binding site at enhancer Eα in the dynamic chromatin organization of the Tcra-Tcrd locus. Nucleic Acids Res 2020; 48:9621-9636. [PMID: 32853367 PMCID: PMC7515734 DOI: 10.1093/nar/gkaa711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/03/2020] [Accepted: 08/20/2020] [Indexed: 12/25/2022] Open
Abstract
The regulation of T cell receptor Tcra gene rearrangement has been extensively studied. The enhancer Eα plays an essential role in Tcra rearrangement by establishing a recombination centre in the Jα array and a chromatin hub for interactions between Vα and Jα genes. But the mechanism of the Eα and its downstream CTCF binding site (here named EACBE) in dynamic chromatin regulation is unknown. The Hi-C data showed that the EACBE is located at the sub-TAD boundary which separates the Tcra–Tcrd locus and the downstream region including the Dad1 gene. The EACBE is required for long-distance regulation of the Eα on the proximal Vα genes, and its deletion impaired the Tcra rearrangement. We also noticed that the EACBE and Eα regulate the genes in the downstream sub-TAD via asymmetric chromatin extrusion. This study provides a new insight into the role of CTCF binding sites at TAD boundaries in gene regulation.
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Affiliation(s)
- Hao Zhao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Zhaoqiang Li
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yongchang Zhu
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Shasha Bian
- Henan Medical Genetics Institute, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan Province, China
| | - Yan Zhang
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Litao Qin
- Henan Medical Genetics Institute, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan Province, China
| | - Abani Kanta Naik
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Jiangtu He
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhenhai Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Bingtao Hao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Henan Medical Genetics Institute, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan Province, China
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20
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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] [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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21
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Park JE, Botting RA, Domínguez Conde C, Popescu DM, Lavaert M, Kunz DJ, Goh I, Stephenson E, Ragazzini R, Tuck E, Wilbrey-Clark A, Roberts K, Kedlian VR, Ferdinand JR, He X, Webb S, Maunder D, Vandamme N, Mahbubani KT, Polanski K, Mamanova L, Bolt L, Crossland D, de Rita F, Fuller A, Filby A, Reynolds G, Dixon D, Saeb-Parsy K, Lisgo S, Henderson D, Vento-Tormo R, Bayraktar OA, Barker RA, Meyer KB, Saeys Y, Bonfanti P, Behjati S, Clatworthy MR, Taghon T, Haniffa M, Teichmann SA. A cell atlas of human thymic development defines T cell repertoire formation. Science 2020; 367:367/6480/eaay3224. [PMID: 32079746 DOI: 10.1126/science.aay3224] [Citation(s) in RCA: 320] [Impact Index Per Article: 80.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 01/16/2020] [Indexed: 11/03/2022]
Abstract
The thymus provides a nurturing environment for the differentiation and selection of T cells, a process orchestrated by their interaction with multiple thymic cell types. We used single-cell RNA sequencing to create a cell census of the human thymus across the life span and to reconstruct T cell differentiation trajectories and T cell receptor (TCR) recombination kinetics. Using this approach, we identified and located in situ CD8αα+ T cell populations, thymic fibroblast subtypes, and activated dendritic cell states. In addition, we reveal a bias in TCR recombination and selection, which is attributed to genomic position and the kinetics of lineage commitment. Taken together, our data provide a comprehensive atlas of the human thymus across the life span with new insights into human T cell development.
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Affiliation(s)
- Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rachel A Botting
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | | | - Dorin-Mirel Popescu
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marieke Lavaert
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Daniel J Kunz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK.,Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Issac Goh
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Emily Stephenson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, Francis Crick Institute, London NW1 1AT, UK.,Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Veronika R Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John R Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Simone Webb
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Daniel Maunder
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David Crossland
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.,Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Fabrizio de Rita
- Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Andrew Fuller
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew Filby
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gary Reynolds
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David Dixon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Deborah Henderson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Omer A Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Roger A Barker
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK.,WT-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Paola Bonfanti
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, Francis Crick Institute, London NW1 1AT, UK.,Great Ormond Street Institute of Child Health, University College London, London, UK.,Institute of Immunity and Transplantation, University College London, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Department of Paediatrics, University of Cambridge, Cambridge CB2 0SP, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK.,Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Tom Taghon
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium. .,Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. .,Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. .,Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
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22
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Park JE, Botting RA, Domínguez Conde C, Popescu DM, Lavaert M, Kunz DJ, Goh I, Stephenson E, Ragazzini R, Tuck E, Wilbrey-Clark A, Roberts K, Kedlian VR, Ferdinand JR, He X, Webb S, Maunder D, Vandamme N, Mahbubani KT, Polanski K, Mamanova L, Bolt L, Crossland D, de Rita F, Fuller A, Filby A, Reynolds G, Dixon D, Saeb-Parsy K, Lisgo S, Henderson D, Vento-Tormo R, Bayraktar OA, Barker RA, Meyer KB, Saeys Y, Bonfanti P, Behjati S, Clatworthy MR, Taghon T, Haniffa M, Teichmann SA. A cell atlas of human thymic development defines T cell repertoire formation. Science 2020. [DOI: 10.1126/science.aay3224 32079746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Rachel A. Botting
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | | | - Dorin-Mirel Popescu
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Marieke Lavaert
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Daniel J. Kunz
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Issac Goh
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Emily Stephenson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roberta Ragazzini
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, Francis Crick Institute, London NW1 1AT, UK
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Veronika R. Kedlian
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - John R. Ferdinand
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
| | - Xiaoling He
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
| | - Simone Webb
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Daniel Maunder
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Krishnaa T. Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David Crossland
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Fabrizio de Rita
- Department of Adult Congenital Heart Disease and Paediatric Cardiology/Cardiothoracic Surgery, Freeman Hospital, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Andrew Fuller
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andrew Filby
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Gary Reynolds
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David Dixon
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Steven Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Deborah Henderson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Omer A. Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Roger A. Barker
- John van Geest Centre for Brain Repair, University of Cambridge, Cambridge CB2 0PY, UK
- WT-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
| | - Kerstin B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Paola Bonfanti
- Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, Francis Crick Institute, London NW1 1AT, UK
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Institute of Immunity and Transplantation, University College London, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0SP, UK
| | - Menna R. Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Tom Taghon
- Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge CB3 0HE, UK
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23
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Zhao H, Li Z, Zhu Y, Hao B. A linear-amplification VDJ-seq technique for quantification of immunoglobulin and T cell receptor diversity. Genome 2019; 63:145-153. [PMID: 31825677 DOI: 10.1139/gen-2019-0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The V(D)J recombination is essential for generating a highly diverse repertoire of antigen receptors expressed on T and B lymphocytes. Here, we developed a linear-amplification VDJ-seq technique for quantifying V(D)J recombination of antigen receptor genes. This technique takes advantage of linear amplification using in vitro transcription and reverse transcription to avoid bias generated by the PCR amplification of low copy number of target DNA. The unrearranged alleles are removed by in vitro cleavage with the CRISPR-Cas9 system. The linear-amplification VDJ-seq assay was applied in quantification of the Vκ-Jκ recombination of the mouse Igκ gene with Jκ capture primers. The Jκ genes were detected in 95.86% of clean reads with more than half containing the Vκ gene, indicating high specificity of capturing and amplification. We also applied this approach to quantify the usage of Jα within the Trav12 gene family of the Tcra gene.
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Affiliation(s)
- Hao Zhao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Zhaoqiang Li
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Yongchang Zhu
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China
| | - Bingtao Hao
- Guangdong Provincial Key Laboratory of Tumor Immunotherapy, Cancer Research Institute, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P.R. China.,Henan Medical Genetics Institute, People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Zhengzhou, Henan Province, P.R. China
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24
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Pakasticali N, Gill T, Chobrutskiy BI, Tong WL, Ramsamooj M, Blanck G. TRAV gene segments further away from the TRAJ gene segment cluster appear more commonly in human tumor and blood samples. Mol Immunol 2019; 116:174-179. [PMID: 31704500 DOI: 10.1016/j.molimm.2019.10.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/17/2019] [Accepted: 10/13/2019] [Indexed: 10/25/2022]
Abstract
We considered the possibility that the greater the distance between an immune receptor V and J, the more likely the V usage. Such a hypothesis is supported by results from mouse experiments. And, such a hypothesis is consistent with the fundamental nature of recombination and genomic distance: the further the distance, the greater the chance of a DNA break. Thus, we exploited the vast dataset of V and J recombination reads available for the human TRA gene, particularly from cancer and blood specimens, to assess the frequency of TRAV usage with respect to distance from the TRAJ cluster. Results indicated that, indeed, over the entire TRAV cluster, there is a greater chance of V usage the further the distance from the J cluster. These results do not address causation, and are not consistent for certain individual V gene segments, but the results do indicate that overall, the larger the distance between the V and J gene segment cluster, the more likely the appearance of at least a subset of TRAV segments, particularly among tumor infiltrating lymphocytes. With a similar approach, the distal TRAV gene segments were also found to be more commonly associated with a subset of distal TRAJ segments. These results have implications for restrictions on the apparent TRA repertoire in disease settings.
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Affiliation(s)
- Nagehan Pakasticali
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States; Department of Basic Sciences, National University of Health Sciences, Pinellas Park, Florida, 33781, United States
| | - Tommy Gill
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States
| | - Boris I Chobrutskiy
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States
| | - Wei Lue Tong
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States
| | - Michael Ramsamooj
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States
| | - George Blanck
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, 33612, United States; Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, 33612, United States.
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25
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Schuldt NJ, Binstadt BA. Dual TCR T Cells: Identity Crisis or Multitaskers? JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:637-644. [PMID: 30670579 PMCID: PMC11112972 DOI: 10.4049/jimmunol.1800904] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/21/2018] [Indexed: 05/25/2024]
Abstract
Dual TCR T cells are a common and natural product of TCR gene rearrangement and thymocyte development. As much as one third of the T cell population may have the capability to express two different TCR specificities on the cell surface. This discovery provoked a reconsideration of the classic model of thymic selection. Many potential roles for dual TCR T cells have since been hypothesized, including posing an autoimmune hazard, dominating alloreactive T cell responses, inducing allergy, and expanding the TCR repertoire to improve protective immunity. Yet, since the initial wave of publications following the discovery of dual TCR T cells, research in the area has slowed. In this study, we aim to provide a brief but comprehensive history of dual TCR T cell research, re-evaluate past observations in the context of current knowledge of the immune system, and identify key issues for future study.
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Affiliation(s)
- Nathaniel J Schuldt
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454; and Center for Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Bryce A Binstadt
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55454; and Center for Immunology, University of Minnesota, Minneapolis, MN 55455
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26
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Loguercio S, Barajas-Mora EM, Shih HY, Krangel MS, Feeney AJ. Variable Extent of Lineage-Specificity and Developmental Stage-Specificity of Cohesin and CCCTC-Binding Factor Binding Within the Immunoglobulin and T Cell Receptor Loci. Front Immunol 2018; 9:425. [PMID: 29593713 PMCID: PMC5859386 DOI: 10.3389/fimmu.2018.00425] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/16/2018] [Indexed: 12/19/2022] Open
Abstract
CCCTC-binding factor (CTCF) is largely responsible for the 3D architecture of the genome, in concert with the action of cohesin, through the creation of long-range chromatin loops. Cohesin is hypothesized to be the main driver of these long-range chromatin interactions by the process of loop extrusion. Here, we performed ChIP-seq for CTCF and cohesin in two stages each of T and B cell differentiation and examined the binding pattern in all six antigen receptor (AgR) loci in these lymphocyte progenitors and in mature T and B cells, ES cells, and fibroblasts. The four large AgR loci have many bound CTCF sites, most of which are only occupied in lymphocytes, while only the CTCF sites at the end of each locus near the enhancers or J genes tend to be bound in non-lymphoid cells also. However, despite the generalized lymphocyte restriction of CTCF binding in AgR loci, the Igκ locus is the only locus that also shows significant lineage-specificity (T vs. B cells) and developmental stage-specificity (pre-B vs. pro-B) in CTCF binding. We show that cohesin binding shows greater lineage- and stage-specificity than CTCF at most AgR loci, providing more specificity to the loops. We also show that the culture of pro-B cells in IL7, a common practice to expand the number of cells before ChIP-seq, results in a CTCF-binding pattern resembling pre-B cells, as well as other epigenetic and transcriptional characteristics of pre-B cells. Analysis of the orientation of the CTCF sites show that all sites within the large V portions of the Igh and TCRβ loci have the same orientation. This suggests either a lack of requirement for convergent CTCF sites creating loops, or indicates an absence of any loops between CTCF sites within the V region portion of those loci but only loops to the convergent sites at the D-J-enhancer end of each locus. The V region portions of the Igκ and TCRα/δ loci, by contrast, have CTCF sites in both orientations, providing many options for creating CTCF-mediated convergent loops throughout the loci. CTCF/cohesin loops, along with transcription factors, drives contraction of AgR loci to facilitate the creation of a diverse repertoire of antibodies and T cell receptors.
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Affiliation(s)
- Salvatore Loguercio
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - E. Mauricio Barajas-Mora
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
| | - Han-Yu Shih
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Michael S. Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Ann J. Feeney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States
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