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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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2
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Xu M, Ito-Kureha T, Kang HS, Chernev A, Raj T, Hoefig KP, Hohn C, Giesert F, Wang Y, Pan W, Ziętara N, Straub T, Feederle R, Daniel C, Adler B, König J, Feske S, Tsokos GC, Wurst W, Urlaub H, Sattler M, Kisielow J, Wulczyn FG, Łyszkiewicz M, Heissmeyer V. The thymocyte-specific RNA-binding protein Arpp21 provides TCR repertoire diversity by binding to the 3'-UTR and promoting Rag1 mRNA expression. Nat Commun 2024; 15:2194. [PMID: 38467629 PMCID: PMC10928157 DOI: 10.1038/s41467-024-46371-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
The regulation of thymocyte development by RNA-binding proteins (RBPs) is largely unexplored. We identify 642 RBPs in the thymus and focus on Arpp21, which shows selective and dynamic expression in early thymocytes. Arpp21 is downregulated in response to T cell receptor (TCR) and Ca2+ signals. Downregulation requires Stim1/Stim2 and CaMK4 expression and involves Arpp21 protein phosphorylation, polyubiquitination and proteasomal degradation. Arpp21 directly binds RNA through its R3H domain, with a preference for uridine-rich motifs, promoting the expression of target mRNAs. Analysis of the Arpp21-bound transcriptome reveals strong interactions with the Rag1 3'-UTR. Arpp21-deficient thymocytes show reduced Rag1 expression, delayed TCR rearrangement and a less diverse TCR repertoire. This phenotype is recapitulated in Rag1 3'-UTR mutant mice harboring a deletion of the Arpp21 response region. These findings show how thymocyte-specific Arpp21 promotes Rag1 expression to enable TCR repertoire diversity until signals from the TCR terminate Arpp21 and Rag1 activities.
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Affiliation(s)
- Meng Xu
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany
- Department of Integrated Traditional Chinese and Western Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Taku Ito-Kureha
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center (BNMRZ), Garching, Germany
| | - Aleksandar Chernev
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Göttingen, Germany
| | - Timsse Raj
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Kai P Hoefig
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany
| | - Christine Hohn
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Yinhu Wang
- Department of Pathology, New York University, Grossman School of Medicine, New York, NY, USA
| | - Wenliang Pan
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Natalia Ziętara
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
- Cancer Immunology and Immune Modulation, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Tobias Straub
- Institute for Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, German Research Center for Environmental Health, Neuherberg, Germany
| | - Carolin Daniel
- Research Unit Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Barbara Adler
- Max von Pettenkofer Institute, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Stefan Feske
- Department of Pathology, New York University, Grossman School of Medicine, New York, NY, USA
| | - George C Tsokos
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Developmental Genetics, Munich School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE) site Munich, Munich, Germany
| | - Henning Urlaub
- Max Planck Institute for Multidisciplinary Sciences, Bioanalytical Mass Spectrometry, Göttingen, Germany
- University Medical Center Göttingen, Department of Clinical Chemistry, Bioanalytics Group, Göttingen, Germany
- Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Michael Sattler
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Neuherberg, Germany
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience and Bavarian NMR Center (BNMRZ), Garching, Germany
| | - Jan Kisielow
- Institute for Molecular Health Sciences, ETH Zürich, Zürich, Switzerland.
- Repertoire Immune Medicines (Switzerland) AG, Schlieren, Switzerland.
| | - F Gregory Wulczyn
- Institute for Integrative Neuroanatomie, Charite-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Marcin Łyszkiewicz
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany.
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany.
| | - Vigo Heissmeyer
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, Munich, Germany.
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany.
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3
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Worth AN, Palmer VL, Schabla NM, Perry GA, Fraser-Philbin AN, Swanson PC. Receptor editing constrains development of phosphatidyl choline-specific B cells in V H12-transgenic mice. Cell Rep 2022; 39:110899. [PMID: 35705027 DOI: 10.1016/j.celrep.2022.110899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/22/2022] [Accepted: 05/10/2022] [Indexed: 11/03/2022] Open
Abstract
B1 B cells reactive to phosphatidyl choline (PtC) exhibit restricted immunoglobulin heavy chain (HC) and light chain (LC) combinations, exemplified by VH12/Vκ4/5H. Two checkpoints are thought to focus PtC+ B cell maturation in VH12-transgenic mice (VH12 mice): V-J rearrangements encoding a "permissive" LC capable of VH12 HC pairing are selected first, followed by positive selection based on PtC binding, often requiring LC receptor editing to salvage PtC- B cells and acquire PtC reactivity. However, evidence obtained from breeding VH12 mice to editing-defective dnRAG1 mice and analyzing LC sequences from PtC+ and PtC- B cell subsets instead suggests that receptor editing functions after initial positive selection to remove PtC+ B cells in VH12 mice. This offers a mechanism to constrain natural, polyreactive B cells to limit their frequency. Sequencing also reveals occasional in-frame hybrid LC genes, reminiscent of type 2 gene replacement, that, testing suggests, arise via a recombination-activating gene (RAG)-independent mechanism.
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Affiliation(s)
- Alexandra N Worth
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Victoria L Palmer
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - N Max Schabla
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA; Shoreline Biosciences, San Diego, CA 92121, USA
| | - Greg A Perry
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Anna N Fraser-Philbin
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA
| | - Patrick C Swanson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE 68178, USA.
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4
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Structural insights into the evolution of the RAG recombinase. Nat Rev Immunol 2022; 22:353-370. [PMID: 34675378 DOI: 10.1038/s41577-021-00628-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 11/09/2022]
Abstract
Adaptive immunity in jawed vertebrates relies on the assembly of antigen receptor genes by the recombination activating gene 1 (RAG1)-RAG2 (collectively RAG) recombinase in a reaction known as V(D)J recombination. Extensive biochemical and structural evidence indicates that RAG and V(D)J recombination evolved from the components of a RAG-like (RAGL) transposable element through a process known as transposon molecular domestication. This Review describes recent advances in our understanding of the functional and structural transitions that occurred during RAG evolution. We use the structures of RAG and RAGL enzymes to trace the evolutionary adaptations that yielded a RAG recombinase with exquisitely regulated cleavage activity and a multilayered array of mechanisms to suppress transposition. We describe how changes in modes of DNA binding, alterations in the dynamics of protein-DNA complexes, single amino acid mutations and a modular design likely enabled RAG family enzymes to survive and spread in the genomes of eukaryotes. These advances highlight the insight that can be gained from viewing evolution of vertebrate immunity through the lens of comparative genome analyses coupled with structural biology and biochemistry.
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5
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The CRL4VPRBP(DCAF1) E3 ubiquitin ligase directs constitutive RAG1 degradation in a non-lymphoid cell line. PLoS One 2021; 16:e0258683. [PMID: 34648572 PMCID: PMC8516306 DOI: 10.1371/journal.pone.0258683] [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: 04/09/2021] [Accepted: 10/02/2021] [Indexed: 11/19/2022] Open
Abstract
The development of B and T lymphocytes critically depends on RAG1/2 endonuclease activity to mediate antigen receptor gene assembly by V(D)J recombination. Although control of RAG1/2 activity through cell cycle- and ubiquitin-dependent degradation of RAG2 has been studied in detail, relatively little is known about mechanisms regulating RAG1 stability. We recently demonstrated that VprBP/DCAF1, a substrate adaptor for the CRL4 E3 ubiquitin ligase complex, is required to maintain physiological levels of RAG1 protein in murine B cells by facilitating RAG1 turnover. Loss of VprBP/DCAF1 in vivo results in elevated RAG1 expression, excessive V(D)J recombination, and immunoglobulin light chain repertoire skewing. Here we show that RAG1 is constitutively degraded when ectopically expressed in a human fibroblast cell line. Consistent with our findings in murine B cells, RAG1 turnover under these conditions is sensitive to loss of VprBP, as well as CRL4 or proteasome inhibition. Further evidence indicates that RAG1 degradation is ubiquitin-dependent and that RAG1 association with the CRL4VPRBP/DCAF1 complex is independent of CUL4 activation status. Taken together, these findings suggest V(D)J recombination co-opts an evolutionarily conserved and constitutively active mechanism to ensure rapid RAG1 turnover to restrain excessive RAG activity.
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6
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Beilinson HA, Glynn RA, Yadavalli AD, Xiao J, Corbett E, Saribasak H, Arya R, Miot C, Bhattacharyya A, Jones JM, Pongubala JM, Bassing CH, Schatz DG. The RAG1 N-terminal region regulates the efficiency and pathways of synapsis for V(D)J recombination. J Exp Med 2021; 218:e20210250. [PMID: 34402853 PMCID: PMC8374863 DOI: 10.1084/jem.20210250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/30/2021] [Accepted: 07/30/2021] [Indexed: 11/29/2022] Open
Abstract
Immunoglobulin and T cell receptor gene assembly depends on V(D)J recombination initiated by the RAG1-RAG2 recombinase. The RAG1 N-terminal region (NTR; aa 1-383) has been implicated in regulatory functions whose influence on V(D)J recombination and lymphocyte development in vivo is poorly understood. We generated mice in which RAG1 lacks ubiquitin ligase activity (P326G), the major site of autoubiquitination (K233R), or its first 215 residues (Δ215). While few abnormalities were detected in R1.K233R mice, R1.P326G mice exhibit multiple features indicative of reduced recombination efficiency, including an increased Igκ+:Igλ+ B cell ratio and decreased recombination of Igh, Igκ, Igλ, and Tcrb loci. Previous studies indicate that synapsis of recombining partners during Igh recombination occurs through two pathways: long-range scanning and short-range collision. We find that R1Δ215 mice exhibit reduced short-range Igh and Tcrb D-to-J recombination. Our findings indicate that the RAG1 NTR regulates V(D)J recombination and lymphocyte development by multiple pathways, including control of the balance between short- and long-range recombination.
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Affiliation(s)
- Helen A. Beilinson
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Rebecca A. Glynn
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Anurupa Devi Yadavalli
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Jianxiong Xiao
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Elizabeth Corbett
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Huseyin Saribasak
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
| | - Rahul Arya
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Charline Miot
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Anamika Bhattacharyya
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC
| | - Jessica M. Jones
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC
| | - Jagan M.R. Pongubala
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Craig H. Bassing
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David G. Schatz
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, CT
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
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7
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Chen Y, Lear TB, Evankovich JW, Larsen MB, Lin B, Alfaras I, Kennerdell JR, Salminen L, Camarco DP, Lockwood KC, Tuncer F, Liu J, Myerburg MM, McDyer JF, Liu Y, Finkel T, Chen BB. A high-throughput screen for TMPRSS2 expression identifies FDA-approved compounds that can limit SARS-CoV-2 entry. Nat Commun 2021; 12:3907. [PMID: 34162861 PMCID: PMC8222394 DOI: 10.1038/s41467-021-24156-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
SARS-CoV-2 (2019-nCoV) is the pathogenic coronavirus responsible for the global pandemic of COVID-19 disease. The Spike (S) protein of SARS-CoV-2 attaches to host lung epithelial cells through the cell surface receptor ACE2, a process dependent on host proteases including TMPRSS2. Here, we identify small molecules that reduce surface expression of TMPRSS2 using a library of 2,560 FDA-approved or current clinical trial compounds. We identify homoharringtonine and halofuginone as the most attractive agents, reducing endogenous TMPRSS2 expression at sub-micromolar concentrations. These effects appear to be mediated by a drug-induced alteration in TMPRSS2 protein stability. We further demonstrate that halofuginone modulates TMPRSS2 levels through proteasomal-mediated degradation that involves the E3 ubiquitin ligase component DDB1- and CUL4-associated factor 1 (DCAF1). Finally, cells exposed to homoharringtonine and halofuginone, at concentrations of drug known to be achievable in human plasma, demonstrate marked resistance to SARS-CoV-2 infection in both live and pseudoviral in vitro models. Given the safety and pharmacokinetic data already available for the compounds identified in our screen, these results should help expedite the rational design of human clinical trials designed to combat active COVID-19 infection.
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Affiliation(s)
- Yanwen Chen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
- Department of Gastroenterology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Travis B Lear
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - John W Evankovich
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mads B Larsen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
| | - Bo Lin
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
| | - Irene Alfaras
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
| | | | - Laura Salminen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
| | - Daniel P Camarco
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
| | | | - Ferhan Tuncer
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
| | - Jie Liu
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA
| | - Michael M Myerburg
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA
| | - John F McDyer
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuan Liu
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA.
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA.
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Toren Finkel
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA.
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Medicine, Division of Cardiology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Bill B Chen
- Aging Institute, University of Pittsburgh/UPMC, Pittsburgh, PA, USA.
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA, USA.
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA.
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8
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Dar AA, Sawada K, Dybas JM, Moser EK, Lewis EL, Park E, Fazelinia H, Spruce LA, Ding H, Seeholzer SH, Oliver PM. The E3 ubiquitin ligase Cul4b promotes CD4+ T cell expansion by aiding the repair of damaged DNA. PLoS Biol 2021; 19:e3001041. [PMID: 33524014 PMCID: PMC7888682 DOI: 10.1371/journal.pbio.3001041] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 02/17/2021] [Accepted: 01/15/2021] [Indexed: 12/26/2022] Open
Abstract
The capacity for T cells to become activated and clonally expand during pathogen invasion is pivotal for protective immunity. Our understanding of how T cell receptor (TCR) signaling prepares cells for this rapid expansion remains limited. Here we provide evidence that the E3 ubiquitin ligase Cullin-4b (Cul4b) regulates this process. The abundance of total and neddylated Cul4b increased following TCR stimulation. Disruption of Cul4b resulted in impaired proliferation and survival of activated T cells. Additionally, Cul4b-deficient CD4+ T cells accumulated DNA damage. In T cells, Cul4b preferentially associated with the substrate receptor DCAF1, and Cul4b and DCAF1 were found to interact with proteins that promote the sensing or repair of damaged DNA. While Cul4b-deficient CD4+ T cells showed evidence of DNA damage sensing, downstream phosphorylation of SMC1A did not occur. These findings reveal an essential role for Cul4b in promoting the repair of damaged DNA to allow survival and expansion of activated T cells.
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Affiliation(s)
- Asif A. Dar
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Keisuke Sawada
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Joseph M. Dybas
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Biomedical Health and Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Emily K. Moser
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Emma L. Lewis
- Medical Scientist Training Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Eddie Park
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Hossein Fazelinia
- Division of Cell Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Lynn A. Spruce
- Division of Cell Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Hua Ding
- Division of Cell Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Steven H. Seeholzer
- Division of Cell Pathology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Paula M. Oliver
- Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
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9
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Schabla NM, Mondal K, Swanson PC. DCAF1 (VprBP): emerging physiological roles for a unique dual-service E3 ubiquitin ligase substrate receptor. J Mol Cell Biol 2020; 11:725-735. [PMID: 30590706 PMCID: PMC6821201 DOI: 10.1093/jmcb/mjy085] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/01/2018] [Accepted: 12/21/2018] [Indexed: 12/12/2022] Open
Abstract
Cullin-RING ligases (CRLs) comprise a large group of modular eukaryotic E3 ubiquitin ligases. Within this family, the CRL4 ligase (consisting of the Cullin4 [CUL4] scaffold protein, the Rbx1 RING finger domain protein, the DNA damage-binding protein 1 [DDB1], and one of many DDB1-associated substrate receptor proteins) has been intensively studied in recent years due to its involvement in regulating various cellular processes, its role in cancer development and progression, and its subversion by viral accessory proteins. Initially discovered as a target for hijacking by the human immunodeficiency virus accessory protein r, the normal targets and function of the CRL4 substrate receptor protein DDB1–Cul4-associated factor 1 (DCAF1; also known as VprBP) had remained elusive, but newer studies have begun to shed light on these questions. Here, we review recent progress in understanding the diverse physiological roles of this DCAF1 in supporting various general and cell type-specific cellular processes in its context with the CRL4 E3 ligase, as well as another HECT-type E3 ligase with which DCAF1 also associates, called EDD/UBR5. We also discuss emerging questions and areas of future study to uncover the dynamic roles of DCAF1 in normal physiology.
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Affiliation(s)
- N Max Schabla
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE, USA
| | - Koushik Mondal
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE, USA
| | - Patrick C Swanson
- Department of Medical Microbiology and Immunology, Creighton University, 2500 California Plaza, Omaha, NE, USA
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10
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Abstract
V(D)J recombination assembles and diversifies Ig and T cell receptor genes in developing B and T lymphocytes. The reaction is initiated by the RAG1-RAG2 protein complex which binds and cleaves at discrete gene segments in the antigen receptor loci. To identify mechanisms that regulate V(D)J recombination, we used proximity-dependent biotin identification to analyze the interactomes of full-length and truncated forms of RAG1 in pre-B cells. This revealed an association of RAG1 with numerous nucleolar proteins in a manner dependent on amino acids 216 to 383 and allowed identification of a motif required for nucleolar localization. Experiments in transformed pre-B cell lines and cultured primary pre-B cells reveal a strong correlation between disruption of nucleoli, reduced association of RAG1 with a nucleolar marker, and increased V(D)J recombination activity. Mutation of the RAG1 nucleolar localization motif boosts recombination while removal of the first 215 amino acids of RAG1, required for efficient egress from nucleoli, reduces recombination activity. Our findings indicate that nucleolar sequestration of RAG1 is a negative regulatory mechanism in V(D)J recombination and identify regions of the RAG1 N-terminal region that control nucleolar association and egress.
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Smith AL, Scott JNF, Boyes J. The ESC: The Dangerous By-Product of V(D)J Recombination. Front Immunol 2019; 10:1572. [PMID: 31333681 PMCID: PMC6620893 DOI: 10.3389/fimmu.2019.01572] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/24/2019] [Indexed: 11/18/2022] Open
Abstract
V(D)J recombination generates antigen receptor diversity by mixing and matching individual variable (V), diversity (D), and joining (J) gene segments. An obligate by-product of many of these reactions is the excised signal circle (ESC), generated by excision of the DNA from between the gene segments. Initially, the ESC was believed to be inert and formed to protect the genome from reactive broken DNA ends but more recent work suggests that the ESC poses a substantial threat to genome stability. Crucially, the recombinase re-binds to the ESC, which can result in it being re-integrated back into the genome, to cause potentially oncogenic insertion events. In addition, very recently, the ESC/recombinase complex was found to catalyze breaks at recombination signal sequences (RSSs) throughout the genome, via a “cut-and-run” mechanism. Remarkably, the ESC/recombinase complex triggers these breaks at key leukemia driver genes, implying that this reaction could be a significant cause of lymphocyte genome instability. Here, we explore these alternate pathways and discuss their relative dangers to lymphocyte genome stability.
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Affiliation(s)
- Alastair L Smith
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - James N F Scott
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Joan Boyes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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