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Moud BN, Ober F, O’Neill TJ, Krappmann D. MALT1 substrate cleavage: what is it good for? Front Immunol 2024; 15:1412347. [PMID: 38863711 PMCID: PMC11165066 DOI: 10.3389/fimmu.2024.1412347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024] Open
Abstract
CARD-BCL10-MALT1 (CBM) signalosomes connect distal signaling of innate and adaptive immune receptors to proximal signaling pathways and immune activation. Four CARD scaffold proteins (CARD9, 10, 11, 14) can form seeds that nucleate the assembly of BCL10-MALT1 filaments in a cell- and stimulus-specific manner. MALT1 (also known as PCASP1) serves a dual function within the assembled CBM complexes. By recruiting TRAF6, MALT1 acts as a molecular scaffold that initiates IκB kinase (IKK)/NF-κB and c-Jun N-terminal kinase (JNK)/AP-1 signaling. In parallel, proximity-induced dimerization of the paracaspase domain activates the MALT1 protease which exerts its function by cleaving a set of specific substrates. While complete MALT1 ablation leads to immune deficiency, selective destruction of either scaffolding or protease function provokes autoimmune inflammation. Thus, balanced MALT1-TRAF6 recruitment and MALT1 substrate cleavage are critical to maintain immune homeostasis and to promote optimal immune activation. Further, MALT1 protease activity drives the survival of aggressive lymphomas and other non-hematologic solid cancers. However, little is known about the relevance of the cleavage of individual substrates for the pathophysiological functions of MALT1. Unbiased serendipity, screening and computational predictions have identified and validated ~20 substrates, indicating that MALT1 targets a quite distinct set of proteins. Known substrates are involved in CBM auto-regulation (MALT1, BCL10 and CARD10), regulation of signaling and adhesion (A20, CYLD, HOIL-1 and Tensin-3), or transcription (RelB) and mRNA stability/translation (Regnase-1, Roquin-1/2 and N4BP1), indicating that MALT1 often targets multiple proteins involved in similar cellular processes. Here, we will summarize what is known about the fate and functions of individual MALT1 substrates and how their cleavage contributes to the biological functions of the MALT1 protease. We will outline what is needed to better connect critical pathophysiological roles of the MALT1 protease with the cleavage of distinct substrates.
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Affiliation(s)
| | | | | | - Daniel Krappmann
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
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2
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Zuo Z, Roux ME, Dagdas YF, Rodriguez E, Petersen M. PAT mRNA decapping factors are required for proper development in Arabidopsis. FEBS Lett 2024; 598:1008-1021. [PMID: 38605280 DOI: 10.1002/1873-3468.14872] [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: 02/27/2024] [Revised: 04/10/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024]
Abstract
Evolutionarily conserved protein associated with topoisomerase II (PAT1) proteins activate mRNA decay through binding mRNA and recruiting decapping factors to optimize posttranscriptional reprogramming. Here, we generated multiple mutants of pat1, pat1 homolog 1 (path1), and pat1 homolog 2 (path2) and discovered that pat triple mutants exhibit extremely stunted growth and all mutants with pat1 exhibit leaf serration while mutants with pat1 and path1 display short petioles. All three PATs can be found localized to processing bodies and all PATs can target ASYMMETRIC LEAVES 2-LIKE 9 transcripts for decay to finely regulate apical hook and lateral root development. In conclusion, PATs exhibit both specific and redundant functions during different plant growth stages and our observations underpin the selective regulation of the mRNA decay machinery for proper development.
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Affiliation(s)
- Zhangli Zuo
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Milena Edna Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Yasin F Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Austria
| | - Eleazar Rodriguez
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
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3
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Wang H, Zhang D, Chen M, Meng X, Bai S, Xin P, Yan J, Chu J, Li J, Yu H. Genome editing of 3' UTR-embedded inhibitory region enables generation of gene knock-up alleles in plants. PLANT COMMUNICATIONS 2024; 5:100745. [PMID: 37946411 PMCID: PMC10943523 DOI: 10.1016/j.xplc.2023.100745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Affiliation(s)
- Hongwen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Dahan Zhang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingjiang Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Shiwei Bai
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Peiyong Xin
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jijun Yan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Yazhouwan National Laboratory, Sanya 572024, China
| | - Hong Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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4
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Yoshinaga M, Takeuchi O. RNA Metabolism Governs Immune Function and Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1444:145-161. [PMID: 38467978 DOI: 10.1007/978-981-99-9781-7_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Inflammation is a complex process that protects our body from various insults such as infection, injury, and stress. Proper inflammation is beneficial to eliminate the insults and maintain organ homeostasis, however, it can become detrimental if uncontrolled. To tightly regulate inflammation, post-transcriptional mechanisms governing RNA metabolism play a crucial role in monitoring the expression of immune-related genes, such as tumor necrosis factor (TNF) and interleukin-6 (IL-6). These mechanisms involve the coordinated action of various RNA-binding proteins (RBPs), including the Regnase family, Roquin, and RNA methyltransferases, which are responsible for mRNA decay and/or translation regulation. The collaborative efforts of these RBPs are essential in preventing aberrant immune response activation and consequently safeguarding against inflammatory and autoimmune diseases. This review provides an overview of recent advancements in our understanding of post-transcriptional regulation within the immune system and explores the specific roles of individual RBPs in RNA metabolism and regulation.
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Affiliation(s)
- Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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5
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Wimberger N, Ober F, Avar G, Grau M, Xu W, Lenz G, Menden MP, Krappmann D. Oncogene-induced MALT1 protease activity drives posttranscriptional gene expression in malignant lymphomas. Blood 2023; 142:1985-2001. [PMID: 37623434 PMCID: PMC10733837 DOI: 10.1182/blood.2023021299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/13/2023] [Accepted: 07/26/2023] [Indexed: 08/26/2023] Open
Abstract
Constitutive mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) activity drives survival of malignant lymphomas addicted to chronic B-cell receptor signaling, oncogenic CARD11, or the API2-MALT1 (also BIRC3::MALT1) fusion oncoprotein. Although MALT1 scaffolding induces NF-κB-dependent survival signaling, MALT1 protease function is thought to augment NF-κB activation by cleaving signaling mediators and transcriptional regulators in B-cell lymphomas. However, the pathological role of MALT1 protease function in lymphomagenesis is not well understood. Here, we show that TRAF6 controls MALT1-dependent activation of NF-κB transcriptional responses but is dispensable for MALT1 protease activation driven by oncogenic CARD11. To uncouple enzymatic and nonenzymatic functions of MALT1, we analyzed TRAF6-dependent and -independent as well as MALT1 protease-dependent gene expression profiles downstream of oncogenic CARD11 and API2-MALT1. The data suggest that by cleaving and inactivating the RNA binding proteins Regnase-1 and Roquin-1/2, MALT1 protease induces posttranscriptional upregulation of many genes including NFKBIZ/IκBζ, NFKBID/IκBNS, and ZC3H12A/Regnase-1 in activated B-cell-like diffuse large B-cell lymphoma (ABC DLBCL). We demonstrate that oncogene-driven MALT1 activity in ABC DLBCL cells regulates NFKBIZ and NFKBID induction on an mRNA level via releasing a brake imposed by Regnase-1 and Roquin-1/2. Furthermore, MALT1 protease drives posttranscriptional gene induction in the context of the API2-MALT1 fusion created by the recurrent t(11;18)(q21;q21) translocation in MALT lymphoma. Thus, MALT1 paracaspase acts as a bifurcation point for enhancing transcriptional and posttranscriptional gene expression in malignant lymphomas. Moreover, the identification of MALT1 protease-selective target genes provides specific biomarkers for the clinical evaluation of MALT1 inhibitors.
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Affiliation(s)
- Nicole Wimberger
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets Therapeutic Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Franziska Ober
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets Therapeutic Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Göksu Avar
- Department of Computational Health, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Michael Grau
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Muenster, Muenster, Germany
| | - Wendan Xu
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Muenster, Muenster, Germany
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Muenster, Muenster, Germany
| | - Michael P. Menden
- Department of Computational Health, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, Australia
| | - Daniel Krappmann
- Research Unit Signaling and Translation, Group Signaling and Immunity, Molecular Targets Therapeutic Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
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6
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Schmidt H, Raj T, O'Neill TJ, Muschaweckh A, Giesert F, Negraschus A, Hoefig KP, Behrens G, Esser L, Baumann C, Feederle R, Plaza-Sirvent C, Geerlof A, Gewies A, Isay SE, Ruland J, Schmitz I, Wurst W, Korn T, Krappmann D, Heissmeyer V. Unrestrained cleavage of Roquin-1 by MALT1 induces spontaneous T cell activation and the development of autoimmunity. Proc Natl Acad Sci U S A 2023; 120:e2309205120. [PMID: 37988467 PMCID: PMC10691344 DOI: 10.1073/pnas.2309205120] [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: 06/07/2023] [Accepted: 10/02/2023] [Indexed: 11/23/2023] Open
Abstract
Constitutive activation of the MALT1 paracaspase in conventional T cells of Malt1TBM/TBM (TRAF6 Binding Mutant = TBM) mice causes fatal inflammation and autoimmunity, but the involved targets and underlying molecular mechanisms are unknown. We genetically rendered a single MALT1 substrate, the RNA-binding protein (RBP) Roquin-1, insensitive to MALT1 cleavage. These Rc3h1Mins/Mins mice showed normal immune homeostasis. Combining Rc3h1Mins/Mins alleles with those encoding for constitutively active MALT1 (TBM) prevented spontaneous T cell activation and restored viability of Malt1TBM/TBM mice. Mechanistically, we show how antigen/MHC recognition is translated by MALT1 into Roquin cleavage and derepression of Roquin targets. Increasing T cell receptor (TCR) signals inactivated Roquin more effectively, and only high TCR strength enabled derepression of high-affinity targets to promote Th17 differentiation. Induction of experimental autoimmune encephalomyelitis (EAE) revealed increased cleavage of Roquin-1 in disease-associated Th17 compared to Th1 cells in the CNS. T cells from Rc3h1Mins/Mins mice did not efficiently induce the high-affinity Roquin-1 target IκBNS in response to TCR stimulation, showed reduced Th17 differentiation, and Rc3h1Mins/Mins mice were protected from EAE. These data demonstrate how TCR signaling and MALT1 activation utilize graded cleavage of Roquin to differentially regulate target mRNAs that control T cell activation and differentiation as well as the development of autoimmunity.
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Affiliation(s)
- Henrik Schmidt
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Timsse Raj
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Thomas J. O'Neill
- Research Unit Signaling and Translation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Andreas Muschaweckh
- Institute for Experimental Neuroimmunology, Technical University of Munich, School of Medicine, Munich81675, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Arlinda Negraschus
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Kai P. Hoefig
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich81337, Germany
| | - Gesine Behrens
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Lena Esser
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
| | - Christina Baumann
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich81337, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Carlos Plaza-Sirvent
- Department of Molecular Immunology, ZKF2, Ruhr-University Bochum, Bochum44801, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Andreas Gewies
- Research Unit Signaling and Translation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Sophie E. Isay
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich81675, Germany
| | - Jürgen Ruland
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich81675, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich81675, Germany
| | - Ingo Schmitz
- Department of Molecular Immunology, ZKF2, Ruhr-University Bochum, Bochum44801, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
- Max-Planck-Institute of Psychiatry, Munich80804, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences, Technische Universität München, Freising85354, Germany
| | - Thomas Korn
- Institute for Experimental Neuroimmunology, Technical University of Munich, School of Medicine, Munich81675, Germany
- Munich Cluster for Systems Neurology, Munich81377, Germany
| | - Daniel Krappmann
- Research Unit Signaling and Translation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg85764, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Medical Faculty, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried82152, Germany
- Research Unit Molecular Immune Regulation, Molecular Targets and Therapeutics Center, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich81337, Germany
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7
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Zhu WS, Wheeler BD, Ansel KM. RNA circuits and RNA-binding proteins in T cells. Trends Immunol 2023; 44:792-806. [PMID: 37599172 PMCID: PMC10890840 DOI: 10.1016/j.it.2023.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023]
Abstract
RNA is integral to the regulatory circuits that control cell identity and behavior. Cis-regulatory elements in mRNAs interact with RNA-binding proteins (RBPs) that can alter RNA sequence, stability, and translation into protein. Similarly, long noncoding RNAs (lncRNAs) scaffold ribonucleoprotein complexes that mediate transcriptional and post-transcriptional regulation of gene expression. Indeed, cell programming is fundamental to multicellular life and, in this era of cellular therapies, it is of particular interest in T cells. Here, we review key concepts and recent advances in our understanding of the RNA circuits and RBPs that govern mammalian T cell differentiation and immune function.
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Affiliation(s)
- Wandi S Zhu
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - Benjamin D Wheeler
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA 94143, USA.
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8
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Horlacher M, Cantini G, Hesse J, Schinke P, Goedert N, Londhe S, Moyon L, Marsico A. A systematic benchmark of machine learning methods for protein-RNA interaction prediction. Brief Bioinform 2023; 24:bbad307. [PMID: 37635383 PMCID: PMC10516373 DOI: 10.1093/bib/bbad307] [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: 01/31/2023] [Revised: 06/15/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
RNA-binding proteins (RBPs) are central actors of RNA post-transcriptional regulation. Experiments to profile-binding sites of RBPs in vivo are limited to transcripts expressed in the experimental cell type, creating the need for computational methods to infer missing binding information. While numerous machine-learning based methods have been developed for this task, their use of heterogeneous training and evaluation datasets across different sets of RBPs and CLIP-seq protocols makes a direct comparison of their performance difficult. Here, we compile a set of 37 machine learning (primarily deep learning) methods for in vivo RBP-RNA interaction prediction and systematically benchmark a subset of 11 representative methods across hundreds of CLIP-seq datasets and RBPs. Using homogenized sample pre-processing and two negative-class sample generation strategies, we evaluate methods in terms of predictive performance and assess the impact of neural network architectures and input modalities on model performance. We believe that this study will not only enable researchers to choose the optimal prediction method for their tasks at hand, but also aid method developers in developing novel, high-performing methods by introducing a standardized framework for their evaluation.
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Affiliation(s)
- Marc Horlacher
- Computational Health Center, Helmholtz Center Munich, Germany
- School of Computation, Information and Technology, Technical University Munich (TUM), Germany
| | - Giulia Cantini
- Computational Health Center, Helmholtz Center Munich, Germany
| | - Julian Hesse
- Computational Health Center, Helmholtz Center Munich, Germany
| | - Patrick Schinke
- Computational Health Center, Helmholtz Center Munich, Germany
| | - Nicolas Goedert
- Computational Health Center, Helmholtz Center Munich, Germany
| | | | - Lambert Moyon
- Computational Health Center, Helmholtz Center Munich, Germany
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9
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Zuo Z, Roux ME, Chevalier JR, Dagdas YF, Yamashino T, Højgaard SD, Knight E, Østergaard L, Rodriguez E, Petersen M. The mRNA decapping machinery targets LBD3/ASL9 to mediate apical hook and lateral root development. Life Sci Alliance 2023; 6:e202302090. [PMID: 37385753 PMCID: PMC10310928 DOI: 10.26508/lsa.202302090] [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: 04/11/2023] [Revised: 06/15/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023] Open
Abstract
Multicellular organisms perceive and transduce multiple cues to optimize development. Key transcription factors drive developmental changes, but RNA processing also contributes to tissue development. Here, we report that multiple decapping deficient mutants share developmental defects in apical hook, primary and lateral root growth. More specifically, LATERAL ORGAN BOUNDARIES DOMAIN 3 (LBD3)/ASYMMETRIC LEAVES 2-LIKE 9 (ASL9) transcripts accumulate in decapping deficient plants and can be found in complexes with decapping components. Accumulation of ASL9 inhibits apical hook and lateral root formation. Interestingly, exogenous auxin application restores lateral roots formation in both ASL9 over-expressors and mRNA decay-deficient mutants. Likewise, mutations in the cytokinin transcription factors type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs) ARR10 and ARR12 restore the developmental defects caused by over-accumulation of capped ASL9 transcript upon ASL9 overexpression. Most importantly, loss-of-function of asl9 partially restores apical hook and lateral root formation in both dcp5-1 and pat triple decapping deficient mutants. Thus, the mRNA decay machinery directly targets ASL9 transcripts for decay, possibly to interfere with cytokinin/auxin responses, during development.
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Affiliation(s)
- Zhangli Zuo
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Milena E Roux
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan R Chevalier
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Yasin F Dagdas
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Takafumi Yamashino
- Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University, Nagoya, Japan
| | - Søren D Højgaard
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Emilie Knight
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Lars Østergaard
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Eleazar Rodriguez
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Morten Petersen
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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10
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Bechara R, Vagner S, Mariette X. Post-transcriptional checkpoints in autoimmunity. Nat Rev Rheumatol 2023; 19:486-502. [PMID: 37311941 DOI: 10.1038/s41584-023-00980-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Post-transcriptional regulation is a fundamental process in gene expression that has a role in diverse cellular processes, including immune responses. A core concept underlying post-transcriptional regulation is that protein abundance is not solely determined by transcript abundance. Indeed, transcription and translation are not directly coupled, and intervening steps occur between these processes, including the regulation of mRNA stability, localization and alternative splicing, which can impact protein abundance. These steps are controlled by various post-transcription factors such as RNA-binding proteins and non-coding RNAs, including microRNAs, and aberrant post-transcriptional regulation has been implicated in various pathological conditions. Indeed, studies on the pathogenesis of autoimmune and inflammatory diseases have identified various post-transcription factors as important regulators of immune cell-mediated and target effector cell-mediated pathological conditions. This Review summarizes current knowledge regarding the roles of post-transcriptional checkpoints in autoimmunity, as evidenced by studies in both haematopoietic and non-haematopoietic cells, and discusses the relevance of these findings for developing new anti-inflammatory therapies.
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Affiliation(s)
- Rami Bechara
- Université Paris-Saclay, Inserm, CEA, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB/IDMIT/UMR1184), Le Kremlin Bicêtre, France.
| | - Stephan Vagner
- Institut Curie, CNRS UMR3348, INSERM U1278, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Xavier Mariette
- Université Paris-Saclay, Inserm, CEA, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB/IDMIT/UMR1184), Le Kremlin Bicêtre, France
- Assistance Publique - Hôpitaux de Paris, Hôpital Bicêtre, Department of Rheumatology, Le Kremlin Bicêtre, France
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11
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Hormone Regulation of CCCH Zinc Finger Proteins in Plants. Int J Mol Sci 2022; 23:ijms232214288. [PMID: 36430765 PMCID: PMC9698766 DOI: 10.3390/ijms232214288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
Abstract
CCCH zinc finger proteins contain one to six tandem CCCH motifs composed of three cysteine and one histidine residues and have been widely found in eukaryotes. Plant CCCH proteins control a wide range of developmental and adaptive processes through DNA-protein, RNA-protein and/or protein-protein interactions. The complex networks underlying these processes regulated by plant CCCH proteins are often involved in phytohormones as signal molecules. In this review, we described the evolution of CCCH proteins from green algae to vascular plants and summarized the functions of plant CCCH proteins that are influenced by six major hormones, including abscisic acid, gibberellic acid, brassinosteroid, jasmonate, ethylene and auxin. We further compared the regulatory mechanisms of plant and animal CCCH proteins via hormone signaling. Among them, Arabidopsis AtC3H14, 15 and human hTTP, three typical CCCH proteins, are able to integrate multiple hormones to participate in various biological processes.
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12
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Roles of RNA-binding proteins in immune diseases and cancer. Semin Cancer Biol 2022; 86:310-324. [PMID: 35351611 DOI: 10.1016/j.semcancer.2022.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/03/2022] [Accepted: 03/21/2022] [Indexed: 01/27/2023]
Abstract
Genetic information that is transcribed from DNA to mRNA, and then translated from mRNA to protein, is regulated by complex and sophisticated post-transcriptional mechanisms. Recently, it has become clear that mRNA degradation not only acts to remove unnecessary mRNA, but is also closely associated with the regulation of translation initiation, and is essential for maintaining cellular homeostasis. Various RNA-binding proteins (RBPs) have been reported to play central roles in the mechanisms of mRNA stability and translation initiation through various signal transduction pathways, and to modulate gene expression faster than the transcription process via post-transcriptional modifications in response to intracellular and extracellular stimuli, without de novo protein synthesis. On the other hand, inflammation is necessary for the elimination of pathogens associated with infection, and is tightly controlled to avoid the overexpression of inflammatory cytokines, such as interleukin 6 (IL-6) and tumor necrosis factor (TNF). It is increasingly becoming clear that RBPs play important roles in the post-transcriptional regulation of these immune responses. Furthermore, it has been shown that the aberrant regulation of RBPs leads to chronic inflammation and autoimmune diseases. Although it has been recognized since the time of Rudolf Virchow in the 19th century that cancer-associated inflammation contributes to tumor onset and progression, involvement of the disruption of the balance between anti-tumor immunity via the immune surveillance system and pro-tumor immunity by cancer-associated inflammation in the malignant transformation of cancer remains elusive. Recently, the dysregulated expression and activation of representative RBPs involved in regulation of the production of pro-inflammatory cytokines have been shown to be involved in tumor progression. In this review, we summarize the recent progress in our understanding of the functional roles of these RBPs in several types of immune responses, and the involvement of RBP dysregulation in the pathogenesis of immune diseases and cancer, and discuss possible therapeutic strategies against cancer by targeting RBPs, coupled with immunotherapy.
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13
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Rosas Mejia O, Claeys TA, Williams A, Zafar A, Robinson RT. IL12RB1 allele bias in human T H cells is regulated by functional SNPs in its 3'UTR. Cytokine 2022; 158:155993. [PMID: 36007427 DOI: 10.1016/j.cyto.2022.155993] [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: 04/05/2022] [Revised: 07/25/2022] [Accepted: 08/01/2022] [Indexed: 11/26/2022]
Abstract
Allele bias is an epigenetic mechanism wherein only the maternal- or paternal-derived allele of a gene is preferentially expressed. Allele bias is used by T cells to regulate expression of numerous genes, including those which govern their development and response to cytokines. Here we demonstrate that human TH cell expression of the cytokine receptor gene IL12RB1 is subject to allele bias, and the extent to which this bias occurs is influenced by cells' differentiation status and two polymorphic sites in the IL12RB1 3'UTR. The single nucleotide polymorphisms (SNPs) at these sites, rs3746190 and rs404733, function to increase expression of their encoding allele. Modeling suggests this is due to a stabilizing effect of these SNPs on the predicted mRNA secondary structure. The SNP rs3746190 is also proximal to the predicted binding site of microRNA miR-1277, raising the possibility that miR-1277 cannot exert suppression in the presence of rs3746190. Functional experiments demonstrate, however, that miR-1277 suppression of IL12RB1 3'UTR expression-which itself has not been previously reported-is nevertheless independent of rs3746190. Collectively, these data demonstrate that rs3746190 and rs404733 are functional SNPs which regulate IL12RB1 allele bias in human TH cells.
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Affiliation(s)
- Oscar Rosas Mejia
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, OH, USA
| | - Tiffany A Claeys
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, OH, USA
| | - Amanda Williams
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, OH, USA
| | - Ayesha Zafar
- University of the Punjab, Lahore, Pakistan; University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Richard T Robinson
- Department of Microbial Infection & Immunity, The Ohio State University, Columbus, OH, USA.
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14
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Liu Y, Cui DX, Pan Y, Yu SH, Zheng LW, Wan M. Metabolic-epigenetic nexus in regulation of stem cell fate. World J Stem Cells 2022; 14:490-502. [PMID: 36157525 PMCID: PMC9350619 DOI: 10.4252/wjsc.v14.i7.490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/31/2022] [Accepted: 07/11/2022] [Indexed: 02/06/2023] Open
Abstract
Stem cell fate determination is one of the central questions in stem cell biology, and although its regulation has been studied at genomic and proteomic levels, a variety of biological activities in cells occur at the metabolic level. Metabolomics studies have established the metabolome during stem cell differentiation and have revealed the role of metabolites in stem cell fate determination. While metabolism is considered to play a biological regulatory role as an energy source, recent studies have suggested the nexus between metabolism and epigenetics because several metabolites function as cofactors and substrates in epigenetic mechanisms, including histone modification, DNA methylation, and microRNAs. Additionally, the epigenetic modification is sensitive to the dynamic metabolites and consequently leads to changes in transcription. The nexus between metabolism and epigenetics proposes a novel stem cell-based therapeutic strategy through manipulating metabolites. In the present review, we summarize the possible nexus between metabolic and epigenetic regulation in stem cell fate determination, and discuss the potential preventive and therapeutic strategies via targeting metabolites.
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Affiliation(s)
- Yi Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Di-Xin Cui
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Yue Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Si-Han Yu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Li-Wei Zheng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Pediatric Dentistry, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Mian Wan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, Sichuan Province, China
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15
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Tants JN, Becker LM, McNicoll F, Müller-McNicoll M, Schlundt A. NMR-derived secondary structure of the full-length Ox40 mRNA 3'UTR and its multivalent binding to the immunoregulatory RBP Roquin. Nucleic Acids Res 2022; 50:4083-4099. [PMID: 35357505 PMCID: PMC9023295 DOI: 10.1093/nar/gkac212] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 12/31/2022] Open
Abstract
Control of posttranscriptional mRNA decay is a crucial determinant of cell homeostasis and differentiation. mRNA lifetime is governed by cis-regulatory elements in their 3′ untranslated regions (UTR). Despite ongoing progress in the identification of cis elements we have little knowledge about the functional and structural integration of multiple elements in 3′UTR regulatory hubs and their recognition by mRNA-binding proteins (RBPs). Structural analyses are complicated by inconsistent mapping and prediction of RNA fold, by dynamics, and size. We here, for the first time, provide the secondary structure of a complete mRNA 3′UTR. We use NMR spectroscopy in a divide-and-conquer strategy complemented with SAXS, In-line probing and SHAPE-seq applied to the 3′UTR of Ox40 mRNA, which encodes a T-cell co-receptor repressed by the protein Roquin. We provide contributions of RNA elements to Roquin-binding. The protein uses its extended bi-modal ROQ domain to sequentially engage in a 2:1 stoichiometry with a 3′UTR core motif. We observe differential binding of Roquin to decay elements depending on their structural embedment. Our data underpins the importance of studying RNA regulation in a full sequence and structural context. This study serves as a paradigm for an approach in analysing structured RNA-regulatory hubs and their binding by RBPs.
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Affiliation(s)
- Jan-Niklas Tants
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Lea Marie Becker
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - François McNicoll
- Goethe University Frankfurt, Institute for Molecular Biosciences, Max-von-Laue-Str. 13, 60438 Frankfurt, Germany
| | - Michaela Müller-McNicoll
- Goethe University Frankfurt, Institute for Molecular Biosciences, Max-von-Laue-Str. 13, 60438 Frankfurt, Germany
| | - Andreas Schlundt
- Goethe University Frankfurt, Institute for Molecular Biosciences and Biomagnetic Resonance Centre (BMRZ), Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
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16
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Behrens G, Heissmeyer V. Cooperation of RNA-Binding Proteins – a Focus on Roquin Function in T Cells. Front Immunol 2022; 13:839762. [PMID: 35251035 PMCID: PMC8894612 DOI: 10.3389/fimmu.2022.839762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/31/2022] [Indexed: 12/18/2022] Open
Abstract
Post-transcriptional gene regulation by RNA-binding proteins (RBPs) is important in the prevention of inflammatory and autoimmune diseases. With respect to T cell activation and differentiation, the RBPs Roquin-1/2 and Regnase-1 play pivotal roles by inducing degradation and/or translational silencing of target mRNAs. These targets encode important proinflammatory mediators and thus Roquin and Regnase-1 functions dampen cellular programs that can lead to inflammation and autoimmune disease. Recent findings demonstrate direct physical interaction of both RBPs. Here, we propose that cooperativity of trans-acting factors may be more generally used to reinforce the regulatory impact on selected targets and promote specific cell fate decisions. We develop this concept for Roquin and Regnase-1 function in resting and activated T cells and discuss the involvement in autoimmunity as well as how the therapeutic potential can be used in anti-tumor therapies.
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Affiliation(s)
- Gesine Behrens
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
- *Correspondence: Vigo Heissmeyer,
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17
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García-Espinoza JA, Muñoz-Valle JF, García-Chagollán M, Hernández-Bello J, Palafox-Sánchez CA, López-Villalobos EF, Sánchez-Zuno GA, Martínez-Bonilla GE, Cerpa-Cruz S, Carrillo-Ballesteros FJ, Oregon-Romero E. ICOS Gene Polymorphisms (IVS1 + 173 T/C and c. 1624 C/T) in Primary Sjögren's Syndrome Patients: Analysis of ICOS Expression. Curr Issues Mol Biol 2022; 44:764-776. [PMID: 35723338 PMCID: PMC8929044 DOI: 10.3390/cimb44020053] [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: 11/26/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Primary Sjögren’s syndrome (pSS) is a systemic autoimmune disease, which affects exocrine glands. T cell activation is a trigger mechanism in the immune response. Hyperreactivity of T cells and antibody production are features in pSS. ICOS can be critical in the pathogenesis of pSS. Methods: A total of 134 pSS patients and 134 control subjects (CS) were included. Genotyping was performed by PCR-RFLP. ICOS mRNA expression was quantified by real-time PCR, and CD4+ ICOS+ T cells were determined by flow cytometry. Results: The ICOS IVS1 + 173 T>C polymorphisms were not associated with susceptibility to pSS (p = 0.393, CI = 0.503−1.311). However, the c.1624 C>T polymorphism was associated with a reduction in the risk of development of pSS (p = 0.015, CI = 0.294−0.884). An increase in ICOS mRNA expression in patients was observed (3.7-fold). Furthermore, pSS patients showed an increase in membranal-ICOS expression (mICOS). High expression of mICOS (MFI) was associated with lymphocytic infiltration. Conclusions: The IVS1 + 173 polymorphism is not a genetic marker for the development of pSS, while c.1624 T allele was associated with a low risk. However, elevated mICOS expression in pSS patients with high lymphocytic infiltration was found. ICOS may have an important role in the immunopathogenesis of pSS and should be analyzed in T cell subsets in pSS patients as a possible disease marker.
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Affiliation(s)
- José Antonio García-Espinoza
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.A.G.-E.); (J.F.M.-V.); (M.G.-C.); (J.H.-B.); (C.A.P.-S.); (E.F.L.-V.); (G.A.S.-Z.)
| | - José Francisco Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.A.G.-E.); (J.F.M.-V.); (M.G.-C.); (J.H.-B.); (C.A.P.-S.); (E.F.L.-V.); (G.A.S.-Z.)
| | - Mariel García-Chagollán
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.A.G.-E.); (J.F.M.-V.); (M.G.-C.); (J.H.-B.); (C.A.P.-S.); (E.F.L.-V.); (G.A.S.-Z.)
| | - Jorge Hernández-Bello
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.A.G.-E.); (J.F.M.-V.); (M.G.-C.); (J.H.-B.); (C.A.P.-S.); (E.F.L.-V.); (G.A.S.-Z.)
| | - Claudia Azucena Palafox-Sánchez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.A.G.-E.); (J.F.M.-V.); (M.G.-C.); (J.H.-B.); (C.A.P.-S.); (E.F.L.-V.); (G.A.S.-Z.)
| | - Erika Fabiola López-Villalobos
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.A.G.-E.); (J.F.M.-V.); (M.G.-C.); (J.H.-B.); (C.A.P.-S.); (E.F.L.-V.); (G.A.S.-Z.)
| | - Gabriela Athziri Sánchez-Zuno
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.A.G.-E.); (J.F.M.-V.); (M.G.-C.); (J.H.-B.); (C.A.P.-S.); (E.F.L.-V.); (G.A.S.-Z.)
| | - Gloria Esther Martínez-Bonilla
- Servicio de Reumatología, O.P.D. Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (G.E.M.-B.); (S.C.-C.)
| | - Sergio Cerpa-Cruz
- Servicio de Reumatología, O.P.D. Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44280, Mexico; (G.E.M.-B.); (S.C.-C.)
| | - Francisco Josue Carrillo-Ballesteros
- Departamento de Farmacobiología, Centro Universitarios de Ciencias Exactas e Ingenierias, Universidad de Guadalajara, Guadalajara 44430, Mexico;
| | - Edith Oregon-Romero
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Mexico; (J.A.G.-E.); (J.F.M.-V.); (M.G.-C.); (J.H.-B.); (C.A.P.-S.); (E.F.L.-V.); (G.A.S.-Z.)
- Correspondence: ; Tel.: +52-1-3310585200 (ext. 34200)
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18
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Behrens G, Edelmann SL, Raj T, Kronbeck N, Monecke T, Davydova E, Wong EH, Kifinger L, Giesert F, Kirmaier ME, Hohn C, de Jonge LS, Pisfil MG, Fu M, Theurich S, Feske S, Kawakami N, Wurst W, Niessing D, Heissmeyer V. Disrupting Roquin-1 interaction with Regnase-1 induces autoimmunity and enhances antitumor responses. Nat Immunol 2021; 22:1563-1576. [PMID: 34811541 PMCID: PMC8996344 DOI: 10.1038/s41590-021-01064-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/30/2021] [Indexed: 12/15/2022]
Abstract
Roquin and Regnase-1 proteins bind and post-transcriptionally regulate proinflammatory target messenger RNAs to maintain immune homeostasis. Either the sanroque mutation in Roquin-1 or loss of Regnase-1 cause systemic lupus erythematosus-like phenotypes. Analyzing mice with T cells that lack expression of Roquin-1, its paralog Roquin-2 and Regnase-1 proteins, we detect overlapping or unique phenotypes by comparing individual and combined inactivation. These comprised spontaneous activation, metabolic reprogramming and persistence of T cells leading to autoimmunity. Here, we define an interaction surface in Roquin-1 for binding to Regnase-1 that included the sanroque residue. Mutations in Roquin-1 impairing this interaction and cooperative regulation of targets induced T follicular helper cells, germinal center B cells and autoantibody formation. These mutations also improved the functionality of tumor-specific T cells by promoting their accumulation in the tumor and reducing expression of exhaustion markers. Our data reveal the physical interaction of Roquin-1 with Regnase-1 as a hub to control self-reactivity and effector functions in immune cell therapies.
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Affiliation(s)
- Gesine Behrens
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Stephanie L Edelmann
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
| | - Timsse Raj
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Nina Kronbeck
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Thomas Monecke
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
| | - Elena Davydova
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Elaine H Wong
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Lisa Kifinger
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
| | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Martin E Kirmaier
- Cancer and Immunometabolism Research Group at the Gene Center, Ludwig-Maximilians-Universität in Munich, Munich, Germany
- Department of Medicine III, LMU University Hospital, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Christine Hohn
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Laura S de Jonge
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine at the Biomedical Center, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Mingui Fu
- Department of Basic Medical Science, School of Medicine, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Sebastian Theurich
- Cancer and Immunometabolism Research Group at the Gene Center, Ludwig-Maximilians-Universität in Munich, Munich, Germany
- Department of Medicine III, LMU University Hospital, Ludwig-Maximilians-Universität in Munich, Munich, Germany
| | - Stefan Feske
- Department of Pathology, New York University School of Medicine, New York, NY, USA
| | - Naoto Kawakami
- Institute of Clinical Neuroimmunology, University Hospital and Biomedical Center, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- German Center for Neurodegenerative Diseases (DZNE) Site Munich, Munich, Germany
- Technische Universität München, Lehrstuhl für Entwicklungsgenetik c/o Helmholtz Zentrum München, Munich, Germany
| | - Dierk Niessing
- Institute of Pharmaceutical Biotechnology, Ulm University, Ulm, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Planegg-Martinsried, Germany.
- Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany.
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19
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O'Neill TJ, Seeholzer T, Gewies A, Gehring T, Giesert F, Hamp I, Graß C, Schmidt H, Kriegsmann K, Tofaute MJ, Demski K, Poth T, Rosenbaum M, Schnalzger T, Ruland J, Göttlicher M, Kriegsmann M, Naumann R, Heissmeyer V, Plettenburg O, Wurst W, Krappmann D. TRAF6 prevents fatal inflammation by homeostatic suppression of MALT1 protease. Sci Immunol 2021; 6:eabh2095. [PMID: 34767456 DOI: 10.1126/sciimmunol.abh2095] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Thomas J O'Neill
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Thomas Seeholzer
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Andreas Gewies
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Torben Gehring
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Florian Giesert
- Institute for Developmental Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Isabel Hamp
- Institute for Medicinal Chemistry, Helmholtz Zentrum München-German Research Center for Environmental Health, 30167 Hannover, Germany.,Centre of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Carina Graß
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Henrik Schmidt
- Institute for Immunology, Biomedical Center Munich, LMU Munich, 82152 Martinsried, Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marie J Tofaute
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Katrin Demski
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Tanja Poth
- Center for Model System and Comparative Pathology (CMCP), Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Marc Rosenbaum
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany
| | - Theresa Schnalzger
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany
| | - Jürgen Ruland
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, 81675 Munich, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Martin Göttlicher
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.,School of Medicine, Technical University of Munich, Munich, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Ronald Naumann
- Max Planck Institute of Molecular Cell Biology and Genetics, Transgenic Core Facility, 01307 Dresden, Germany
| | - Vigo Heissmeyer
- Institute for Immunology, Biomedical Center Munich, LMU Munich, 82152 Martinsried, Germany.,Research Unit Molecular Immune Regulation, Helmholtz Zentrum München-German Research Center for Environmental Health, 81377 München, Germany
| | - Oliver Plettenburg
- Institute for Medicinal Chemistry, Helmholtz Zentrum München-German Research Center for Environmental Health, 30167 Hannover, Germany.,Centre of Biomolecular Drug Research (BMWZ), Institute of Organic Chemistry, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Wolfgang Wurst
- Institute for Developmental Genetics, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.,German Center for Neurodegenerative Diseases (DZNE), Site Munich, Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Technische Universität München, Lehrstuhl für Entwicklungsgenetik c/o Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Daniel Krappmann
- Research Unit Cellular Signal Integration, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany
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20
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Nicolet BP, Zandhuis ND, Lattanzio VM, Wolkers MC. Sequence determinants as key regulators in gene expression of T cells. Immunol Rev 2021; 304:10-29. [PMID: 34486113 PMCID: PMC9292449 DOI: 10.1111/imr.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
T cell homeostasis, T cell differentiation, and T cell effector function rely on the constant fine-tuning of gene expression. To alter the T cell state, substantial remodeling of the proteome is required. This remodeling depends on the intricate interplay of regulatory mechanisms, including post-transcriptional gene regulation. In this review, we discuss how the sequence of a transcript influences these post-transcriptional events. In particular, we review how sequence determinants such as sequence conservation, GC content, and chemical modifications define the levels of the mRNA and the protein in a T cell. We describe the effect of different forms of alternative splicing on mRNA expression and protein production, and their effect on subcellular localization. In addition, we discuss the role of sequences and structures as binding hubs for miRNAs and RNA-binding proteins in T cells. The review thus highlights how the intimate interplay of post-transcriptional mechanisms dictate cellular fate decisions in T cells.
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Affiliation(s)
- Benoit P. Nicolet
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Nordin D. Zandhuis
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - V. Maria Lattanzio
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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21
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Mino T, Takeuchi O. Regnase-1-related endoribonucleases in health and immunological diseases. Immunol Rev 2021; 304:97-110. [PMID: 34514623 DOI: 10.1111/imr.13023] [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] [Received: 06/17/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022]
Abstract
Dynamic changes in gene expression are key factors in the development and activation of immune cells. RNA metabolism is one of the critical steps for the control of gene expression. Together with transcriptional regulation, mRNA decay by specific ribonucleases (RNases) plays a vital role in shaping gene expression. In addition to the canonical exoribonuclease-mediated mRNA degradation through the recognition of cis-elements in mRNA 3' untranslated regions by RNA-binding proteins (RBPs), endoribonucleases are involved in the control of mRNAs in immune cells. In this review, we gleam insights on how Regnase-1, an endoribonuclease necessary for regulating immune cell activation and maintenance of immune homeostasis, degrades RNAs involved in immune cell activation. Additionally, we provide insights on recent studies which uncover the role of Regnase-1-related RNases, including Regnase-2, Regnase-3, and Regnase-4, as well as N4BP1 and KHNYN, in immune regulation and antiviral immunity. As the dysregulation of immune mRNA decay leads to pathologies such as autoimmune diseases or impaired activation of immune responses, RNases are deemed as essential components of regulatory feedback mechanisms that modulate inflammation. Given the critical role of RNases in autoimmunity, RNases can be perceived as emerging targets in the development of novel therapeutics.
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Affiliation(s)
- Takashi Mino
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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22
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Schott J, Reitter S, Lindner D, Grosser J, Bruer M, Shenoy A, Geiger T, Mathes A, Dobreva G, Stoecklin G. Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density. Nat Methods 2021; 18:1068-1074. [PMID: 34480152 DOI: 10.1038/s41592-021-01250-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 07/23/2021] [Indexed: 01/21/2023]
Abstract
In general, mRNAs are assumed to be loaded with ribosomes instantly upon entry into the cytoplasm. To measure ribosome density (RD) on nascent mRNA, we developed nascent Ribo-Seq by combining Ribo-Seq with progressive 4-thiouridine labeling. In mouse macrophages, we determined experimentally the lag between the appearance of nascent mRNA and its association with ribosomes, which was calculated to be 20-22 min for bulk mRNA. In mouse embryonic stem cells, nRibo-Seq revealed an even stronger lag of 35-38 min in ribosome loading. After stimulation of macrophages with lipopolysaccharide, the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments, which gives rise to distorted RD measurements under conditions where mRNA amounts are far from steady-state expression. As a result, we demonstrate that transcriptional changes affect RD in a passive way.
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Affiliation(s)
- Johanna Schott
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany. .,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany.
| | - Sonja Reitter
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Doris Lindner
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Jan Grosser
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Marius Bruer
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Anjana Shenoy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Geiger
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Arthur Mathes
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
| | - Gergana Dobreva
- Department of Anatomy and Developmental Biology, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,German Center for Cardiovascular Research (DZHK), Heidelberg, Germany
| | - Georg Stoecklin
- Mannheim Institute for Innate Immunoscience (MI3), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Center for Molecular Biology of Heidelberg University (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
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23
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Zhou M, Lu W, Li B, Yuan X, Liu M, Han J, Liu X, Li A. Roquin2 suppresses breast cancer progression by inhibiting tumor angiogenesis via selectively destabilizing proangiogenic factors mRNA. Int J Biol Sci 2021; 17:2884-2898. [PMID: 34345214 PMCID: PMC8326130 DOI: 10.7150/ijbs.59891] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022] Open
Abstract
Tumor angiogenesis is an essential step in tumor growth and metastasis. The initiation of tumor angiogenesis is dictated by a shift in the balance between proangiogenic and antiangiogenic gene expression programs. Roquin2 is a zinc-finger RNA-binding protein with important roles in mediating the expression of inflammatory genes, such as TNF, IL6 and PTGS2, which are also important angiogenic factors. In this study, we demonstrate that Roquin2 functions as a potent tumor angiogenesis regulator that inhibits breast tumor-induced angiogenesis by selectively destabilizing mRNA of proangiogenic gene transcripts, including endoglin (ENG), endothelin-1 (EDN1), vascular endothelial growth factor B (VEGFB) and platelet derived growth factor C (PDGFC). Roquin2 recognizes and binds the stem-loop structure in the 3'untranslated region (3'UTR) of these mRNAs via its ROQ domain to destabilize mRNA. Moreover, we found that Roquin2 expression was reduced in breast cancer cells and tissues, and associated with poor prognosis in breast cancer patients. Overexpression of Roquin2 inhibited breast tumor-induced angiogenesis in vitro and in vivo, whereas silencing Roquin2 enhanced tumor angiogenesis. In vivo induction of Roquin2 by adenovirus significantly suppressed breast tumor growth, metastasis and angiogenesis. Taken together, our results identify that Roquin2 is a novel breast cancer suppressor that inhibits tumor angiogenesis by selectively downregulating the expression of proangiogenic genes.
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Affiliation(s)
- Meicen Zhou
- Department of Endocrinology, Beijing Jishuitan Hospatial, The 4 th Clinical Medical College of Peking University, Beijing, 100035, China
| | - Wenbao Lu
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Bingwei Li
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xiaochen Yuan
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Mingming Liu
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Jianqun Han
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Xueting Liu
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
| | - Ailing Li
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
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24
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Freen-van Heeren JJ. Post-transcriptional control of T-cell cytokine production: Implications for cancer therapy. Immunology 2021; 164:57-72. [PMID: 33884612 DOI: 10.1111/imm.13339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 03/22/2021] [Accepted: 03/30/2021] [Indexed: 01/05/2023] Open
Abstract
As part of the adaptive immune system, T cells are vital for the eradication of infected and malignantly transformed cells. To perform their protective function, T cells produce effector molecules that are either directly cytotoxic, such as granzymes, perforin, interferon-γ and tumour necrosis factor α, or attract and stimulate (immune) cells, such as interleukin-2. As these molecules can also induce immunopathology, tight control of their production is required. Indeed, inflammatory cytokine production is regulated on multiple levels. Firstly, locus accessibility and transcription factor availability and activity determine the amount of mRNA produced. Secondly, post-transcriptional mechanisms, influencing mRNA splicing/codon usage, stability, decay, localization and translation rate subsequently determine the amount of protein that is produced. In the immune suppressive environments of tumours, T cells gradually lose the capacity to produce effector molecules, resulting in tumour immune escape. Recently, the role of post-transcriptional regulation in fine-tuning T-cell effector function has become more appreciated. Furthermore, several groups have shown that exhausted or dysfunctional T cells from cancer patients or murine models possess mRNA for inflammatory mediators, but fail to produce effector molecules, hinting that post-transcriptional events also play a role in hampering tumour-infiltrating lymphocyte effector function. Here, the post-transcriptional regulatory events governing T-cell cytokine production are reviewed, with a specific focus on the importance of post-transcriptional regulation in anti-tumour responses. Furthermore, potential approaches to circumvent tumour-mediated dampening of T-cell effector function through the (dis)engagement of post-transcriptional events are explored, such as CRISPR/Cas9-mediated genome editing or chimeric antigen receptors.
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25
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Corral VM, Schultz ER, Eisenstein RS, Connell GJ. Roquin is a major mediator of iron-regulated changes to transferrin receptor-1 mRNA stability. iScience 2021; 24:102360. [PMID: 33898949 PMCID: PMC8058555 DOI: 10.1016/j.isci.2021.102360] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/18/2020] [Accepted: 03/23/2021] [Indexed: 11/21/2022] Open
Abstract
Transferrin receptor-1 (TfR1) has essential iron transport and proposed signal transduction functions. Proper TfR1 regulation is a requirement for hematopoiesis, neurological development, and the homeostasis of tissues including the intestine and muscle, while dysregulation is associated with cancers and immunodeficiency. TfR1 mRNA degradation is highly regulated, but the identity of the degradation activity remains uncertain. Here, we show with gene knockouts and siRNA knockdowns that two Roquin paralogs are major mediators of iron-regulated changes to the steady-state TfR1 mRNA level within four different cell types (HAP1, HUVEC, L-M, and MEF). Roquin is demonstrated to destabilize the TfR1 mRNA, and its activity is fully dependent on three hairpin loops within the TfR1 mRNA 3′-UTR that are essential for iron-regulated instability. We further show in L-M cells that TfR1 mRNA degradation does not require ongoing translation, consistent with Roquin-mediated instability. We conclude that Roquin is a major effector of TfR1 mRNA abundance. Roquin is a major mediator of iron-regulated TfR1 mRNA instability Roquin-mediated instability requires three stem loops within the TfR1 3′-UTR Iron-regulated TfR1 mRNA instability can occur in the absence of Regnase-1
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Affiliation(s)
- Victor M Corral
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eric R Schultz
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Richard S Eisenstein
- Department of Nutritional Sciences, University of Wisconsin, Madison, WI 53706, USA
| | - Gregory J Connell
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
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26
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Zhou M, Lu W, Li B, Liu X, Li A. TARBP2 promotes tumor angiogenesis and metastasis by destabilizing antiangiogenic factor mRNAs. Cancer Sci 2021; 112:1289-1299. [PMID: 33484209 PMCID: PMC7935780 DOI: 10.1111/cas.14820] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Tumor angiogenesis is a crucial step in the further growth and metastasis of solid tumors. However, its regulatory mechanism remains unclear. Here, we showed that TARBP2, an RNA‐binding protein, played a role in promoting tumor‐induced angiogenesis both in vitro and in vivo through degrading the mRNAs of antiangiogenic factors, including thrombospondin1/2 (THBS1/2), tissue inhibitor of metalloproteinases 1 (TIMP1), and serpin family F member 1 (SERPINF1), by targeting their 3′untranslated regions (3′UTRs). Overexpression of TARBP2 promotes tumor cell–induced angiogenesis, while its knockdown inhibits tumor angiogenesis. Clinical cohort analysis revealed that high expression level of TARBP2 was associated with poor survival of lung cancer and breast cancer patients. Mechanistically, TARBP2 physically interacts with the stem‐loop structure located in the 3′UTR of antiangiogenic transcripts, leading to mRNA destabilization by the dsRNA‐binding domains 1/2 (dsRBDs1/2). Notably, the expression level of TARBP2 in human tumor tissue is negatively correlated with the expression of antiangiogenic factors, including THBS1/2, and brain‐specific angiogenesis inhibitor 1 (BAI1). Moreover, TARBP2 expression is strongly associated with tumor angiogenesis in a group of human lung cancer samples. Collectively, our results highlight that TARBP2 is a novel tumor angiogenesis regulator that could promote tumor angiogenesis by selectively downregulating antiangiogenic gene expression.
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Affiliation(s)
- Meicen Zhou
- Department of Endocrinology, Beijing Jishuitan Hospital, The 4th Clinical Medical College of Peking University, Beijing, China
| | - Wenbao Lu
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bingwei Li
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xueting Liu
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ailing Li
- Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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27
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Zhang Y, Wei Z, Dong H, Zhou J, Yuan J, Ni B, Wu Y, Han C, Tian Y. Regulation of mRNA stability by RBPs and noncoding RNAs contributing to the pathogenicity of Th17 cells. RNA Biol 2020; 18:647-656. [PMID: 33302787 DOI: 10.1080/15476286.2020.1862567] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Th17 cells remain one of the most important subsets of T cells in numerous autoimmune and chronic inflammatory diseases. Posttranscriptional regulation (PTR), especially mRNA stability, has recently emerged as an important mechanism that controls the fate of Th17 cells. This review summarizes the current knowledge on RNA-binding proteins (RBPs), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) that induce mRNA stability changes and their roles in mediating the differentiation, proliferation, function, and migration of Th17 cells. In addition, we summarize the role of RNA modifications and nonsense-mediated mRNA decay (NMD) in Th17 cells. Ongoing research will help to identify practical applications for the regulation of mRNA stability and provide potential targets to prevent and treat Th17-related autoimmune diseases.
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Affiliation(s)
- Yiwei Zhang
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China.,Department of Orthopedics, The First Affiliated Hospital of Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Zhiyuan Wei
- Department of Orthopedics, The First Affiliated Hospital of Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Hui Dong
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Jian Zhou
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Jizhao Yuan
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Bing Ni
- Department of Pathophysiology, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Chao Han
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Yi Tian
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
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28
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Binas O, Tants JN, Peter SA, Janowski R, Davydova E, Braun J, Niessing D, Schwalbe H, Weigand JE, Schlundt A. Structural basis for the recognition of transiently structured AU-rich elements by Roquin. Nucleic Acids Res 2020; 48:7385-7403. [PMID: 32491174 PMCID: PMC7367199 DOI: 10.1093/nar/gkaa465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/16/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022] Open
Abstract
Adenylate/uridylate-rich elements (AREs) are the most common cis-regulatory elements in the 3′-untranslated region (UTR) of mRNAs, where they fine-tune turnover by mediating mRNA decay. They increase plasticity and efficacy of mRNA regulation and are recognized by several ARE-specific RNA-binding proteins (RBPs). Typically, AREs are short linear motifs with a high content of complementary A and U nucleotides and often occur in multiple copies. Although thermodynamically rather unstable, the high AU-content might enable transient secondary structure formation and modify mRNA regulation by RBPs. We have recently suggested that the immunoregulatory RBP Roquin recognizes folded AREs as constitutive decay elements (CDEs), resulting in shape-specific ARE-mediated mRNA degradation. However, the structural evidence for a CDE-like recognition of AREs by Roquin is still lacking. We here present structures of CDE-like folded AREs, both in their free and protein-bound form. Moreover, the AREs in the UCP3 3′-UTR are additionally bound by the canonical ARE-binding protein AUF1 in their linear form, adopting an alternative binding-interface compared to the recognition of their CDE structure by Roquin. Strikingly, our findings thus suggest that AREs can be recognized in multiple ways, allowing control over mRNA regulation by adapting distinct conformational states, thus providing differential accessibility to regulatory RBPs.
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Affiliation(s)
- Oliver Binas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ), 60438 Frankfurt, Germany
| | - Jan-Niklas Tants
- Institute for Molecular Biosciences, Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ), 60438 Frankfurt, Germany
| | - Stephen A Peter
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Robert Janowski
- Institute of Structural Biology, Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Elena Davydova
- Institute of Structural Biology, Helmholtz-Zentrum München, 85764 Neuherberg, Germany
| | - Johannes Braun
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Dierk Niessing
- Institute of Structural Biology, Helmholtz-Zentrum München, 85764 Neuherberg, Germany.,Institute of Pharmaceutical Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ), 60438 Frankfurt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt 64287, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ), 60438 Frankfurt, Germany
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29
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Francisco-Velilla R, Azman EB, Martinez-Salas E. Impact of RNA-Protein Interaction Modes on Translation Control: The Versatile Multidomain Protein Gemin5. Bioessays 2019; 41:e1800241. [PMID: 30919488 DOI: 10.1002/bies.201800241] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/04/2019] [Indexed: 12/12/2022]
Abstract
The fate of cellular RNAs is largely dependent on their structural conformation, which determines the assembly of ribonucleoprotein (RNP) complexes. Consequently, RNA-binding proteins (RBPs) play a pivotal role in the lifespan of RNAs. The advent of highly sensitive in cellulo approaches for studying RNPs reveals the presence of unprecedented RNA-binding domains (RBDs). Likewise, the diversity of the RNA targets associated with a given RBP increases the code of RNA-protein interactions. Increasing evidence highlights the biological relevance of RNA conformation for recognition by specific RBPs and how this mutual interaction affects translation control. In particular, noncanonical RBDs present in proteins such as Gemin5, Roquin-1, Staufen, and eIF3 eventually determine translation of selective targets. Collectively, recent studies on RBPs interacting with RNA in a structure-dependent manner unveil new pathways for gene expression regulation, reinforcing the pivotal role of RNP complexes in genome decoding.
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Affiliation(s)
- Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain
| | - Embarc-Buh Azman
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain
| | - Encarnacion Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolás Cabrera 1, 28049, Madrid, Spain
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30
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Criscitiello MF, Kraev I, Lange S. Deiminated proteins in extracellular vesicles and serum of llama (Lama glama)-Novel insights into camelid immunity. Mol Immunol 2019; 117:37-53. [PMID: 31733447 PMCID: PMC7112542 DOI: 10.1016/j.molimm.2019.10.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/05/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023]
Abstract
Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, causing functional and structural changes in target proteins. Protein deimination causes generation of neo-epitopes, affects gene regulation and also allows for protein moonlighting. Furthermore, PADs have been found to be a phylogenetically conserved regulator for extracellular vesicle (EVs) release. EVs are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins in serum and serum-EVs are described for the first time in camelids, using the llama (Lama glama L. 1758) as a model animal. We report a poly-dispersed population of llama serum EVs, positive for phylogenetically conserved EV-specific markers and characterised by TEM. In serum, 103 deiminated proteins were overall identified, including key immune and metabolic mediators including complement components, immunoglobulin-based nanobodies, adiponectin and heat shock proteins. In serum, 60 deiminated proteins were identified that were not in EVs, and 25 deiminated proteins were found to be unique to EVs, with 43 shared deiminated protein hits between both serum and EVs. Deiminated histone H3, a marker of neutrophil extracellular trap formation, was also detected in llama serum. PAD homologues were identified in llama serum by Western blotting, via cross reaction with human PAD antibodies, and detected at an expected 70 kDa size. This is the first report of deiminated proteins in serum and EVs of a camelid species, highlighting a hitherto unrecognized post-translational modification in key immune and metabolic proteins in camelids, which may be translatable to and inform a range of human metabolic and inflammatory pathologies.
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Affiliation(s)
- Michael F Criscitiello
- Comparative Immunogenetics Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, 77843, USA; Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M Health Science Center, Texas A&M University, College Station, TX, 77843, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK.
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31
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Tavernier SJ, Athanasopoulos V, Verloo P, Behrens G, Staal J, Bogaert DJ, Naesens L, De Bruyne M, Van Gassen S, Parthoens E, Ellyard J, Cappello J, Morris LX, Van Gorp H, Van Isterdael G, Saeys Y, Lamkanfi M, Schelstraete P, Dehoorne J, Bordon V, Van Coster R, Lambrecht BN, Menten B, Beyaert R, Vinuesa CG, Heissmeyer V, Dullaers M, Haerynck F. A human immune dysregulation syndrome characterized by severe hyperinflammation with a homozygous nonsense Roquin-1 mutation. Nat Commun 2019; 10:4779. [PMID: 31636267 PMCID: PMC6803705 DOI: 10.1038/s41467-019-12704-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 09/24/2019] [Indexed: 12/15/2022] Open
Abstract
Hyperinflammatory syndromes are life-threatening disorders caused by overzealous immune cell activation and cytokine release, often resulting from defects in negative feedback mechanisms. In the quintessential hyperinflammatory syndrome familial hemophagocytic lymphohistiocytosis (HLH), inborn errors of cytotoxicity result in effector cell accumulation, immune dysregulation and, if untreated, tissue damage and death. Here, we describe a human case with a homozygous nonsense R688* RC3H1 mutation suffering from hyperinflammation, presenting as relapsing HLH. RC3H1 encodes Roquin-1, a posttranscriptional repressor of immune-regulatory proteins such as ICOS, OX40 and TNF. Comparing the R688* variant with the murine M199R variant reveals a phenotypic resemblance, both in immune cell activation, hypercytokinemia and disease development. Mechanistically, R688* Roquin-1 fails to localize to P-bodies and interact with the CCR4-NOT deadenylation complex, impeding mRNA decay and dysregulating cytokine production. The results from this unique case suggest that impaired Roquin-1 function provokes hyperinflammation by a failure to quench immune activation. Roquin-1 is a posttranscriptional regulator that controls the expression of many immune-related genes such as ICOS and TNFA. Here, the authors report a homozygous R688* loss of function mutation in Roquin-1 in a patient with syndromic uncontrolled hyperinflammation associated with immune cell activation and hypercytokinemia.
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Affiliation(s)
- S J Tavernier
- Primary Immune Deficiency Research Lab, Department of Internal Medicine and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,VIB Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - V Athanasopoulos
- Department of Immunology and Infectious Disease and Center for Personalised Immunology (NHMRC Centre for Research Excellence), John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Centre for Personalised Immunology (CACPI), Shanghai Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - P Verloo
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - G Behrens
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
| | - J Staal
- VIB Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - D J Bogaert
- Primary Immune Deficiency Research Lab, Department of Internal Medicine and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - L Naesens
- Primary Immune Deficiency Research Lab, Department of Internal Medicine and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - M De Bruyne
- Primary Immune Deficiency Research Lab, Department of Internal Medicine and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - S Van Gassen
- VIB Center for Inflammation Research, Unit of Data Mining and Modeling for Biomedicine, Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
| | - E Parthoens
- VIB Bioimaging Core, VIB Center for Inflammation Research, Ghent, Belgium
| | - J Ellyard
- Department of Immunology and Infectious Disease and Center for Personalised Immunology (NHMRC Centre for Research Excellence), John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - J Cappello
- Department of Immunology and Infectious Disease and Center for Personalised Immunology (NHMRC Centre for Research Excellence), John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - L X Morris
- The Australian Phenomics Facility, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - H Van Gorp
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium.,VIB Center for Inflammation Research, Ghent, Belgium
| | - G Van Isterdael
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
| | - Y Saeys
- VIB Center for Inflammation Research, Unit of Data Mining and Modeling for Biomedicine, Ghent, Belgium.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Gent, Belgium
| | - M Lamkanfi
- Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium.,VIB Center for Inflammation Research, Ghent, Belgium
| | - P Schelstraete
- Department of Internal Medicine and Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - J Dehoorne
- Department of Internal Medicine and Pediatrics, Division of Pediatric Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - V Bordon
- Department of Internal Medicine and Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - R Van Coster
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - B N Lambrecht
- Department of Internal Medicine and Pediatrics, Division of Pulmonology, Ghent University Hospital, Ghent, Belgium.,VIB Center for Inflammation Research, Unit for Immunoregulation and Mucosal Immunology, Ghent, Belgium.,Department of Pulmonary Medicine, ErasmusMC, Rotterdam, The Netherlands
| | - B Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - R Beyaert
- VIB Center for Inflammation Research, Unit of Molecular Signal Transduction in Inflammation, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - C G Vinuesa
- Department of Immunology and Infectious Disease and Center for Personalised Immunology (NHMRC Centre for Research Excellence), John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Centre for Personalised Immunology (CACPI), Shanghai Renji Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - V Heissmeyer
- Institute for Immunology, Biomedical Center, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.,Research Unit Molecular Immune Regulation, Helmholtz Zentrum München, Munich, Germany
| | - M Dullaers
- Primary Immune Deficiency Research Lab, Department of Internal Medicine and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium.,Ablynx, a Sanofi Company, Zwijnaarde, Belgium
| | - F Haerynck
- Primary Immune Deficiency Research Lab, Department of Internal Medicine and Pediatrics, Centre for Primary Immunodeficiency Ghent, Jeffrey Modell Diagnosis and Research Centre, Ghent University Hospital, Ghent, Belgium. .,Department of Internal Medicine and Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium.
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Yoshinaga M, Takeuchi O. RNA binding proteins in the control of autoimmune diseases. Immunol Med 2019; 42:53-64. [DOI: 10.1080/25785826.2019.1655192] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Human cytomegalovirus induces and exploits Roquin to counteract the IRF1-mediated antiviral state. Proc Natl Acad Sci U S A 2019; 116:18619-18628. [PMID: 31451648 DOI: 10.1073/pnas.1909314116] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RNA represents a pivotal component of host-pathogen interactions. Human cytomegalovirus (HCMV) infection causes extensive alteration in host RNA metabolism, but the functional relationship between the virus and cellular RNA processing remains largely unknown. Through loss-of-function screening, we show that HCMV requires multiple RNA-processing machineries for efficient viral lytic production. In particular, the cellular RNA-binding protein Roquin, whose expression is actively stimulated by HCMV, plays an essential role in inhibiting the innate immune response. Transcriptome profiling revealed Roquin-dependent global down-regulation of proinflammatory cytokines and antiviral genes in HCMV-infected cells. Furthermore, using cross-linking immunoprecipitation (CLIP)-sequencing (seq), we identified IFN regulatory factor 1 (IRF1), a master transcriptional activator of immune responses, as a Roquin target gene. Roquin reduces IRF1 expression by directly binding to its mRNA, thereby enabling suppression of a variety of antiviral genes. This study demonstrates how HCMV exploits host RNA-binding protein to prevent a cellular antiviral response and offers mechanistic insight into the potential development of CMV therapeutics.
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Yoshinaga M, Takeuchi O. Post-transcriptional control of immune responses and its potential application. Clin Transl Immunology 2019; 8:e1063. [PMID: 31236273 DOI: 10.1002/cti2.1063] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/14/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022] Open
Abstract
Inflammation is the host response against stresses such as infection. Although the inflammation process is required for the elimination of pathogens, uncontrolled inflammation leads to tissue destruction and inflammatory diseases. To avoid this, the inflammatory response is tightly controlled by multiple layers of regulation. Post-transcriptional control of inflammatory mRNAs is increasingly understood to perform critical roles in this process. This is mediated primarily by a set of RNA binding proteins (RBPs) including tristetraprolin, Roquin and Regnase-1, and RNA methylases. These key regulators coordinate the inflammatory response by modulating mRNA pools in both immune and local nonimmune cells. In this review, we provide an overview of the post-transcriptional coordination of immune responses in various tissues and discuss how RBP-mediated regulation of inflammation may be harnessed as a potential class of treatments for inflammatory diseases.
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Affiliation(s)
- Masanori Yoshinaga
- Department of Medical Chemistry Graduate School of Medicine Kyoto University Kyoto Japan
| | - Osamu Takeuchi
- Department of Medical Chemistry Graduate School of Medicine Kyoto University Kyoto Japan
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Chinese‐German Cooperation Group Tumor Immunology: Another inspiring Meeting in Deidesheim. Eur J Immunol 2019; 49:826-830. [DOI: 10.1002/eji.201970065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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