1
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Li C, Moro S, Shostak K, O'Reilly FJ, Donzeau M, Graziadei A, McEwen AG, Desplancq D, Poussin-Courmontagne P, Bachelart T, Fiskin M, Berrodier N, Pichard S, Brillet K, Orfanoudakis G, Poterszman A, Torbeev V, Rappsilber J, Davey NE, Chariot A, Zanier K. Molecular mechanism of IKK catalytic dimer docking to NF-κB substrates. Nat Commun 2024; 15:7692. [PMID: 39227404 PMCID: PMC11371828 DOI: 10.1038/s41467-024-52076-0] [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: 08/27/2023] [Accepted: 08/27/2024] [Indexed: 09/05/2024] Open
Abstract
The inhibitor of κB (IκB) kinase (IKK) is a central regulator of NF-κB signaling. All IKK complexes contain hetero- or homodimers of the catalytic IKKβ and/or IKKα subunits. Here, we identify a YDDΦxΦ motif, which is conserved in substrates of canonical (IκBα, IκBβ) and alternative (p100) NF-κB pathways, and which mediates docking to catalytic IKK dimers. We demonstrate a quantitative correlation between docking affinity and IKK activity related to IκBα phosphorylation/degradation. Furthermore, we show that phosphorylation of the motif's conserved tyrosine, an event previously reported to promote IκBα accumulation and inhibition of NF-κB gene expression, suppresses the docking interaction. Results from integrated structural analyzes indicate that the motif binds to a groove at the IKK dimer interface. Consistently, suppression of IKK dimerization also abolishes IκBα substrate binding. Finally, we show that an optimized bivalent motif peptide inhibits NF-κB signaling. This work unveils a function for IKKα/β dimerization in substrate motif recognition.
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Affiliation(s)
- Changqing Li
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France
| | - Stefano Moro
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France
| | - Kateryna Shostak
- Laboratory of Cancer Biology, GIGA Cancer, University of Liege, CHU, Sart-Tilman, 4000, Liege, Belgium
| | - Francis J O'Reilly
- Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, Berlin, Germany
| | - Mariel Donzeau
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France
| | - Andrea Graziadei
- Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, Berlin, Germany
| | - Alastair G McEwen
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) / INSERM UMR-S 1258 / CNRS UMR7104/ Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Dominique Desplancq
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France
| | - Pierre Poussin-Courmontagne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) / INSERM UMR-S 1258 / CNRS UMR7104/ Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Thomas Bachelart
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France
| | - Mert Fiskin
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France
| | - Nicolas Berrodier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) / INSERM UMR-S 1258 / CNRS UMR7104/ Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Simon Pichard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) / INSERM UMR-S 1258 / CNRS UMR7104/ Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Karl Brillet
- Institut Biologie Moléculaire et Cellulaire (IBMC), CNRS UPR9002, 2 allée Konrad Roentgen, 67000, Strasbourg, France
| | - Georges Orfanoudakis
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France
| | - Arnaud Poterszman
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC) / INSERM UMR-S 1258 / CNRS UMR7104/ Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France
| | - Vladimir Torbeev
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France
| | - Juri Rappsilber
- Institute of Biotechnology, Technische Universität Berlin, Gustav-Meyer-Allee 25, Berlin, Germany
| | - Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
| | - Alain Chariot
- Laboratory of Cancer Biology, GIGA Cancer, University of Liege, CHU, Sart-Tilman, 4000, Liege, Belgium
- WELBIO department, WEL Research Institute, avenue Pasteur, 6, 1300, Wavre, Belgium
| | - Katia Zanier
- Biotechnology and Cell Signaling (CNRS/Université de Strasbourg, UMR7242), Ecole Superieure de Biotechnologie de Strasbourg, Boulevard Sébastien Brant, 67400, Illkirch, France.
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2
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An J, Marwaha A, Laxer RM. Autoinflammatory Diseases: A Review. J Rheumatol 2024; 51:848-861. [PMID: 38879186 DOI: 10.3899/jrheum.2023-1209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2024] [Indexed: 07/17/2024]
Abstract
Autoinflammatory disease (AID) is a vast spectrum of disorders characterized by recurrent attacks of sterile inflammation. Since the first cloning of the familial Mediterranean fever gene in 1997, there has been a rapid rate of discovery of new AIDs. As of 2022, there have been 485 inborn errors of immunity documented by the International Union of Immunological Societies, for which many display aspects of autoinflammation. The pathophysiology of AIDs is complex. Although many are caused by rare mutations in genes that govern innate immunity, others are polygenic, where disease expression is thought to be triggered by environmental factors in genetically predisposed hosts. AIDs range in prevalence from common entities like gout to ultrarare monogenic diseases. Whereas AIDs were initially studied in pediatric populations, it is now apparent that they can present in adulthood and even in the elderly. AIDs can be clinically challenging given their rarity, as well as the heterogeneity in presentation and underlying etiology. Although the care of AIDs can span medical disciplines, the rheumatologist often plays a central role given the inflammatory nature of these illnesses. In this review, we explore the current understanding of the pathophysiology of these complex conditions and propose a classification system for AIDs. We place an emphasis on AIDs that present to the adult rheumatologist and discuss important AIDs that can mimic more classic rheumatic diseases such as systemic lupus erythematosus and inflammatory arthritis. Finally, we offer an approach to the clinical assessment, diagnosis, and management of AIDs.
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Affiliation(s)
- Jason An
- J. An, MD, MSc, Division of Rheumatology, Hospital for Sick Children, University of Toronto, Toronto, Ontario;
| | - Ashish Marwaha
- A. Marwaha, MD, PhD, Department of Medical Genetics, Alberta Children's Hospital, University of Calgary, Calgary, Alberta
| | - Ronald M Laxer
- R.M. Laxer, MDCM, Division of Rheumatology, Hospital for Sick Children, University of Toronto, and Division of Rheumatology, Department of Medicine, St. Michael's Hospital, University of Toronto, Toronto, Ontario, Canada
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3
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Seyrek K, Ivanisenko NV, König C, Lavrik IN. Modulation of extrinsic apoptotic pathway by intracellular glycosylation. Trends Cell Biol 2024; 34:728-741. [PMID: 38336591 DOI: 10.1016/j.tcb.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
The importance of post-translational modifications (PTMs), particularly O-GlcNAcylation, of cytoplasmic proteins in apoptosis has been neglected for quite a while. Modification of cytoplasmic proteins by a single N-acetylglucosamine sugar is a dynamic and reversible PTM exhibiting properties more like phosphorylation than classical O- and N-linked glycosylation. Due to the sparse information existing, we have only limited understanding of how GlcNAcylation affects cell death. Deciphering the role of GlcNAcylation in cell fate may provide further understanding of cell fate decisions. This review focus on the modulation of extrinsic apoptotic pathway via GlcNAcylation carried out by O-GlcNAc transferase (OGT) or by other bacterial effector proteins.
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Affiliation(s)
- Kamil Seyrek
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Nikita V Ivanisenko
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Corinna König
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Inna N Lavrik
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems (CDS), Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany.
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4
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Chen YG, Rieser E, Bhamra A, Surinova S, Kreuzaler P, Ho MH, Tsai WC, Peltzer N, de Miguel D, Walczak H. LUBAC enables tumor-promoting LTβ receptor signaling by activating canonical NF-κB. Cell Death Differ 2024:10.1038/s41418-024-01355-w. [PMID: 39215104 DOI: 10.1038/s41418-024-01355-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
Lymphotoxin β receptor (LTβR), a member of the TNF receptor superfamily (TNFR-SF), is essential for development and maturation of lymphoid organs. In addition, LTβR activation promotes carcinogenesis by inducing a proinflammatory secretome. Yet, we currently lack a detailed understanding of LTβR signaling. In this study we discovered the linear ubiquitin chain assembly complex (LUBAC) as a previously unrecognized and functionally crucial component of the native LTβR signaling complex (LTβR-SC). Mechanistically, LUBAC-generated linear ubiquitin chains enable recruitment of NEMO, OPTN and A20 to the LTβR-SC, where they act coordinately to regulate the balance between canonical and non-canonical NF-κB pathways. Thus, different from death receptor signaling, where LUBAC prevents inflammation through inhibition of cell death, in LTβR signaling LUBAC is required for inflammatory signaling by enabling canonical and interfering with non-canonical NF-κB activation. This results in a LUBAC-dependent LTβR-driven inflammatory, protumorigenic secretome. Intriguingly, in liver cancer patients with high LTβR expression, high expression of LUBAC correlates with poor prognosis, providing clinical relevance for LUBAC-mediated inflammatory LTβR signaling.
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Affiliation(s)
- Yu-Guang Chen
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
- Division of Hematology/Oncology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Eva Rieser
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- CECAD Research Centre, University of Cologne, Cologne, Germany
| | - Amandeep Bhamra
- Proteomics Research Translational Technology Platform, UCL Ciancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, UK
| | - Silvia Surinova
- Proteomics Research Translational Technology Platform, UCL Ciancer Institute and Cancer Research UK UCL Centre, University College London (UCL), London, UK
| | - Peter Kreuzaler
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- CECAD Research Centre, University of Cologne, Cologne, Germany
| | - Meng-Hsing Ho
- Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Wen-Chiuan Tsai
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Nieves Peltzer
- CECAD Research Centre, University of Cologne, Cologne, Germany
- Department of Translational Genomics and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Medical Faculty, Cologne, Germany
- Department of Genome Editing, University of Stuttgart, Stuttgart, Germany
| | - Diego de Miguel
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- CECAD Research Centre, University of Cologne, Cologne, Germany
- Aragon Health Research Institute (IIS Aragon), Biomedical Research Centre of Aragon (CIBA), Zaragoza, Spain
| | - Henning Walczak
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK.
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany.
- CECAD Research Centre, University of Cologne, Cologne, Germany.
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5
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Michel MA, Scutts S, Komander D. Secondary interactions in ubiquitin-binding domains achieve linkage or substrate specificity. Cell Rep 2024; 43:114545. [PMID: 39052481 PMCID: PMC11372445 DOI: 10.1016/j.celrep.2024.114545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/24/2024] [Accepted: 07/10/2024] [Indexed: 07/27/2024] Open
Abstract
Small ubiquitin-binding domains (UBDs) recognize small surface patches on ubiquitin with weak affinity, and it remains a conundrum how specific cellular responses may be achieved. Npl4-type zinc-finger (NZF) domains are ∼30 amino acid, compact UBDs that can provide two ubiquitin-binding interfaces, imposing linkage specificity to explain signaling outcomes. We here comprehensively characterize the linkage preference of human NZF domains. TAB2 prefers Lys6 and Lys63 linkages phosphorylated on Ser65, explaining why TAB2 recognizes depolarized mitochondria. Surprisingly, most NZF domains do not display chain linkage preference, despite conserved, secondary interaction surfaces. This suggests that some NZF domains may specifically bind ubiquitinated substrates by simultaneously recognizing substrate and an attached ubiquitin. We show biochemically and structurally that the NZF1 domain of the E3 ligase HOIPbinds preferentially to site-specifically ubiquitinated forms of NEMO and optineurin. Thus, despite their small size, UBDs may impose signaling specificity via multivalent interactions with ubiquitinated substrates.
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Affiliation(s)
- Martin A Michel
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK
| | - Simon Scutts
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department for Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, CB2 0QH Cambridge, UK; The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department for Medical Biology, University of Melbourne, Melbourne, VIC 3000, Australia.
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6
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Janusova S, Paprckova D, Michalik J, Uleri V, Drobek A, Salyova E, Chorfi L, Neuwirth A, Andreyeva A, Prochazka J, Sedlacek R, Draber P, Stepanek O. ABIN1 is a negative regulator of effector functions in cytotoxic T cells. EMBO Rep 2024; 25:3456-3485. [PMID: 38877170 PMCID: PMC11315980 DOI: 10.1038/s44319-024-00179-6] [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: 12/02/2023] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
T cells are pivotal in the adaptive immune defense, necessitating a delicate balance between robust response against infections and self-tolerance. Their activation involves intricate cross-talk among signaling pathways triggered by the T-cell antigen receptors (TCR) and co-stimulatory or inhibitory receptors. The molecular regulation of these complex signaling networks is still incompletely understood. Here, we identify the adaptor protein ABIN1 as a component of the signaling complexes of GITR and OX40 co-stimulation receptors. T cells lacking ABIN1 are hyper-responsive ex vivo, exhibit enhanced responses to cognate infections, and superior ability to induce experimental autoimmune diabetes in mice. ABIN1 negatively regulates p38 kinase activation and late NF-κB target genes. P38 is at least partially responsible for the upregulation of the key effector proteins IFNG and GZMB in ABIN1-deficient T cells after TCR stimulation. Our findings reveal the intricate role of ABIN1 in T-cell regulation.
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MESH Headings
- Animals
- Humans
- Mice
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/genetics
- Diabetes Mellitus, Type 1/immunology
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Glucocorticoid-Induced TNFR-Related Protein
- Interferon-gamma/metabolism
- Lymphocyte Activation/immunology
- Lymphocyte Activation/genetics
- Mice, Inbred C57BL
- Mice, Knockout
- NF-kappa B/metabolism
- p38 Mitogen-Activated Protein Kinases/metabolism
- Receptors, Antigen, T-Cell/metabolism
- Receptors, OX40/metabolism
- Receptors, OX40/genetics
- Signal Transduction
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Cytotoxic/metabolism
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Affiliation(s)
- Sarka Janusova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Darina Paprckova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Juraj Michalik
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Valeria Uleri
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Ales Drobek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eva Salyova
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Louise Chorfi
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ales Neuwirth
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Arina Andreyeva
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radislav Sedlacek
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Peter Draber
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Laboratory of Immunity & Cell Communication, Division BIOCEV, First Faculty of Medicine, Charles University, Vestec, Czech Republic
| | - Ondrej Stepanek
- Laboratory of Adaptive Immunity, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic.
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7
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Du J, Wang Z. Regulation of RIPK1 Phosphorylation: Implications for Inflammation, Cell Death, and Therapeutic Interventions. Biomedicines 2024; 12:1525. [PMID: 39062098 PMCID: PMC11275223 DOI: 10.3390/biomedicines12071525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/04/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Receptor-interacting protein kinase 1 (RIPK1) plays a crucial role in controlling inflammation and cell death. Its function is tightly controlled through post-translational modifications, enabling its dynamic switch between promoting cell survival and triggering cell death. Phosphorylation of RIPK1 at various sites serves as a critical mechanism for regulating its activity, exerting either activating or inhibitory effects. Perturbations in RIPK1 phosphorylation status have profound implications for the development of severe inflammatory diseases in humans. This review explores the intricate regulation of RIPK1 phosphorylation and dephosphorylation and highlights the potential of targeting RIPK1 phosphorylation as a promising therapeutic strategy for mitigating human diseases.
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Affiliation(s)
- Jingchun Du
- Department of Clinical Immunology, Kingmed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou 510182, China
| | - Zhigao Wang
- Center for Regenerative Medicine, Heart Institute, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 560 Channelside Drive, Tampa, FL 33602, USA
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8
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Luan Y, Long W, Dai L, Tao P, Deng Z, Xia Z. Linear ubiquitination regulates the KSHV replication and transcription activator protein to control infection. Nat Commun 2024; 15:5515. [PMID: 38951495 PMCID: PMC11217414 DOI: 10.1038/s41467-024-49887-6] [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: 11/19/2023] [Accepted: 06/21/2024] [Indexed: 07/03/2024] Open
Abstract
Like many other viruses, KSHV has two life cycle modes: the latent phase and the lytic phase. The RTA protein from KSHV is essential for lytic reactivation, but how this protein's activity is regulated is not fully understood. Here, we report that linear ubiquitination regulates the activity of RTA during KSHV lytic reactivation and de novo infection. Overexpressing OTULIN inhibits KSHV lytic reactivation, whereas knocking down OTULIN or overexpressing HOIP enhances it. Intriguingly, we found that RTA is linearly polyubiquitinated by HOIP at K516 and K518, and these modifications control the RTA's nuclear localization. OTULIN removes linear polyubiquitin chains from cytoplasmic RTA, preventing its nuclear import. The RTA orthologs encoded by the EB and MHV68 viruses are also linearly polyubiquitinated and regulated by OTULIN. Our study establishes that linear polyubiquitination plays a critically regulatory role in herpesvirus infection, adding virus infection to the list of biological processes known to be controlled by linear polyubiquitination.
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Affiliation(s)
- Yi Luan
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Infection and Immunity, Henan Academy of Innovations in Medical Science, Zhengzhou, China
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Wenying Long
- Center for Clinical Research, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, Zhejiang, China
| | - Lisi Dai
- Department of Pathology & Pathophysiology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Surgical Oncology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- School of Basic Medical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Panfeng Tao
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhifen Deng
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- Institute of Infection and Immunity, Henan Academy of Innovations in Medical Science, Zhengzhou, China
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zongping Xia
- Clinical Systems Biology Laboratories, Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
- Institute of Infection and Immunity, Henan Academy of Innovations in Medical Science, Zhengzhou, China.
- Department of Neurology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
- NHC Key Laboratory of Prevention and Treatment of Cerebrovascular Diseases, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
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9
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Takeda Y, Ueki M, Matsuhiro J, Walinda E, Tanaka T, Yamada M, Fujita H, Takezaki S, Kobayashi I, Tamaki S, Nagata S, Miyake N, Matsumoto N, Osawa M, Yasumi T, Heike T, Ohtake F, Saito MK, Toguchida J, Takita J, Ariga T, Iwai K. A de novo dominant-negative variant is associated with OTULIN-related autoinflammatory syndrome. J Exp Med 2024; 221:e20231941. [PMID: 38652464 PMCID: PMC11040501 DOI: 10.1084/jem.20231941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
OTULIN-related autoinflammatory syndrome (ORAS), a severe autoinflammatory disease, is caused by biallelic pathogenic variants of OTULIN, a linear ubiquitin-specific deubiquitinating enzyme. Loss of OTULIN attenuates linear ubiquitination by inhibiting the linear ubiquitin chain assembly complex (LUBAC). Here, we report a patient who harbors two rare heterozygous variants of OTULIN (p.P152L and p.R306Q). We demonstrated accumulation of linear ubiquitin chains upon TNF stimulation and augmented TNF-induced cell death in mesenchymal stem cells differentiated from patient-derived iPS cells, which confirms that the patient has ORAS. However, although the de novo p.R306Q variant exhibits attenuated deubiquitination activity without reducing the amount of OTULIN, the deubiquitination activity of the p.P152L variant inherited from the mother was equivalent to that of the wild-type. Patient-derived MSCs in which the p.P152L variant was replaced with wild-type also exhibited augmented TNF-induced cell death and accumulation of linear chains. The finding that ORAS can be caused by a dominant-negative p.R306Q variant of OTULIN furthers our understanding of disease pathogenesis.
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Affiliation(s)
- Yukiko Takeda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Ueki
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Junpei Matsuhiro
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Tanaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masafumi Yamada
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
- Department of Food and Human Wellness, Rakuno Gakuen University, Ebetsu, Japan
| | - Hiroaki Fujita
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shunichiro Takezaki
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ichiro Kobayashi
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Sakura Tamaki
- Department of Regeneration Science and Engineering, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sanae Nagata
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsujiro Osawa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshio Heike
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Megumu K. Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Junya Toguchida
- Department of Regeneration Science and Engineering, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadashi Ariga
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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10
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Xu LL, Gan T, Li Y, Chen P, Shi SF, Liu LJ, Lv JC, Zhang H, Zhou XJ. Combined Genetic Association and Differed Expression Analysis of UBE2L3 Uncovers a Genetic Regulatory Role of (Immuno)proteasome in IgA Nephropathy. KIDNEY DISEASES (BASEL, SWITZERLAND) 2024; 10:167-180. [PMID: 38835407 PMCID: PMC11149991 DOI: 10.1159/000537987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/20/2024] [Indexed: 06/06/2024]
Abstract
Introduction IgA nephropathy (IgAN) is a leading cause of end-stage renal disease. The exact pathogenesis of IgAN is not well defined, but some genetic studies have led to a novel discovery that the (immuno)proteasome probably plays an important role in IgAN. Methods We firstly analyzed the association of variants in the UBE2L3 region with susceptibility to IgAN in 3,495 patients and 9,101 controls, and then analyzed the association between lead variant and clinical phenotypes in 1,803 patients with regular follow-up data. The blood mRNA levels of members of the ubiquitin-proteasome system including UBE2L3 were analyzed in peripheral blood mononuclear cells from 53 patients and 28 healthy controls. The associations between UBE2L3 and the expression levels of genes involved in Gd-IgA1 production were also explored. Results The rs131654 showed the most significant association signal in UBE2L3 region (OR: 1.10, 95% CI: 1.04-1.16, p = 2.29 × 10-3), whose genotypes were also associated with the levels of Gd-IgA1 (p = 0.04). The rs131654 was observed to exert cis-eQTL effects on UBE2L3 in various tissues and cell types, particularly in immune cell types in multiple databases. The UBE2L3, LUBAC, and proteasome subunits were highly expressed in patients compared with healthy controls. High expression levels of UBE2L3 were not only associated with higher proteinuria (r = 0.34, p = 0.01) and lower eGFR (r = -0.28, p = 0.04), but also positively correlated with the gene expression of LUBAC and other proteasome subunits. Additionally, mRNA expression levels of UBE2L3 were also positively correlated with IL-6 and RELA, but negatively correlated with the expression levels of the key enzyme in the process of glycosylation including C1GALT1 and C1GALT1C1. Conclusion In conclusion, by combined genetic association and differed expression analysis of UBE2L3, our data support a role of genetically conferred dysregulation of the (immuno)proteasome in regulating galactose-deficient IgA1 in the development of IgAN.
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Affiliation(s)
- Lin-Lin Xu
- Renal Division, Peking University First Hospital, Beijing, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Ting Gan
- Renal Division, Peking University First Hospital, Beijing, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Yang Li
- Renal Division, Peking University First Hospital, Beijing, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Pei Chen
- Renal Division, Peking University First Hospital, Beijing, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Su-Fang Shi
- Renal Division, Peking University First Hospital, Beijing, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Li-Jun Liu
- Renal Division, Peking University First Hospital, Beijing, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Ji-Cheng Lv
- Renal Division, Peking University First Hospital, Beijing, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Beijing, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Beijing, China
- Kidney Genetics Center, Peking University Institute of Nephrology, Beijing, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment, Peking University, Ministry of Education, Beijing, China
- Research Units of Diagnosis and Treatment of Immune-mediated Kidney Diseases, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing, China
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11
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Bibert S, Quinodoz M, Perriot S, Krebs FS, Jan M, Malta RC, Collinet E, Canales M, Mathias A, Faignart N, Roulet-Perez E, Meylan P, Brouillet R, Opota O, Lozano-Calderon L, Fellmann F, Guex N, Zoete V, Asner S, Rivolta C, Du Pasquier R, Bochud PY. Herpes simplex encephalitis due to a mutation in an E3 ubiquitin ligase. Nat Commun 2024; 15:3969. [PMID: 38730242 PMCID: PMC11087577 DOI: 10.1038/s41467-024-48287-0] [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: 11/28/2022] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Encephalitis is a rare and potentially fatal manifestation of herpes simplex type 1 infection. Following genome-wide genetic analyses, we identified a previously uncharacterized and very rare heterozygous variant in the E3 ubiquitin ligase WWP2, in a 14-month-old girl with herpes simplex encephalitis. The p.R841H variant (NM_007014.4:c.2522G > A) impaired TLR3 mediated signaling in inducible pluripotent stem cells-derived neural precursor cells and neurons; cells bearing this mutation were also more susceptible to HSV-1 infection compared to control cells. The p.R841H variant increased TRIF ubiquitination in vitro. Antiviral immunity was rescued following the correction of p.R841H by CRISPR-Cas9 technology. Moreover, the introduction of p.R841H in wild type cells reduced such immunity, suggesting that this mutation is linked to the observed phenotypes.
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Affiliation(s)
- Stéphanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Sylvain Perriot
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Fanny S Krebs
- Department of Oncology UNIL-CHUV, Computer-Aided Molecular Engineering, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Maxime Jan
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Rita C Malta
- Pediatric Infectious Diseases and Vaccinology Unit, Woman-Mother-Child Department, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Emilie Collinet
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathieu Canales
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Amandine Mathias
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nicole Faignart
- Department of Pediatrics, Child Neurology Unit, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Eliane Roulet-Perez
- Department of Pediatrics, Child Neurology Unit, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pascal Meylan
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - René Brouillet
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Leyder Lozano-Calderon
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Vincent Zoete
- Department of Oncology UNIL-CHUV, Computer-Aided Molecular Engineering, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Molecular Modelling Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandra Asner
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
- Pediatric Infectious Diseases and Vaccinology Unit, Woman-Mother-Child Department, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Renaud Du Pasquier
- Department of Clinical Neurosciences, Laboratory of Neuroimmunology, Neuroscience Research Centre, University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Clinical Neurosciences, Service of Neurology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland.
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12
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Gao H, Chen Z, Zhao L, Ji C, Xing F. Cellular functions, molecular signalings and therapeutic applications: Translational potential of deubiquitylating enzyme USP9X as a drug target in cancer treatment. Biochim Biophys Acta Rev Cancer 2024; 1879:189099. [PMID: 38582329 DOI: 10.1016/j.bbcan.2024.189099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/13/2023] [Accepted: 03/31/2024] [Indexed: 04/08/2024]
Abstract
Protein ubiquitination, one of the most significant post-translational modifications, plays an important role in controlling the proteins activity in diverse cellular processes. The reversible process of protein ubiquitination, known as deubiquitination, has emerged as a critical mechanism for maintaining cellular homeostasis. The deubiquitinases (DUBs), which participate in deubiquitination process are increasingly recognized as potential candidates for drug discovery. Among these DUBs, ubiquitin-specific protease 9× (USP9X), a highly conserved member of the USP family, exhibits versatile functions in various cellular processes, including the regulation of cell cycle, protein endocytosis, apoptosis, cell polarity, immunological microenvironment, and stem cell characteristics. The dysregulation and abnormal activities of USP9X are influenced by intricate cellular signaling pathway crosstalk and upstream non-coding RNAs. The complex expression patterns and controversial clinical significance of USP9X in cancers suggest its potential as a prognostic biomarker. Furthermore, USP9X inhibitors has shown promising antitumor activity and holds the potential to overcome therapeutic resistance in preclinical models. However, a comprehensive summary of the role and molecular functions of USP9X in cancer progression is currently lacking. In this review, we provide a comprehensive delineation of USP9X participation in numerous critical cellular processes, complicated signaling pathways within the tumor microenvironment, and its potential translational applications to combat therapeutic resistance. By systematically summarizing the updated molecular mechanisms of USP9X in cancer biology, this review aims to contribute to the advancement of cancer therapeutics and provide essential insights for specialists and clinicians in the development of improved cancer treatment strategies.
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Affiliation(s)
- Hongli Gao
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Zhiguang Chen
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Liang Zhao
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Ce Ji
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Fei Xing
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang 110004, China.
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13
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Abstract
Regulated cell death mediated by dedicated molecular machines, known as programmed cell death, plays important roles in health and disease. Apoptosis, necroptosis and pyroptosis are three such programmed cell death modalities. The caspase family of cysteine proteases serve as key regulators of programmed cell death. During apoptosis, a cascade of caspase activation mediates signal transduction and cellular destruction, whereas pyroptosis occurs when activated caspases cleave gasdermins, which can then form pores in the plasma membrane. Necroptosis, a form of caspase-independent programmed necrosis mediated by RIPK3 and MLKL, is inhibited by caspase-8-mediated cleavage of RIPK1. Disruption of cellular homeostatic mechanisms that are essential for cell survival, such as normal ionic and redox balance and lysosomal flux, can also induce cell death without invoking programmed cell death mechanisms. Excitotoxicity, ferroptosis and lysosomal cell death are examples of such cell death modes. In this Review, we provide an overview of the major cell death mechanisms, highlighting the latest insights into their complex regulation and execution, and their relevance to human diseases.
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Affiliation(s)
- Junying Yuan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Shanghai, China.
- Shanghai Key Laboratory of Aging Studies, Shanghai, China.
| | - Dimitry Ofengeim
- Sanofi, Rare and Neurological Diseases Research, Cambridge, MA, USA.
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14
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Fu Y, Li L, Zhang X, Deng Z, Wu Y, Chen W, Liu Y, He S, Wang J, Xie Y, Tu Z, Lyu Y, Wei Y, Wang S, Cui CP, Liu CH, Zhang L. Systematic HOIP interactome profiling reveals critical roles of linear ubiquitination in tissue homeostasis. Nat Commun 2024; 15:2974. [PMID: 38582895 PMCID: PMC10998861 DOI: 10.1038/s41467-024-47289-2] [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: 08/03/2023] [Accepted: 03/27/2024] [Indexed: 04/08/2024] Open
Abstract
Linear ubiquitination catalyzed by HOIL-1-interacting protein (HOIP), the key component of the linear ubiquitination assembly complex, plays fundamental roles in tissue homeostasis by executing domain-specific regulatory functions. However, a proteome-wide analysis of the domain-specific interactome of HOIP across tissues is lacking. Here, we present a comprehensive mass spectrometry-based interactome profiling of four HOIP domains in nine mouse tissues. The interaction dataset provides a high-quality HOIP interactome resource with an average of approximately 90 interactors for each bait per tissue. HOIP tissue interactome presents a systematic understanding of linear ubiquitination functions in each tissue and also shows associations of tissue functions to genetic diseases. HOIP domain interactome characterizes a set of previously undefined linear ubiquitinated substrates and elucidates the cross-talk among HOIP domains in physiological and pathological processes. Moreover, we show that linear ubiquitination of Integrin-linked protein kinase (ILK) decreases focal adhesion formation and promotes the detachment of Shigella flexneri-infected cells. Meanwhile, Hoip deficiency decreases the linear ubiquitination of Smad ubiquitination regulatory factor 1 (SMURF1) and enhances its E3 activity, finally causing a reduced bone mass phenotype in mice. Overall, our work expands the knowledge of HOIP-interacting proteins and provides a platform for further discovery of linear ubiquitination functions in tissue homeostasis.
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Affiliation(s)
- Yesheng Fu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Lei Li
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Xin Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Zhikang Deng
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Ying Wu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Wenzhe Chen
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yuchen Liu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Shan He
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Jian Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yuping Xie
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Zhiwei Tu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yadi Lyu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Yange Wei
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Shujie Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Chun-Ping Cui
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China
| | - Cui Hua Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Lingqiang Zhang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 100850, China.
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15
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Cheng D, Zhu J, Liu G, Gack MU, MacDuff DA. HOIL1 mediates MDA5 activation through ubiquitination of LGP2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.02.587772. [PMID: 38617308 PMCID: PMC11014604 DOI: 10.1101/2024.04.02.587772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The RIG-I-like receptors (RLRs), RIG-I and MDA5, are innate sensors of RNA virus infections that are critical for mounting a robust antiviral immune response. We have shown previously that HOIL1, a component of the Linear Ubiquitin Chain Assembly Complex (LUBAC), is essential for interferon (IFN) induction in response to viruses sensed by MDA5, but not for viruses sensed by RIG-I. LUBAC contains two unusual E3 ubiquitin ligases, HOIL1 and HOIP. HOIP generates methionine-1-linked polyubiquitin chains, whereas HOIL1 has recently been shown to conjugate ubiquitin onto serine and threonine residues. Here, we examined the differential requirement for HOIL1 and HOIP E3 ligase activities in RLR-mediated IFN induction. We determined that HOIL1 E3 ligase activity was critical for MDA5-dependent IFN induction, while HOIP E3 ligase activity played only a modest role in promoting IFN induction. HOIL1 E3 ligase promoted MDA5 oligomerization, its translocation to mitochondrial-associated membranes, and the formation of MAVS aggregates. We identified that HOIL1 can interact with and facilitate the ubiquitination of LGP2, a positive regulator of MDA5 oligomerization. In summary, our work identifies LGP2 ubiquitination by HOIL1 in facilitating the activation of MDA5 and the induction of a robust IFN response.
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Affiliation(s)
- Deion Cheng
- . Department of Microbiology and Immunology, University of Illinois Chicago College of Medicine, Chicago, Illinois, USA
| | - Junji Zhu
- . Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, Florida, USA
| | - GuanQun Liu
- . Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, Florida, USA
| | - Michaela U. Gack
- . Cleveland Clinic Florida Research and Innovation Center, Port St. Lucie, Florida, USA
| | - Donna A. MacDuff
- . Department of Microbiology and Immunology, University of Illinois Chicago College of Medicine, Chicago, Illinois, USA
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16
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Preedy MK, White MRH, Tergaonkar V. Cellular heterogeneity in TNF/TNFR1 signalling: live cell imaging of cell fate decisions in single cells. Cell Death Dis 2024; 15:202. [PMID: 38467621 PMCID: PMC10928192 DOI: 10.1038/s41419-024-06559-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 03/13/2024]
Abstract
Cellular responses to TNF are inherently heterogeneous within an isogenic cell population and across different cell types. TNF promotes cell survival by activating pro-inflammatory NF-κB and MAPK signalling pathways but may also trigger apoptosis and necroptosis. Following TNF stimulation, the fate of individual cells is governed by the balance of pro-survival and pro-apoptotic signalling pathways. To elucidate the molecular mechanisms driving heterogenous responses to TNF, quantifying TNF/TNFR1 signalling at the single-cell level is crucial. Fluorescence live-cell imaging techniques offer real-time, dynamic insights into molecular processes in single cells, allowing for detection of rapid and transient changes, as well as identification of subpopulations, that are likely to be missed with traditional endpoint assays. Whilst fluorescence live-cell imaging has been employed extensively to investigate TNF-induced inflammation and TNF-induced cell death, it has been underutilised in studying the role of TNF/TNFR1 signalling pathway crosstalk in guiding cell-fate decisions in single cells. Here, we outline the various opportunities for pathway crosstalk during TNF/TNFR1 signalling and how these interactions may govern heterogenous responses to TNF. We also advocate for the use of live-cell imaging techniques to elucidate the molecular processes driving cell-to-cell variability in single cells. Understanding and overcoming cellular heterogeneity in response to TNF and modulators of the TNF/TNFR1 signalling pathway could lead to the development of targeted therapies for various diseases associated with aberrant TNF/TNFR1 signalling, such as rheumatoid arthritis, metabolic syndrome, and cancer.
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Affiliation(s)
- Marcus K Preedy
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, D3308, Dover Street, Manchester, M13 9PT, England, UK
| | - Michael R H White
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Michael Smith Building, D3308, Dover Street, Manchester, M13 9PT, England, UK.
| | - Vinay Tergaonkar
- Laboratory of NF-κB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, MD7, Singapore, 117596, Singapore.
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17
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Mitra S, Chen B, Shelton JM, Nitschke S, Wu J, Covington L, Dear M, Lynn T, Verma M, Nitschke F, Fuseya Y, Iwai K, Evers BM, Minassian BA. Myofiber-type-dependent 'boulder' or 'multitudinous pebble' formations across distinct amylopectinoses. Acta Neuropathol 2024; 147:46. [PMID: 38411740 DOI: 10.1007/s00401-024-02698-x] [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: 11/23/2023] [Revised: 01/13/2024] [Accepted: 01/24/2024] [Indexed: 02/28/2024]
Abstract
At least five enzymes including three E3 ubiquitin ligases are dedicated to glycogen's spherical structure. Absence of any reverts glycogen to a structure resembling amylopectin of the plant kingdom. This amylopectinosis (polyglucosan body formation) causes fatal neurological diseases including adult polyglucosan body disease (APBD) due to glycogen branching enzyme deficiency, Lafora disease (LD) due to deficiencies of the laforin glycogen phosphatase or the malin E3 ubiquitin ligase and type 1 polyglucosan body myopathy (PGBM1) due to RBCK1 E3 ubiquitin ligase deficiency. Little is known about these enzymes' functions in glycogen structuring. Toward understanding these functions, we undertake a comparative murine study of the amylopectinoses of APBD, LD and PGBM1. We discover that in skeletal muscle, polyglucosan bodies form as two main types, small and multitudinous ('pebbles') or giant and single ('boulders'), and that this is primarily determined by the myofiber types in which they form, 'pebbles' in glycolytic and 'boulders' in oxidative fibers. This pattern recapitulates what is known in the brain in LD, innumerable dust-like in astrocytes and single giant sized in neurons. We also show that oxidative myofibers are relatively protected against amylopectinosis, in part through highly increased glycogen branching enzyme expression. We present evidence of polyglucosan body size-dependent cell necrosis. We show that sex influences amylopectinosis in genotype, brain region and myofiber-type-specific fashion. RBCK1 is a component of the linear ubiquitin chain assembly complex (LUBAC), the only known cellular machinery for head-to-tail linear ubiquitination critical to numerous cellular pathways. We show that the amylopectinosis of RBCK1 deficiency is not due to loss of linear ubiquitination, and that another function of RBCK1 or LUBAC must exist and operate in the shaping of glycogen. This work opens multiple new avenues toward understanding the structural determinants of the mammalian carbohydrate reservoir critical to neurologic and neuromuscular function and disease.
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Affiliation(s)
- Sharmistha Mitra
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA.
| | - Baozhi Chen
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA
| | - John M Shelton
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9148, USA
| | - Silvia Nitschke
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA
| | - Jun Wu
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA
| | - Lindsay Covington
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9148, USA
| | - Mathew Dear
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA
| | - Tori Lynn
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA
| | - Mayank Verma
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA
| | - Felix Nitschke
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA
| | - Yasuhiro Fuseya
- Department of Molecular and Cellular Physiology, Kyoto University School of Medicine, Kyoto, 606-8501, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Kyoto University School of Medicine, Kyoto, 606-8501, Japan
| | - Bret M Evers
- Departments of Pathology and Ophthalmology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75390-9073, USA
| | - Berge A Minassian
- Division of Neurology, Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390-9063, USA.
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18
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Ito Y, Kobori T, Urashima Y, Ito T, Hotta K, Obata T. Moesin affects the plasma membrane expression and the immune checkpoint function of CD47 in human ovarian clear cell carcinoma. J Reprod Immunol 2024; 161:104185. [PMID: 38141516 DOI: 10.1016/j.jri.2023.104185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/25/2023]
Abstract
Among major histological subtypes of epithelial ovarian cancer, a higher incidence of ovarian clear cell carcinoma (OCCC) is observed in East Asian populations, particularly in Japan. Despite recent progress in the immune checkpoint inhibitors for a wide variety of cancer cell types, patients with OCCC exhibit considerably low response rates to these drugs. Hence, urgent efforts are needed to develop a novel immunotherapeutic approach for OCCC. CD47, a transmembrane protein, is overexpressed in almost all cancer cells and disrupts macrophage phagocytic activity in cancer cells. Ezrin-Radixin-Moesin (ERM) family member of proteins serve as scaffold proteins by crosslinking certain transmembrane proteins with the actin cytoskeleton, contributing to their plasma membrane localization. Here, we examined the role of ERM family in the plasma membrane localization and functionality of CD47 in OCCC cell lines derived from Japanese women. Confocal laser scanning microscopy analysis showed colocalization of CD47 with all three ERM in the plasma membrane of OCCC cells. RNA interference-mediated gene silencing of moesin, but not others, decreased the plasma membrane expression and immune checkpoint function of CD47, as determined by flow cytometry and in vitro phagocytosis assay using human macrophage-like cells, respectively. Interestingly, clinical database analysis indicated that moesin expression in OCCC was higher than that in other histological subtypes of ovarian cancers, and the expression of CD47 and moesin increased with the cancer stage. In conclusion, moesin is overexpressed in OCCC and may be the predominant scaffold protein responsible for CD47 plasma membrane localization and function in OCCC.
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Affiliation(s)
- Yui Ito
- Laboratory of Clinical Pharmaceutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-8540, Japan
| | - Takuro Kobori
- Laboratory of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-8540, Japan
| | - Yoko Urashima
- Laboratory of Clinical Pharmaceutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-8540, Japan
| | - Takuya Ito
- Laboratory of Natural Medicines, Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Osaka 584-8540, Japan
| | - Kikuko Hotta
- Laboratory of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-8540, Japan
| | - Tokio Obata
- Laboratory of Clinical Pharmaceutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka 584-8540, Japan.
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19
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Jin Y, Peng Y, Xu J, Yuan Y, Yang N, Zhang Z, Xu L, Li L, Xiong Y, Sun D, Pan Y, Wu R, Fu J. LUBAC promotes angiogenesis and lung tumorigenesis by ubiquitinating and antagonizing autophagic degradation of HIF1α. Oncogenesis 2024; 13:6. [PMID: 38272870 PMCID: PMC10810860 DOI: 10.1038/s41389-024-00508-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Hypoxia-inducible factor 1 (HIF1) is critically important for driving angiogenesis and tumorigenesis. Linear ubiquitin chain assembly complex (LUBAC), the only known ubiquitin ligase capable of catalyzing protein linear ubiquitination to date, is implicated in cell signaling and associated with cancers. However, the role and mechanism of LUBAC in regulating the expression and function of HIF1α, the labile subunit of HIF1, remain to be elucidated. Herein we showed that LUBAC increases HIF1α protein expression in cultured cells and tissues of human lung cancer and enhances HIF1α DNA-binding and transcriptional activities, which are dependent upon LUBAC enzymatic activity. Mechanistically, LUBAC increases HIF1α stability through antagonizing HIF1α decay by the chaperone-mediated autophagy (CMA)-lysosome pathway, thereby potentiating HIF1α activity. We further demonstrated that HIF1α selectively interacts with HOIP (the catalytic subunit of LUBAC) primarily in the cytoplasm. LUBAC catalyzes linear ubiquitination of HIF1α at lysine 362. Linear ubiquitination shields HIF1α from interacting with heat-shock cognate protein of 70 kDa and lysosome-associated membrane protein type 2 A, two components of CMA. Consequently, linear ubiquitination confers protection against CMA-mediated destruction of HIF1α, increasing HIF1α stability and activity. We found that prolyl hydroxylation is not a perquisite for LUBAC's effects on HIF1α. Functionally, LUBAC facilitates proliferation, clonogenic formation, invasion and migration of lung cancer cells. LUBAC also boosts angiogenesis and exacerbates lung cancer growth in mice, which are greatly compromised by inhibition of HIF1α. This work provides novel mechanistic insights into the role of LUBAC in regulating HIF1α homeostasis, tumor angiogenesis and tumorigenesis of lung cancer, making LUBAC an attractive therapeutic target for cancers.
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Affiliation(s)
- Ying Jin
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China.
- Aab Cardiovascular Research Institute and Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
| | - Yazhi Peng
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
| | - Jie Xu
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
| | - Ye Yuan
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Nan Yang
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
| | - Zemei Zhang
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
- Graduate School, Jinzhou Medical University, Liaoning, China
| | - Lei Xu
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
| | - Lin Li
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
| | - Yulian Xiong
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
| | - Dejiao Sun
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
| | - Yamu Pan
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
| | - Ruiqing Wu
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China
| | - Jian Fu
- The Laboratory of Inflammation and Vascular Biology, Institute of Clinical Medicine and Department of Cardiology, Renmin Hospital, Hubei University of Medicine, Hubei, China.
- Aab Cardiovascular Research Institute and Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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20
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Weinelt N, Wächtershäuser KN, Celik G, Jeiler B, Gollin I, Zein L, Smith S, Andrieux G, Das T, Roedig J, Feist L, Rotter B, Boerries M, Pampaloni F, van Wijk SJL. LUBAC-mediated M1 Ub regulates necroptosis by segregating the cellular distribution of active MLKL. Cell Death Dis 2024; 15:77. [PMID: 38245534 PMCID: PMC10799905 DOI: 10.1038/s41419-024-06447-6] [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: 08/10/2023] [Revised: 12/22/2023] [Accepted: 01/05/2024] [Indexed: 01/22/2024]
Abstract
Plasma membrane accumulation of phosphorylated mixed lineage kinase domain-like (MLKL) is a hallmark of necroptosis, leading to membrane rupture and inflammatory cell death. Pro-death functions of MLKL are tightly controlled by several checkpoints, including phosphorylation. Endo- and exocytosis limit MLKL membrane accumulation and counteract necroptosis, but the exact mechanisms remain poorly understood. Here, we identify linear ubiquitin chain assembly complex (LUBAC)-mediated M1 poly-ubiquitination (poly-Ub) as novel checkpoint for necroptosis regulation downstream of activated MLKL in cells of human origin. Loss of LUBAC activity inhibits tumor necrosis factor α (TNFα)-mediated necroptosis, not by affecting necroptotic signaling, but by preventing membrane accumulation of activated MLKL. Finally, we confirm LUBAC-dependent activation of necroptosis in primary human pancreatic organoids. Our findings identify LUBAC as novel regulator of necroptosis which promotes MLKL membrane accumulation in human cells and pioneer primary human organoids to model necroptosis in near-physiological settings.
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Affiliation(s)
- Nadine Weinelt
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Kaja Nicole Wächtershäuser
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Biological Sciences (IZN), Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Gulustan Celik
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Birte Jeiler
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Isabelle Gollin
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Laura Zein
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Sonja Smith
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110, Freiburg, Germany
| | - Tonmoy Das
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110, Freiburg, Germany
| | - Jens Roedig
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Leonard Feist
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Björn Rotter
- GenXPro GmbH, Altenhoeferallee 3, 60438, Frankfurt am Main, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79110, Freiburg, Germany
- German Cancer Consortium (DKTK) partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Francesco Pampaloni
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Biological Sciences (IZN), Goethe University Frankfurt, Max-von-Laue-Strasse 15, 60438, Frankfurt am Main, Germany
| | - Sjoerd J L van Wijk
- Institute for Experimental Paediatric Haematology and Oncology (EPHO), Goethe University Frankfurt, Komturstrasse 3a, 60528, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK) partner site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- University Cancer Centre Frankfurt (UCT), University Hospital Frankfurt, Goethe-University Frankfurt, Frankfurt, Germany.
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21
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Hoshino K, Nakazawa S, Yokobori T, Hagiwara K, Ishii N, Tsukagoshi M, Igarashi T, Araki K, Harimoto N, Tokunaga F, Shirabe K. RNF31 promotes proliferation and invasion of hepatocellular carcinoma via nuclear factor kappaB activation. Sci Rep 2024; 14:346. [PMID: 38172174 PMCID: PMC10764851 DOI: 10.1038/s41598-023-50594-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
RNF31 is a multifunctional RING finger protein implicated in various inflammatory diseases and cancers. It functions as a core component of the linear ubiquitin chain assembly complex (LUBAC), which activates the nuclear factor kappaB (NF-κB) pathway via the generation of the Met1-linked linear ubiquitin chain. We aimed to clarify the role of RNF31 in the pathogenesis of hepatocellular carcinoma (HCC) and its relevance as a therapeutic target. High RNF31 expression in HCC, assessed by both immunohistochemistry and mRNA levels, was related to worse survival rates among patients with HCC. In vitro experiments showed that RNF31 knockdown in HCC cell lines led to decreased cell proliferation and invasion, as well as suppression of tumor necrosis factor (TNF)-α-induced NF-κB activation. Treatment with HOIPIN-8, a specific LUBAC inhibitor that suppresses RNF31 ubiquitin ligase (E3) activity, showed similar effects, resulting in decreased cell proliferation and invasion. Our clinical and in vitro data showed that RNF31 is a prognostic factor for HCC that promotes tumor aggressiveness via NF-κB activation.
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Affiliation(s)
- Kouki Hoshino
- Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan
| | - Seshiru Nakazawa
- Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan.
| | | | - Kei Hagiwara
- Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan
| | - Norihiro Ishii
- Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan
| | - Mariko Tsukagoshi
- Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan
| | - Takamichi Igarashi
- Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan
| | - Kenichiro Araki
- Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan
| | - Norifumi Harimoto
- Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan
| | - Fuminori Tokunaga
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Ken Shirabe
- Department of General Surgical Science, Gunma University Graduate School of Medicine, 3-39-22 Showa-machi, Maebashi, 371-8511, Japan
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22
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Altas B, Rhee HJ, Ju A, Solís HC, Karaca S, Winchenbach J, Kaplan-Arabaci O, Schwark M, Ambrozkiewicz MC, Lee C, Spieth L, Wieser GL, Chaugule VK, Majoul I, Hassan MA, Goel R, Wojcik SM, Koganezawa N, Hanamura K, Rotin D, Pichler A, Mitkovski M, de Hoz L, Poulopoulos A, Urlaub H, Jahn O, Saher G, Brose N, Rhee J, Kawabe H. Nedd4-2-dependent regulation of astrocytic Kir4.1 and Connexin43 controls neuronal network activity. J Cell Biol 2024; 223:e201902050. [PMID: 38032389 PMCID: PMC10689203 DOI: 10.1083/jcb.201902050] [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: 02/14/2019] [Revised: 10/21/2021] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
Nedd4-2 is an E3 ubiquitin ligase in which missense mutation is related to familial epilepsy, indicating its critical role in regulating neuronal network activity. However, Nedd4-2 substrates involved in neuronal network function have yet to be identified. Using mouse lines lacking Nedd4-1 and Nedd4-2, we identified astrocytic channel proteins inwardly rectifying K+ channel 4.1 (Kir4.1) and Connexin43 as Nedd4-2 substrates. We found that the expression of Kir4.1 and Connexin43 is increased upon conditional deletion of Nedd4-2 in astrocytes, leading to an elevation of astrocytic membrane ion permeability and gap junction activity, with a consequent reduction of γ-oscillatory neuronal network activity. Interestingly, our biochemical data demonstrate that missense mutations found in familial epileptic patients produce gain-of-function of the Nedd4-2 gene product. Our data reveal a process of coordinated astrocytic ion channel proteostasis that controls astrocyte function and astrocyte-dependent neuronal network activity and elucidate a potential mechanism by which aberrant Nedd4-2 function leads to epilepsy.
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Affiliation(s)
- Bekir Altas
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- International Max Planck Research School and the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, Göttingen, Germany
- The Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, PhD Program Systems Neuroscience, University of Göttingen, Göttingen, Germany
- Department of Pharmacology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Hong-Jun Rhee
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Anes Ju
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- The Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, PhD Program Systems Neuroscience, University of Göttingen, Göttingen, Germany
| | - Hugo Cruces Solís
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- International Max Planck Research School and the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, Göttingen, Germany
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Samir Karaca
- International Max Planck Research School and the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, Göttingen, Germany
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Jan Winchenbach
- The Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, PhD Program Systems Neuroscience, University of Göttingen, Göttingen, Germany
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Oykum Kaplan-Arabaci
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- The Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, PhD Program Molecular Physiology of the Brain, University of Göttingen, Göttingen, Germany
| | - Manuela Schwark
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Mateusz C. Ambrozkiewicz
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- International Max Planck Research School and the Göttingen Graduate School for Neurosciences, Biophysics and Molecular Biosciences, Göttingen, Germany
- Institute of Cell Biology and Neurobiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - ChungKu Lee
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Lena Spieth
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Georg L. Wieser
- City Campus Light Microscopy Facility, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Viduth K. Chaugule
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Irina Majoul
- Institute of Biology, Center for Structural and Cell Biology in Medicine, University of Lübeck, Lübeck, Germany
| | - Mohamed A. Hassan
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute (GEBRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, Egypt
| | - Rashi Goel
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Sonja M. Wojcik
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Noriko Koganezawa
- Department of Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kenji Hanamura
- Department of Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Daniela Rotin
- The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Miso Mitkovski
- City Campus Light Microscopy Facility, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Livia de Hoz
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Alexandros Poulopoulos
- Department of Pharmacology and Program in Neuroscience, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Olaf Jahn
- Department of Molecular Neurobiology, Neuroproteomics Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Psychiatry and Psychotherapy, Translational Neuroproteomics Group, University Medical Center Göttingen, Göttingen, Germany
| | - Gesine Saher
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - JeongSeop Rhee
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Hiroshi Kawabe
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Department of Pharmacology, Gunma University Graduate School of Medicine, Maebashi, Japan
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe, Japan
- Department of Gerontology, Laboratory of Molecular Life Science, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
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23
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Teague HC, Lefevre C, Rieser E, Wolfram L, de Miguel D, Patricio de Oliveira D, Oliveira M, Mansur DS, Irigoyen N, Walczak H, Ferguson BJ. LUBAC is required for RIG-I sensing of RNA viruses. Cell Death Differ 2024; 31:28-39. [PMID: 38001254 PMCID: PMC10781740 DOI: 10.1038/s41418-023-01233-x] [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: 02/22/2022] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 11/26/2023] Open
Abstract
The ability of cells to mount an interferon response to virus infections depends on intracellular nucleic acid sensing pattern recognition receptors (PRRs). RIG-I is an intracellular PRR that binds short double-stranded viral RNAs to trigger MAVS-dependent signalling. The RIG-I/MAVS signalling complex requires the coordinated activity of multiple kinases and E3 ubiquitin ligases to activate the transcription factors that drive type I and type III interferon production from infected cells. The linear ubiquitin chain assembly complex (LUBAC) regulates the activity of multiple receptor signalling pathways in both ligase-dependent and -independent ways. Here, we show that the three proteins that constitute LUBAC have separate functions in regulating RIG-I signalling. Both HOIP, the E3 ligase capable of generating M1-ubiquitin chains, and LUBAC accessory protein HOIL-1 are required for viral RNA sensing by RIG-I. The third LUBAC component, SHARPIN, is not required for RIG-I signalling. These data cement the role of LUBAC as a positive regulator of RIG-I signalling and as an important component of antiviral innate immune responses.
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Affiliation(s)
- Helena C Teague
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Charlotte Lefevre
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Eva Rieser
- Centre for Cell Death, Cancer and inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London, UK
- Centre for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, Cologne, Germany
| | - Lina Wolfram
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Diego de Miguel
- Centre for Cell Death, Cancer and inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London, UK
- Centre for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, Cologne, Germany
| | - Daniel Patricio de Oliveira
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Marisa Oliveira
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Daniel S Mansur
- Departamento de Microbiologia, Imunologia e Parasitologia, Centro de Ciências Biológicas, Universidade Federal de Santa Catarina (UFSC), Florianópolis, SC, Brazil
| | - Nerea Irigoyen
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Henning Walczak
- Centre for Cell Death, Cancer and inflammation (CCCI), UCL Cancer Institute, University College London, 72 Huntley Street, London, UK
- Centre for Biochemistry, Medical Faculty, University of Cologne, Joseph-Stelzmann-Str. 52, Cologne, Germany
| | - Brian J Ferguson
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, UK.
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24
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Santacroce L, Magrone T. Molluscum Contagiosum Virus: Biology and Immune Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1451:151-170. [PMID: 38801577 DOI: 10.1007/978-3-031-57165-7_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: 05/29/2024]
Abstract
Molluscum contagiosum virus is a poxvirus belonging to the Poxviridae family, which includes Orthopoxvirus, Parapoxvirus, Yantapoxvirus, Molluscipoxvirus, Smallpox virus, Cowpox virus and Monkeypox virus. MCV belongs to the genus Molluscipoxvirus and has a tropism for skin tissue. MCV infects keratinocytes and, after an incubation period of 2 weeks to 6 weeks, causes a breakdown of the skin barrier with the development of papules of variable size depending on the proper functioning of the immune response (both adaptive and acquired). MCV only infects humans and does not cause viraemia. MCV encodes for several inhibitory proteins responsible to circumvent the immune response through different signalling pathways. Individuals who can be infected with MCV are children, immunocompromised individuals such as organ transplant recipients and Human Immunodeficiency Virus (HIV)-infected individuals. Current treatments to manage MCV-induced lesions are different and include the use of immunomodulators, which, however, do not provide an effective response.
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Affiliation(s)
- Luigi Santacroce
- Section of Microbiology and Virology, Interdisciplinary Department of Medicine, School of Medicine, University of Bari, Bari, Italy.
| | - Thea Magrone
- Section of Microbiology and Virology, Interdisciplinary Department of Medicine, School of Medicine, University of Bari, Bari, Italy
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25
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Zhang Y, Xu X, Wang Y, Wang Y, Zhou X, Pan L. Mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN. Biochem Biophys Res Commun 2023; 689:149239. [PMID: 37976837 DOI: 10.1016/j.bbrc.2023.149239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/28/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
HOIL-1L and SHARPIN are two essential regulatory subunits of the linear ubiquitin chain assembly complex (LUBAC), which is the only known E3 ligase complex generating linear ubiquitin chains. In addition to their LUBAC-dependent functions, HOIL-1L and SHARPIN alone play crucial roles in many LUBAC-independent cellular processes. Importantly, deficiency of HOIL-1L or SHARPIN leads to severe disorders in humans or mice. However, the mechanistic bases underlying the multi-functions of HOIL-1L and SHARPIN are still largely unknown. Here, we uncover that HOIL-1L and SHARPIN alone can form homo-dimers through their LTM motifs. We solve two crystal structures of the dimeric LTM motifs of HOIL-1L and SHARPIN, which not only elucidate the detailed molecular mechanism underpinning the dimer formations of HOIL-1L and SHARPIN, but also reveal a general mode shared by the LTM motifs of HOIL-1L and SHARPIN for forming homo-dimer or hetero-dimer. Furthermore, we elucidate that the polyglucosan body myopathy-associated HOIL-1L A18P mutation disturbs the structural folding of HOIL-1L LTM, and disrupts the dimer formation of HOIL-1L. In summary, our study provides mechanistic insights into the homo-dimerization of HOIL-1L and SHARPIN mediated by their LTM motifs, and expands our understandings of the multi-functions of HOIL-1L and SHARPIN as well as the etiology of relevant human disease caused by defective HOIL-1L.
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Affiliation(s)
- Yan Zhang
- Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaolong Xu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yaru Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China
| | - Yingli Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xindi Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lifeng Pan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, China.
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26
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Spano D, Catara G. Targeting the Ubiquitin-Proteasome System and Recent Advances in Cancer Therapy. Cells 2023; 13:29. [PMID: 38201233 PMCID: PMC10778545 DOI: 10.3390/cells13010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/12/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Ubiquitination is a reversible post-translational modification based on the chemical addition of ubiquitin to proteins with regulatory effects on various signaling pathways. Ubiquitination can alter the molecular functions of tagged substrates with respect to protein turnover, biological activity, subcellular localization or protein-protein interaction. As a result, a wide variety of cellular processes are under ubiquitination-mediated control, contributing to the maintenance of cellular homeostasis. It follows that the dysregulation of ubiquitination reactions plays a relevant role in the pathogenic states of human diseases such as neurodegenerative diseases, immune-related pathologies and cancer. In recent decades, the enzymes of the ubiquitin-proteasome system (UPS), including E3 ubiquitin ligases and deubiquitinases (DUBs), have attracted attention as novel druggable targets for the development of new anticancer therapeutic approaches. This perspective article summarizes the peculiarities shared by the enzymes involved in the ubiquitination reaction which, when deregulated, can lead to tumorigenesis. Accordingly, an overview of the main pharmacological interventions based on targeting the UPS that are in clinical use or still in clinical trials is provided, also highlighting the limitations of the therapeutic efficacy of these approaches. Therefore, various attempts to circumvent drug resistance and side effects as well as UPS-related emerging technologies in anticancer therapeutics are discussed.
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Affiliation(s)
- Daniela Spano
- Institute for Endocrinology and Experimental Oncology “G. Salvatore”, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuliana Catara
- Institute of Biochemistry and Cell Biology, National Research Council, Via Pietro Castellino 111, 80131 Naples, Italy
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27
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Furthmann N, Bader V, Angersbach L, Blusch A, Goel S, Sánchez-Vicente A, Krause LJ, Chaban SA, Grover P, Trinkaus VA, van Well EM, Jaugstetter M, Tschulik K, Damgaard RB, Saft C, Ellrichmann G, Gold R, Koch A, Englert B, Westenberger A, Klein C, Jungbluth L, Sachse C, Behrends C, Glatzel M, Hartl FU, Nakamura K, Christine CW, Huang EJ, Tatzelt J, Winklhofer KF. NEMO reshapes the α-Synuclein aggregate interface and acts as an autophagy adapter by co-condensation with p62. Nat Commun 2023; 14:8368. [PMID: 38114471 PMCID: PMC10730909 DOI: 10.1038/s41467-023-44033-0] [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: 02/08/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
NEMO is a ubiquitin-binding protein which regulates canonical NF-κB pathway activation in innate immune signaling, cell death regulation and host-pathogen interactions. Here we identify an NF-κB-independent function of NEMO in proteostasis regulation by promoting autophagosomal clearance of protein aggregates. NEMO-deficient cells accumulate misfolded proteins upon proteotoxic stress and are vulnerable to proteostasis challenges. Moreover, a patient with a mutation in the NEMO-encoding IKBKG gene resulting in defective binding of NEMO to linear ubiquitin chains, developed a widespread mixed brain proteinopathy, including α-synuclein, tau and TDP-43 pathology. NEMO amplifies linear ubiquitylation at α-synuclein aggregates and promotes the local concentration of p62 into foci. In vitro, NEMO lowers the threshold concentrations required for ubiquitin-dependent phase transition of p62. In summary, NEMO reshapes the aggregate surface for efficient autophagosomal clearance by providing a mobile phase at the aggregate interphase favoring co-condensation with p62.
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Affiliation(s)
- Nikolas Furthmann
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Lena Angersbach
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Alina Blusch
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
| | - Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Ana Sánchez-Vicente
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Cluster of Excellence RESOLV, 44801, Bochum, Germany
| | - Sarah A Chaban
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Prerna Grover
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Victoria A Trinkaus
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Eva M van Well
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Maximilian Jaugstetter
- Analytical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Kristina Tschulik
- Cluster of Excellence RESOLV, 44801, Bochum, Germany
- Analytical Chemistry II, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801, Bochum, Germany
| | - Rune Busk Damgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Carsten Saft
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
| | - Gisa Ellrichmann
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
- Department of Neurology, Klinikum Dortmund, University Witten/Herdecke, 44135, Dortmund, Germany
| | - Ralf Gold
- Department of Neurology, St Josef Hospital, Ruhr University Bochum, 44791, Bochum, Germany
| | - Arend Koch
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, 10117, Berlin, Germany
| | - Benjamin Englert
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Neuropathology, Charitéplatz 1, 10117, Berlin, Germany
- Center for Neuropathology and Prion Research, Ludwig-Maximilians University, 81377, Munich, Germany
| | - Ana Westenberger
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Lisa Jungbluth
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Information Processing (IBI-6/Cellular Structural Biology), Forschungszentrum Jülich, Jülich, Germany
| | - Carsten Sachse
- Ernst-Ruska Centre for Microscopy and Spectroscopy with Electrons (ER-C-3/Structural Biology), Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Information Processing (IBI-6/Cellular Structural Biology), Forschungszentrum Jülich, Jülich, Germany
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251, Hamburg, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Munich Cluster for Systems Neurology (SyNergy), 81377, Munich, Germany
| | - Ken Nakamura
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Chadwick W Christine
- Department of Neurology, University of California, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Huang
- Department of Neurology, University of California, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, CA, USA
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany
- Cluster of Excellence RESOLV, 44801, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, 44801, Bochum, Germany.
- Cluster of Excellence RESOLV, 44801, Bochum, Germany.
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28
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Hartley VL, Qaqish AM, Wood MJ, Studnicka BT, Iwai K, Liu TC, MacDuff DA. HOIL1 Regulates Group 3 Innate Lymphoid Cells in the Colon and Protects against Systemic Dissemination, Colonic Ulceration, and Lethality from Citrobacter rodentium Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1823-1834. [PMID: 37902285 PMCID: PMC10841105 DOI: 10.4049/jimmunol.2300351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/19/2023] [Indexed: 10/31/2023]
Abstract
Heme-oxidized IRP2 ubiquitin ligase-1 (HOIL1)-deficient patients experience chronic intestinal inflammation and diarrhea as well as increased susceptibility to bacterial infections. HOIL1 is a component of the linear ubiquitin chain assembly complex that regulates immune signaling pathways, including NF-κB-activating pathways. We have shown previously that HOIL1 is essential for survival following Citrobacter rodentium gastrointestinal infection of mice, but the mechanism of protection by HOIL1 was not examined. C. rodentium is an important murine model for human attaching and effacing pathogens, enteropathogenic and enterohemorrhagic Escherichia coli that cause diarrhea and foodborne illnesses and lead to severe disease in children and immunocompromised individuals. In this study, we found that C. rodentium infection resulted in severe colitis and dissemination of C. rodentium to systemic organs in HOIL1-deficient mice. HOIL1 was important in the innate immune response to limit early replication and dissemination of C. rodentium. Using bone marrow chimeras and cell type-specific knockout mice, we found that HOIL1 functioned in radiation-resistant cells and partly in radiation-sensitive cells and in myeloid cells to limit disease, but it was dispensable in intestinal epithelial cells. HOIL1 deficiency significantly impaired the expansion of group 3 innate lymphoid cells and their production of IL-22 during C. rodentium infection. Understanding the role HOIL1 plays in type 3 inflammation and in limiting the pathogenesis of attaching and effacing lesion-forming bacteria will provide further insight into the innate immune response to gastrointestinal pathogens and inflammatory disorders.
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Affiliation(s)
- Victoria L Hartley
- Department of Microbiology and Immunology, University of Illinois Chicago College of Medicine, Chicago, IL
| | - Arwa M Qaqish
- Department of Microbiology and Immunology, University of Illinois Chicago College of Medicine, Chicago, IL
| | - Matthew J Wood
- Department of Microbiology and Immunology, University of Illinois Chicago College of Medicine, Chicago, IL
| | - Brian T Studnicka
- Department of Microbiology and Immunology, University of Illinois Chicago College of Medicine, Chicago, IL
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Donna A MacDuff
- Department of Microbiology and Immunology, University of Illinois Chicago College of Medicine, Chicago, IL
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29
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McElrath CJ, Benzow S, Zhuo Y, Marchese A. β-arrestin1 is an E3 ubiquitin ligase adaptor for substrate linear polyubiquitination. J Biol Chem 2023; 299:105474. [PMID: 37981209 PMCID: PMC10755771 DOI: 10.1016/j.jbc.2023.105474] [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: 05/18/2023] [Revised: 10/19/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023] Open
Abstract
G protein-coupled receptor (GPCR) signaling and trafficking are regulated by multiple mechanisms, including posttranslational modifications such as ubiquitination by E3 ubiquitin ligases. E3 ligases have been linked to agonist-stimulated ubiquitination of GPCRs via simultaneous binding to βarrestins. In addition, βarrestins have been suggested to assist E3 ligases for ubiquitination of key effector molecules, yet mechanistic insight is lacking. Here, we developed an in vitro reconstituted system and show that βarrestin1 (βarr1) serves as an adaptor between the effector protein signal-transducing adaptor molecule 1 (STAM1) and the E3 ligase atrophin-interacting protein 4. Via mass spectrometry, we identified seven lysine residues within STAM1 that are ubiquitinated and several types of ubiquitin linkages. We provide evidence that βarr1 facilitates the formation of linear polyubiquitin chains at lysine residue 136 on STAM1. This lysine residue is important for stabilizing the βarr1:STAM1 interaction in cells following GPCR activation. Our study identifies atrophin-interacting protein 4 as only the second E3 ligase known to conjugate linear polyubiquitin chains and a possible role for linear ubiquitin chains in GPCR signaling and trafficking.
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Affiliation(s)
- Chandler J McElrath
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Sara Benzow
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Ya Zhuo
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Adriano Marchese
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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30
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Wang P, Tang CT, Li J, Huang X, Jin R, Yin F, Liu Z, Chen Y, Zeng C. The E3 ubiquitin ligase RNF31 mediates the development of ulcerative colitis by regulating NLRP3 inflammasome activation. Int Immunopharmacol 2023; 125:111194. [PMID: 37951199 DOI: 10.1016/j.intimp.2023.111194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/04/2023] [Accepted: 11/05/2023] [Indexed: 11/13/2023]
Abstract
Ulcerative colitis (UC) is characterized by dysregulated inflammation and disruption of the intestinal barrier. The NLRP3 inflammasome, which is composed of NLRP3, ASC, and caspase-1, plays a crucial role in UC pathogenesis by triggering the production of proinflammatory cytokines. In this study, we investigated the regulatory role of RNF31 in NLRP3 inflammasome activation during UC development. Through comprehensive analysis of ulcerative colitis tissues using the GEO database and immunohistochemistry, we found that RNF31 expression was elevated in UC tissues, which prompted further investigation into its function. We constructed an RNF31 knockdown cell model and observed a significant reduction in NLRP3 inflammasome activation, indicating the involvement of RNF31 in regulating NLRP3. Mechanistically, RNF31 could interact with NLRP3 through the RBR structural domain, leading to increased K63-linked ubiquitination of NLRP3 and consequent stabilization. Coimmunoprecipitation experiments revealed a mutual interaction between RNF31 and NLRP3, substantiating their functional association. Finally, an in vivo mouse model with RNF31 knockdown showed a notable reduction in NLRP3 expression, which was accompanied by a decrease in the proinflammatory cytokines IL-18 and IL-1β. The successful attenuation of DSS-induced tissue inflammation by this treatment confirmed the physiological relevance of RNF31-mediated regulation of NLRP3. This study unveils a novel regulatory pathway by which RNF31 affects NLRP3 inflammasome activation, providing new insights into UC pathogenesis and potential therapeutic targets for UC treatment.
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Affiliation(s)
- Peng Wang
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Chao-Tao Tang
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China; Jiangxi Clinical Research Center for Gastroenterology, Nanchang, Jiangxi, China
| | - Jun Li
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xia Huang
- The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Ruiri Jin
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Fang Yin
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Zide Liu
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Youxiang Chen
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China; Jiangxi Clinical Research Center for Gastroenterology, Nanchang, Jiangxi, China
| | - Chunyan Zeng
- Department of Gastroenterology, Digestive Disease Hospital, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China; Jiangxi Clinical Research Center for Gastroenterology, Nanchang, Jiangxi, China.
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31
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Li J, Liu S, Li S. Mechanisms underlying linear ubiquitination and implications in tumorigenesis and drug discovery. Cell Commun Signal 2023; 21:340. [PMID: 38017534 PMCID: PMC10685518 DOI: 10.1186/s12964-023-01239-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/19/2023] [Indexed: 11/30/2023] Open
Abstract
Linear ubiquitination is a distinct type of ubiquitination that involves attaching a head-to-tail polyubiquitin chain to a substrate protein. Early studies found that linear ubiquitin chains are essential for the TNFα- and IL-1-mediated NF-κB signaling pathways. However, recent studies have discovered at least sixteen linear ubiquitination substrates, which exhibit a broader activity than expected and mediate many other signaling pathways beyond NF-κB signaling. Dysregulation of linear ubiquitination in these pathways has been linked to many types of cancers, such as lymphoma, liver cancer, and breast cancer. Since the discovery of linear ubiquitin, extensive effort has been made to delineate the molecular mechanisms of how dysregulation of linear ubiquitination causes tumorigenesis and cancer development. In this review, we highlight newly discovered linear ubiquitination-mediated signaling pathways, recent advances in the role of linear ubiquitin in different types of cancers, and the development of linear ubiquitin inhibitors. Video Abstract.
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Affiliation(s)
- Jack Li
- Department of Biosciences, Rice University, Houston, TX, 77005, USA
| | - Sijin Liu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, People's Republic of China.
| | - Shitao Li
- Department of Microbiology and Immunology, Tulane University, New Orleans, LA, 70112, USA.
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32
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Sakamaki JI, Mizushima N. Ubiquitination of non-protein substrates. Trends Cell Biol 2023; 33:991-1003. [PMID: 37120410 DOI: 10.1016/j.tcb.2023.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/01/2023]
Abstract
The covalent attachment of ubiquitin is a common regulatory mechanism in various proteins. Although it has long been thought that the substrates of ubiquitination are limited to proteins, recent studies have changed this view: ubiquitin can be conjugated to lipids, sugars, and nucleotides. Ubiquitin is linked to these substrates by the action of different classes of ubiquitin ligases that have distinct catalytic mechanisms. Ubiquitination of non-protein substrates likely serves as a signal for the recruitment of other proteins to bring about specific effects. These discoveries have expanded the concept of ubiquitination and have advanced our insight into the biology and chemistry of this well-established modification process. In this review we describe the molecular mechanisms and roles of non-protein ubiquitination and discuss the current limitations.
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Affiliation(s)
- Jun-Ichi Sakamaki
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan.
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Kadirvelu J, Jacobs SE, Liu R, Charles AJ, Yin J, Mabb AM. The E3 ubiquitin ligase RNF216 contains a linear ubiquitin chain-determining-like domain that functions to regulate dendritic arborization and dendritic spine type in hippocampal neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563080. [PMID: 37905043 PMCID: PMC10614953 DOI: 10.1101/2023.10.19.563080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Of the hundreds of E3 ligases found in the human genome, the RING-between RING (RBR) E3 ligase in the LUBAC (linear ubiquitin chain assembly complex) complex HOIP (HOIL-1-interacting protein or RNF31), contains a unique domain called LDD (linear ubiquitin chain determining domain). HOIP is the only E3 ligase known to form linear ubiquitin chains, which regulate inflammatory responses and cell death via activation of the NF-κB pathway. We identified an amino acid sequence within the RNF216 E3 ligase that shares homology to the LDD domain found in HOIP (R2-C). Here, we show that the R2-C domain of RNF216 promotes self-assembly of all ubiquitin chains, with a dominance for those assembled via K63-linkages. Deletion of the R2-C domain altered RNF216 localization, reduced dendritic complexity and changed the distribution of apical dendritic spine morphology types in primary hippocampal neurons. These changes were independent of the RNF216 RBR catalytic activity as expression of a catalytic inactive version of RNF216 had no effect. These data show that the R2-C domain of RNF216 diverges in ubiquitin assembly function from the LDD of HOIP and and functions independently of RNF216 catalytic activity to regulate dendrite development in neurons.
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Affiliation(s)
- Jayashree Kadirvelu
- Neuroscience Institute, Georgia State University, 100 Piedmont Ave., Atlanta, GA 30302, United States
- Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA, 30303, United States
| | - Savannah E. Jacobs
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, United States
| | - Ruochuan Liu
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, United States
| | - Antoinette J. Charles
- Neuroscience Institute, Georgia State University, 100 Piedmont Ave., Atlanta, GA 30302, United States
- Center for Behavioral Neuroscience, Georgia State University, Atlanta, GA, 30303, United States
| | - Jun Yin
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, United States
| | - Angela M. Mabb
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, United States
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Fischer TD, Bunker EN, Zhu PP, Le Guerroué F, Dominguez-Martin E, Scavone F, Cohen R, Yao T, Wang Y, Werner A, Youle RJ. STING induces LUBAC-mediated synthesis of linear ubiquitin chains to stimulate innate immune signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.14.562349. [PMID: 37873486 PMCID: PMC10592814 DOI: 10.1101/2023.10.14.562349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
STING activation by cyclic dinucleotides in mammals induces interferon- and NFκB -related gene expression, and the lipidation of LC3B at Golgi membranes. While mechanisms of the interferon response are well understood, the mechanisms of NFκB activation mediated by STING remain unclear. We report that STING activation induces K63- and M1-linked/linear ubiquitin chain formation at LC3B-associated Golgi membranes. Loss of the LUBAC E3 ubiquitin ligase prevents formation of linear, but not K63-linked ubiquitin chains or STING activation and inhibits STING-induced NFκB and IRF3-mediated signaling in monocytic THP1 cells. The proton channel activity of STING is also important for both K63 and linear ubiquitin chain formation, and NFκB- and interferon-related gene expression. Thus, LUBAC synthesis of linear ubiquitin chains regulates STING-mediated innate immune signaling.
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Affiliation(s)
- Tara D. Fischer
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Eric N. Bunker
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Peng-Peng Zhu
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - François Le Guerroué
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Eunice Dominguez-Martin
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
| | - Francesco Scavone
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO, USA
| | - Robert Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO, USA
| | - Tingting Yao
- Department of Biochemistry and Molecular Biology, Colorado State University; Fort Collins, CO, USA
| | - Yan Wang
- Mass Spectrometry, National Institute of Dental and Craniofacial Research, National Institutes of Health; Bethesda, MD, USA
| | - Achim Werner
- Stem Cell Biochemistry Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health; Bethesda, MD, USA
| | - Richard J. Youle
- Biochemistry Section, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health; Bethesda, MD, USA
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35
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Xu Y, Zheng C, Ashaq MS, Zhou Q, Li Y, Lu C, Zhao B. Regulatory role of E3 ubiquitin ligases in normal B lymphopoiesis and B-cell malignancies. Life Sci 2023; 331:122043. [PMID: 37633415 DOI: 10.1016/j.lfs.2023.122043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/14/2023] [Accepted: 08/23/2023] [Indexed: 08/28/2023]
Abstract
E3 ubiquitin ligases play an essential role in protein ubiquitination, which is involved in the regulation of protein degradation, protein-protein interactions and signal transduction. Increasing evidences have shed light on the emerging roles of E3 ubiquitin ligases in B-cell development and related malignances. This comprehensive review summarizes the current understanding of E3 ubiquitin ligases in B-cell development and their contribution to B-cell malignances, which could help explore the molecular mechanism of normal B-cell development and provide potential therapeutic targets of the related diseases.
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Affiliation(s)
- Yan Xu
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Chengzu Zheng
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Muhammad Sameer Ashaq
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Qian Zhou
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Yuan Li
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Chunhua Lu
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Baobing Zhao
- Key Lab of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pharmacology, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
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36
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Guo J, Sun D, Zhang J, Guo J, Wu Z, Chen Y, Xu Y, Zhou D, Cui Y, Mo Q, Li Y, Zhao T, You Q. The E3 ubiquitin ligase RBCK1: Implications in the tumor immune microenvironment and antiangiogenic therapy of glioma. Comput Struct Biotechnol J 2023; 21:5212-5227. [PMID: 37928949 PMCID: PMC10624590 DOI: 10.1016/j.csbj.2023.10.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023] Open
Abstract
E3 ubiquitin ligases (E3s) play a pivotal role in regulating the specificity of protein ubiquitination, and their significant functions as regulators of immune responses against tumors are attracting considerable interest. RBCK1-an RBR E3 ligase-is involved in immune regulation and tumor development. However, the potential effect of RBCK1 on glioma remains enigmatic. In the present study, we performed comprehensive analyses of multilevel data, which disclosed distribution characteristics of RBCK1 in pan-cancer, especially in glioma. Functional roles of RBCK1 were further confirmed using immunohistochemistry, cell biological assays, and xenograft experiments. Aberrant ascending of RBCK1 in multiple types of cancer was found to remodel the immunosuppressive microenvironment of glioma by regulating immunomodulators, cancer immunity cycles, and immune cell infiltration. Notably, the MES-like/RBCK1High cell population, a unique subset of cells in the microenvironment, suppressed T cell-mediated cell killing in glioma. Elevated expression levels of RBCK1 suggested a glioma subtype characterized by immunosuppression and hypo-responsiveness to immunotherapy but manifesting surprisingly increased responses to anti-angiogenic therapy. In conclusion, anti-RBCK1 target therapy might be beneficial for glioma treatment. Moreover, RBCK1 assisted in predicting molecular subtypes of glioma and response rates of patients to different clinical treatments, which could guide personalized therapy.
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Affiliation(s)
- Jing Guo
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Donglin Sun
- Department of Urology, Shenzhen Hospital, Southern Medical University, Shenzhen 518100, China
| | - Junwei Zhang
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Jie Guo
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Zhenpeng Wu
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yongzhen Chen
- Department of Biotherapy, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
| | - Yujie Xu
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Desheng Zhou
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yachao Cui
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Qi Mo
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Yingchang Li
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Ting Zhao
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Qiang You
- Affiliated Cancer Hospital & Institute, Guangzhou Medical University, 78 Hengzhigang Road, Guangzhou 510095, China
- Key Laboratory of Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou Medical University, Guangzhou 510182, China
- Center for Cancer and Immunology Research, State Key Laboratory of Respiratory Disease, Guangzhou, China
- Department of Biotherapy, Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, China
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Xu X, Wang Y, Zhang Y, Wang Y, Yin Y, Peng C, Gong X, Li M, Zhang Y, Zhang M, Tang Y, Zhou X, Liu H, Pan L. Mechanistic insights into the enzymatic activity of E3 ligase HOIL-1L and its regulation by the linear ubiquitin chain binding. SCIENCE ADVANCES 2023; 9:eadi4599. [PMID: 37831767 PMCID: PMC10575588 DOI: 10.1126/sciadv.adi4599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/11/2023] [Indexed: 10/15/2023]
Abstract
Heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1L) serves as a unique E3 ligase to catalyze the mono-ubiquitination of relevant protein or sugar substrates and plays vital roles in numerous cellular processes in mammals. However, the molecular mechanism underpinning the E3 activity of HOIL-1L and the related regulatory mechanism remain elusive. Here, we report the crystal structure of the catalytic core region of HOIL-1L and unveil the key catalytic triad residues of HOIL-1L. Moreover, we discover that HOIL-1L contains two distinct linear di-ubiquitin binding sites that can synergistically bind to linear tetra-ubiquitin, and the binding of HOIL-1L with linear tetra-ubiquitin can promote its E3 activity. The determined HOIL-1L/linear tetra-ubiquitin complex structure not only elucidates the detailed binding mechanism of HOIL-1L with linear tetra-ubiquitin but also uncovers a unique allosteric ubiquitin-binding site for the activation of HOIL-1L. In all, our findings provide mechanistic insights into the E3 activity of HOIL-1L and its regulation by the linear ubiquitin chain binding.
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Affiliation(s)
- Xiaolong Xu
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yaru Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yan Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Chemistry, College of Science, Shanghai University, Shanghai 200444, China
| | - Yingli Wang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yue Yin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Xinyu Gong
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Miao Li
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
| | - Yuchao Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mingfang Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yubin Tang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xindi Zhou
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Haobo Liu
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lifeng Pan
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou 310024, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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Cao F, Deliz‐Aguirre R, Gerpott FHU, Ziska E, Taylor MJ. Myddosome clustering in IL-1 receptor signaling regulates the formation of an NF-kB activating signalosome. EMBO Rep 2023; 24:e57233. [PMID: 37602973 PMCID: PMC10561168 DOI: 10.15252/embr.202357233] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/22/2023] Open
Abstract
IL-1 receptor (IL-1R) signaling can activate thresholded invariant outputs and proportional outputs that scale with the amount of stimulation. Both responses require the Myddosome, a multiprotein complex. The Myddosome is required for polyubiquitin chain formation and NF-kB signaling. However, how these signals are spatially and temporally regulated to drive switch-like and proportional outcomes is not understood. During IL-1R signaling, Myddosomes dynamically reorganize into multi-Myddosome clusters at the cell membrane. Blockade of clustering using nanoscale extracellular barriers reduces NF-kB activation. Myddosomes function as scaffolds that assemble an NF-kB signalosome consisting of E3-ubiquitin ligases TRAF6 and LUBAC, K63/M1-linked polyubiquitin chains, phospho-IKK, and phospho-p65. This signalosome preferentially assembles at regions of high Myddosome density, which enhances the recruitment of TRAF6 and LUBAC. Extracellular barriers that restrict Myddosome clustering perturbed the recruitment of both ligases. We find that LUBAC was especially sensitive to clustering with 10-fold lower recruitment to single Myddosomes than clustered Myddosomes. These data reveal that the clustering behavior of Myddosomes provides a basis for digital and analog IL-1R signaling.
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Affiliation(s)
- Fakun Cao
- Max Planck Institute for Infection BiologyBerlinGermany
| | | | | | - Elke Ziska
- Max Planck Institute for Infection BiologyBerlinGermany
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Patrick MB, Omar N, Werner CT, Mitra S, Jarome TJ. The ubiquitin-proteasome system and learning-dependent synaptic plasticity - A 10 year update. Neurosci Biobehav Rev 2023; 152:105280. [PMID: 37315660 PMCID: PMC11323321 DOI: 10.1016/j.neubiorev.2023.105280] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 06/16/2023]
Abstract
Over 25 years ago, a seminal paper demonstrated that the ubiquitin-proteasome system (UPS) was involved in activity-dependent synaptic plasticity. Interest in this topic began to expand around 2008 following another seminal paper showing that UPS-mediated protein degradation controlled the "destabilization" of memories following retrieval, though we remained with only a basic understanding of how the UPS regulated activity- and learning-dependent synaptic plasticity. However, over the last 10 years there has been an explosion of papers on this topic that has significantly changed our understanding of how ubiquitin-proteasome signaling regulates synaptic plasticity and memory formation. Importantly, we now know that the UPS controls much more than protein degradation, is involved in plasticity underlying drugs of abuse and that there are significant sex differences in how ubiquitin-proteasome signaling is used for memory storage processes. Here, we aim to provide a critical 10-year update on the role of ubiquitin-proteasome signaling in synaptic plasticity and memory formation, including updated cellular models of how ubiquitin-proteasome activity could be regulating learning-dependent synaptic plasticity in the brain.
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Affiliation(s)
- Morgan B Patrick
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Nour Omar
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Craig T Werner
- Department of Pharmacology and Physiology, Oklahoma State University Center for Health Sciences, Tulsa, OK, USA; National Center for Wellness and Recovery, Oklahoma State University Center for Health Sciences, Tulsa, OK, USA.
| | - Swarup Mitra
- Department of Biomedical Sciences, Joan C Edwards School of Medicine, Marshall University, Huntington, WV, USA.
| | - Timothy J Jarome
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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40
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Almeida SM, Ivantsiv S, Niibori R, Dunham WH, Green BA, Zhao L, Gingras AC, Cordes SP. An interaction between OTULIN and SCRIB uncovers roles for linear ubiquitination in planar cell polarity. Dis Model Mech 2023; 16:dmm049762. [PMID: 37589075 PMCID: PMC10445738 DOI: 10.1242/dmm.049762] [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: 07/12/2022] [Accepted: 07/17/2023] [Indexed: 08/18/2023] Open
Abstract
Planar cell polarity (PCP) plays critical roles in developmental and homeostatic processes. Membrane presentation of PCP complexes containing Van Gogh-like (VANGL) transmembrane proteins is central to PCP and can be directed by the scaffold protein scribble (SCRIB). The role atypical linear ubiquitin (Met1-Ub) chains might play in PCP is unknown. Here, HEK293 cell-based interactomic analyses of the Met1-Ub deubiquitinase OTULIN revealed that OTULIN can interact with SCRIB. Moreover, Met1-Ub chains associated with VANGL2 and PRICKLE1, but not SCRIB, can direct VANGL2 surface presentation. Mouse embryos lacking Otulin showed variable neural tube malformations, including rare open neural tubes, a deficit associated with PCP disruption in mice. In Madin-Darby canine kidney cells, in which the enrichment of VANGL2-GFP proteins at cell-cell contacts represents activated PCP complexes, endogenous OTULIN was recruited to these sites. In the human MDA-MB-231 breast cancer cell model, OTULIN loss caused deficits in Wnt5a-induced filopodia extension and trafficking of transfected HA-VANGL2. Taken together, these findings support a role for linear (de)ubiquitination in PCP signaling. The association of Met1-Ub chains with PCP complex components offers new opportunities for integrating PCP signaling with OTULIN-dependent immune and inflammatory pathways.
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Affiliation(s)
- Stephanie M. Almeida
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sofiia Ivantsiv
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Rieko Niibori
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, ON M5G 1X5, Canada
| | - Wade H. Dunham
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brooke A. Green
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Liang Zhao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sabine P. Cordes
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Ave, Toronto, ON M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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41
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Kim E, Cho H, Lee G, Baek H, Lee IY, Choi EJ. TSG101 Physically Interacts with Linear Ubiquitin Chain Assembly Complex (LUBAC) and Upregulates the TNFα-Induced NF-κB Activation. Mol Cells 2023; 46:430-440. [PMID: 37431163 PMCID: PMC10336271 DOI: 10.14348/molcells.2023.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/21/2023] [Accepted: 03/26/2023] [Indexed: 07/12/2023] Open
Abstract
Linear ubiquitin chain assembly complex (LUBAC) is a ubiquitin E3 ligase complex composed of HOIP, HOIL-1L, and SHARPIN that catalyzes the formation of linear/M1- linked ubiquitin chain. It has been shown to play a pivotal role in the nuclear factor (NF)-κB signaling induced by proinflammatory stimuli. Here, we found that tumor susceptibility gene (TSG101) physically interacts with HOIP, a catalytic component of LUBAC, and potentiates LUBAC activity. Depletion of TSG101 expression by RNA interference decreased TNFα-induced linear ubiquitination and the formation of TNFα receptor 1 signaling complex (TNFRSC). Furthermore, TSG101 facilitated the TNFα-induced stimulation of the NF-κB pathway. Thus, we suggest that TSG101 functions as a positive modulator of HOIP that mediates TNFα-induced NF-κB signaling pathway.
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Affiliation(s)
- Eunju Kim
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Hyunchu Cho
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Gaeul Lee
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Heawon Baek
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - In Young Lee
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Eui-Ju Choi
- Laboratory of Cell Death and Human Diseases, Department of Life Sciences, Korea University, Seoul 02841, Korea
- GNT Science & Technology Center for Health, GNT Pharma Co., Ltd., Yongin 17096, Korea
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42
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Carman LE, Samulevich ML, Aneskievich BJ. Repressive Control of Keratinocyte Cytoplasmic Inflammatory Signaling. Int J Mol Sci 2023; 24:11943. [PMID: 37569318 PMCID: PMC10419196 DOI: 10.3390/ijms241511943] [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: 06/23/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
The overactivity of keratinocyte cytoplasmic signaling contributes to several cutaneous inflammatory and immune pathologies. An important emerging complement to proteins responsible for this overactivity is signal repression brought about by several proteins and protein complexes with the native role of limiting inflammation. The signaling repression by these proteins distinguishes them from transmembrane receptors, kinases, and inflammasomes, which drive inflammation. For these proteins, defects or deficiencies, whether naturally arising or in experimentally engineered skin inflammation models, have clearly linked them to maintaining keratinocytes in a non-activated state or returning cells to a post-inflamed state after a signaling event. Thus, together, these proteins help to resolve acute inflammatory responses or limit the development of chronic cutaneous inflammatory disease. We present here an integrated set of demonstrated or potentially inflammation-repressive proteins or protein complexes (linear ubiquitin chain assembly complex [LUBAC], cylindromatosis lysine 63 deubiquitinase [CYLD], tumor necrosis factor alpha-induced protein 3-interacting protein 1 [TNIP1], A20, and OTULIN) for a comprehensive view of cytoplasmic signaling highlighting protein players repressing inflammation as the needed counterpoints to signal activators and amplifiers. Ebb and flow of players on both sides of this inflammation equation would be of physiological advantage to allow acute response to damage or pathogens and yet guard against chronic inflammatory disease. Further investigation of the players responsible for repressing cytoplasmic signaling would be foundational to developing new chemical-entity pharmacologics to stabilize or enhance their function when clinical intervention is needed to restore balance.
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Affiliation(s)
- Liam E. Carman
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA; (L.E.C.); (M.L.S.)
| | - Michael L. Samulevich
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA; (L.E.C.); (M.L.S.)
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, CT 06269-3092, USA
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43
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Kim Y, Kim EK, Chey Y, Song MJ, Jang HH. Targeted Protein Degradation: Principles and Applications of the Proteasome. Cells 2023; 12:1846. [PMID: 37508510 PMCID: PMC10378610 DOI: 10.3390/cells12141846] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The proteasome is a multi-catalytic protease complex that is involved in protein quality control via three proteolytic activities (i.e., caspase-, trypsin-, and chymotrypsin-like activities). Most cellular proteins are selectively degraded by the proteasome via ubiquitination. Moreover, the ubiquitin-proteasome system is a critical process for maintaining protein homeostasis. Here, we briefly summarize the structure of the proteasome, its regulatory mechanisms, proteins that regulate proteasome activity, and alterations to proteasome activity found in diverse diseases, chemoresistant cells, and cancer stem cells. Finally, we describe potential therapeutic modalities that use the ubiquitin-proteasome system.
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Affiliation(s)
- Yosup Kim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Eun-Kyung Kim
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Yoona Chey
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Min-Jeong Song
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
| | - Ho Hee Jang
- Department of Biochemistry, College of Medicine, Gachon University, Incheon 21999, Republic of Korea
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon 21999, Republic of Korea
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea
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44
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Ito Y, Pan D, Zhang W, Zhang X, Juan TY, Pyrdol JW, Kyrysyuk O, Doench JG, Liu XS, Wucherpfennig KW. Addressing Tumor Heterogeneity by Sensitizing Resistant Cancer Cells to T cell-Secreted Cytokines. Cancer Discov 2023; 13:1186-1209. [PMID: 36811466 PMCID: PMC10164097 DOI: 10.1158/2159-8290.cd-22-1125] [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: 10/07/2022] [Revised: 01/21/2023] [Accepted: 02/14/2023] [Indexed: 02/24/2023]
Abstract
Tumor heterogeneity is a major barrier to cancer therapy, including immunotherapy. Activated T cells can efficiently kill tumor cells following recognition of MHC class I (MHC-I)-bound peptides, but this selection pressure favors outgrowth of MHC-I-deficient tumor cells. We performed a genome-scale screen to discover alternative pathways for T cell-mediated killing of MHC-I-deficient tumor cells. Autophagy and TNF signaling emerged as top pathways, and inactivation of Rnf31 (TNF signaling) and Atg5 (autophagy) sensitized MHC-I-deficient tumor cells to apoptosis by T cell-derived cytokines. Mechanistic studies demonstrated that inhibition of autophagy amplified proapoptotic effects of cytokines in tumor cells. Antigens from apoptotic MHC-I-deficient tumor cells were efficiently cross-presented by dendritic cells, resulting in heightened tumor infiltration by IFNγ-and TNFα-producing T cells. Tumors with a substantial population of MHC-I-deficient cancer cells could be controlled by T cells when both pathways were targeted using genetic or pharmacologic approaches. SIGNIFICANCE Tumor heterogeneity is a major barrier to immunotherapy. We show that MHC-I-deficient tumor cells are forced into apoptosis by T cell-derived cytokines when TNF signaling and autophagy pathways are targeted. This approach enables T cell-mediated elimination of tumors with a substantial population of resistant, MHC-I-deficient tumor cells. This article is highlighted in the In This Issue feature, p. 1027.
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Affiliation(s)
- Yoshinaga Ito
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Immunology, Harvard Medical School, Boston, MA 02115
- Laboratory of Immunopathogenesis, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Deng Pan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Wubing Zhang
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Xixi Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Immunology, Harvard Medical School, Boston, MA 02115
| | - Tiffany Y. Juan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Jason W. Pyrdol
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Oleksandr Kyrysyuk
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - X. Shirley Liu
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Kai W. Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215
- Department of Immunology, Harvard Medical School, Boston, MA 02115
- Department of Neurology, Brigham & Women’s Hospital, Boston, MA 02115
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45
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Mauro D, Manou-Stathopoulou S, Rivellese F, Sciacca E, Goldmann K, Tsang V, Lucey-Clayton I, Pagani S, Alam F, Pyne D, Rajakariar R, Gordon PA, Whiteford J, Bombardieri M, Pitzalis C, Lewis MJ. UBE2L3 regulates TLR7-induced B cell autoreactivity in Systemic Lupus Erythematosus. J Autoimmun 2023; 136:103023. [PMID: 37001433 DOI: 10.1016/j.jaut.2023.103023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023]
Abstract
Both TLR7 and NF-κB hyperactivity are known to contribute to pathogenesis in Systemic Lupus Erythematosus (SLE), driving a pro-interferon response, autoreactive B cell expansion and autoantibody production. UBE2L3 is an SLE susceptibility gene which drives plasmablast/plasma cell expansion in SLE, but its role in TLR7 signalling has not been elucidated. We aimed to investigate the role of UBE2L3 in TLR7-mediated NF-κB activation, and the effect of UBE2L3 inhibition by Dimethyl Fumarate (DMF) on SLE B cell differentiation in vitro. Our data demonstrate that UBE2L3 is critical for activation of NF-κB downstream of TLR7 stimulation, via interaction with LUBAC. DMF, which directly inhibits UBE2L3, significantly inhibited TLR7-induced NF-κB activation, differentiation of memory B cells and plasmablasts, and autoantibody secretion in SLE. DMF also downregulated interferon signature genes and plasma cell transcriptional programmes. These results demonstrate that UBE2L3 inhibition could potentially be used as a therapy in SLE through repurposing of DMF, thus preventing TLR7-driven autoreactive B cell maturation.
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46
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Goel S, Oliva R, Jeganathan S, Bader V, Krause LJ, Kriegler S, Stender ID, Christine CW, Nakamura K, Hoffmann JE, Winter R, Tatzelt J, Winklhofer KF. Linear ubiquitination induces NEMO phase separation to activate NF-κB signaling. Life Sci Alliance 2023; 6:e202201607. [PMID: 36720498 PMCID: PMC9889916 DOI: 10.26508/lsa.202201607] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/09/2023] [Accepted: 01/09/2023] [Indexed: 02/02/2023] Open
Abstract
The NF-κB essential modulator NEMO is the core regulatory component of the inhibitor of κB kinase complex, which is a critical checkpoint in canonical NF-κB signaling downstream of innate and adaptive immune receptors. In response to various stimuli, such as TNF or IL-1β, NEMO binds to linear or M1-linked ubiquitin chains generated by LUBAC, promoting its oligomerization and subsequent activation of the associated kinases. Here we show that M1-ubiquitin chains induce phase separation of NEMO and the formation of NEMO assemblies in cells after exposure to IL-1β. Phase separation is promoted by both binding of NEMO to linear ubiquitin chains and covalent linkage of M1-ubiquitin to NEMO and is essential but not sufficient for its phase separation. Supporting the functional relevance of NEMO phase separation in signaling, a pathogenic NEMO mutant, which is impaired in both binding and linkage to linear ubiquitin chains, does not undergo phase separation and is defective in mediating IL-1β-induced NF-κB activation.
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Affiliation(s)
- Simran Goel
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Rosario Oliva
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Sadasivam Jeganathan
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Laura J Krause
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Simon Kriegler
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Isabelle D Stender
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Ken Nakamura
- Department of Neurology, UCSF, San Francisco, CA, USA
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Jan-Erik Hoffmann
- Protein Chemistry Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I-Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
| | - Jörg Tatzelt
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
- RESOLV Cluster of Excellence, Ruhr University Bochum, Bochum, Germany
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47
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Zhang J, Tu H, Zheng Z, Zhao X, Lin X. RNF31 promotes tumorigenesis via inhibiting RIPK1 kinase-dependent apoptosis. Oncogene 2023; 42:1585-1596. [PMID: 36997719 DOI: 10.1038/s41388-023-02669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 04/01/2023]
Abstract
It is well established that interferon (IFN) and tumor necrosis factor (TNF) could synergistically promote antitumor toxicity and avoid resistance of antigen-negative tumors during cancer immunotherapy. The linear ubiquitin chain assembly complex (LUBAC) has been widely known to regulate receptor-interacting protein kinase-1(RIPK1) kinase activity and TNF-mediated cell death during inflammation and embryogenesis. However, whether LUBAC and RIPK1 kinase activity in tumor microenvironment could regulate antitumor immunity are still not very clear. Here, we demonstrated a cancer cell-intrinsic role of LUBAC complex in tumor microenvironment to promote tumorigenesis. Lacking LUBAC component RNF31 in B16 melanoma cells but not immune cells including macrophages or dendritic cells greatly impaired tumor growth by increasing intratumoral CD8+ T cells infiltration. Mechanistically, we found that tumor cells without RNF31 shown severe apoptosis-mediated cell death caused by TNFα/IFNγ in the tumor microenvironment. Most importantly, we found that RNF31 could limit RIPK1 kinase activity and further prevent tumor cell death in a transcription-independent manner, suggesting a crucial role of RIPK1 kinase activity in tumorigenesis. Together, our results demonstrate an essential role of RNF31 and RIPK1 kinase activity in tumorigenesis and imply that RNF31 inhibition could be harnessed to enhance antitumor toxicity during tumor immunotherapy.
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Affiliation(s)
- Jie Zhang
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, 100084, China
| | - Hailin Tu
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, 100084, China
| | - Zheyu Zheng
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, 100084, China
| | - Xueqiang Zhao
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
- Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, 100084, China
| | - Xin Lin
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China.
- Department of Basic Medical Sciences, Tsinghua University School of Medicine, Beijing, 100084, China.
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48
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Akizuki Y, Morita M, Mori Y, Kaiho-Soma A, Dixit S, Endo A, Shimogawa M, Hayashi G, Naito M, Okamoto A, Tanaka K, Saeki Y, Ohtake F. cIAP1-based degraders induce degradation via branched ubiquitin architectures. Nat Chem Biol 2023; 19:311-322. [PMID: 36316570 DOI: 10.1038/s41589-022-01178-1] [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: 11/25/2021] [Accepted: 09/21/2022] [Indexed: 11/06/2022]
Abstract
Targeted protein degradation through chemical hijacking of E3 ubiquitin ligases is an emerging concept in precision medicine. The ubiquitin code is a critical determinant of the fate of substrates. Although two E3s, CRL2VHL and CRL4CRBN, frequently assemble with proteolysis-targeting chimeras (PROTACs) to attach lysine-48 (K48)-linked ubiquitin chains, the diversity of the ubiquitin code used for chemically induced degradation is largely unknown. Here we show that the efficacy of cIAP1-targeting degraders depends on the K63-specific E2 enzyme UBE2N. UBE2N promotes degradation of cIAP1 induced by cIAP1 ligands and subsequent cancer cell apoptosis. Mechanistically, UBE2N-catalyzed K63-linked ubiquitin chains facilitate assembly of highly complex K48/K63 and K11/K48 branched ubiquitin chains, thereby recruiting p97/VCP, UCH37 and the proteasome. Degradation of neo-substrates directed by cIAP1-recruiting PROTACs also depends on UBE2N. These results reveal an unexpected role for K63-linked ubiquitin chains and UBE2N in degrader-induced proteasomal degradation and demonstrate the diversity of the ubiquitin code used for chemical hijacking.
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Affiliation(s)
- Yoshino Akizuki
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Mai Morita
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Yuki Mori
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan
| | - Ai Kaiho-Soma
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Shivani Dixit
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Akinori Endo
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan
| | - Marie Shimogawa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Gosuke Hayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
| | - Mikihiko Naito
- Social Cooperation Program of Targeted Protein Degradation, Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Akimitsu Okamoto
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Tokyo, Japan
- Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Keiji Tanaka
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan
| | - Yasushi Saeki
- Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan
| | - Fumiaki Ohtake
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Tokyo, Japan.
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan.
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49
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Tan Q, Yao CL. NEMO involves in NF-κB activation by interaction with p65 and promoting its nuclear translocation in large yellow croaker (Larimichthys crocea). FISH & SHELLFISH IMMUNOLOGY 2023; 134:108637. [PMID: 36841517 DOI: 10.1016/j.fsi.2023.108637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/10/2023] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
NEMO (nuclear factor-κB <NF-κB> essential modulator) plays an important role in activating NF-κB signaling pathway, p65 is a pivotal positive-regulator of NF-κB family. However, the role of NEMO in p65-triggered immune activation in teleost is largely unknown. In the present study, the cDNA sequence of LcNEMO was identified from the large yellow croaker (Larimichthys crocea). The predicated LcNEMO protein encoded 565 amino acids, consisting of a N-terminal NEMO domain, followed by two coiled coil (CC) motifs, a CC2-leucine zipper (CC2-LZ) domain, and a C-terminal zinc finger (ZnF) domain. Quantitative PCR showed that the strongest constitutive expression of LcNEMO was detected in blood and the inductive expression of it significantly enhanced after LPS and poly I:C challenge. The effect of LcNEMO on p65, RelB and cRel associated-immune activation detected by dual-luciferase reporter system assay indicated that Lcp65-triggered NF-κB, TNF-α and IL-1β activation could be significantly enhanced by LcNEMO. Furthermore, Co-IP revealed that the protein-protein interaction was existed between LcNEMO and Lcp65. Western blot and confocal microscope observation displayed that Lcp65 nuclear translocation could be promoted by LcNEMO with a dose- and time-dependent manner, which was further verified by RNA interference of LcNEMO expression. Our findings suggest that LcNEMO may be crucial in immune response by promoting p65-mediated immune activation.
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Affiliation(s)
- Qing Tan
- Fisheries College, Jimei University, Xiamen, 361021, PR China
| | - Cui-Luan Yao
- Fisheries College, Jimei University, Xiamen, 361021, PR China.
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50
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Sakamoto Y, Sasaki K, Omatsu M, Hamada K, Nakanishi Y, Itatani Y, Kawada K, Obama K, Seno H, Iwai K. Differential involvement of LUBAC-mediated linear ubiquitination in intestinal epithelial cells and macrophages during intestinal inflammation. J Pathol 2023; 259:304-317. [PMID: 36454102 DOI: 10.1002/path.6042] [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: 06/29/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022]
Abstract
Disruption of the intestinal epithelial barrier and dysregulation of macrophages are major factors contributing to the pathogenesis of inflammatory bowel diseases (IBDs). Activation of NF-κB and cell death are involved in maintaining intestinal homeostasis in a cell type-dependent manner. Although both are regulated by linear ubiquitin chain assembly complex (LUBAC)-mediated linear ubiquitination, the physiological relevance of linear ubiquitination to intestinal inflammation remains unexplored. Here, we used two experimental mouse models of IBD (intraperitoneal LPS and oral dextran sodium sulfate [DSS] administration) to examine the role of linear ubiquitination in intestinal epithelial cells (IECs) and macrophages during intestinal inflammation. We did this by deleting the linear ubiquitination activity of LUBAC specifically from IECs or macrophages. Upon LPS administration, loss of ligase activity in IECs induced mucosal inflammation and augmented IEC death. LPS-mediated death of LUBAC-defective IECs was triggered by TNF. IEC death was rescued by an anti-TNF antibody, and TNF (but not LPS) induced apoptosis of organoids derived from LUBAC-defective IECs. However, augmented TNF-mediated IEC death did not overtly affect the severity of colitis after DSS administration. By contrast, defective LUBAC ligase activity in macrophages ameliorated DSS-induced colitis by attenuating both infiltration of macrophages and expression of inflammatory cytokines. Decreased production of macrophage chemoattractant MCP-1/CCL2, as well as pro-inflammatory IL-6 and TNF, occurred through impaired activation of NF-κB and ERK via loss of ligase activity in macrophages. Taken together, these results indicate that both intraperitoneal LPS and oral DSS administrations are beneficial for evaluating epithelial integrity under inflammatory conditions, as well as macrophage functions in the event of an epithelial barrier breach. The data clarify the cell-specific roles of linear ubiquitination as a critical regulator of TNF-mediated epithelial integrity and macrophage pro-inflammatory responses during intestinal inflammation. © 2022 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Yusuke Sakamoto
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsuhiro Sasaki
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mayuki Omatsu
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kensuke Hamada
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshiro Itatani
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenji Kawada
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazutaka Obama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Seno
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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