1
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Delyea CJ, Forster MD, Luo S, Dubrule BE, Julien O, Bhavsar AP. The Salmonella Effector SspH2 Facilitates Spatially Selective Ubiquitination of NOD1 to Enhance Inflammatory Signaling. Biochemistry 2024; 63:2266-2279. [PMID: 39189508 PMCID: PMC11412229 DOI: 10.1021/acs.biochem.4c00380] [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: 06/28/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 08/28/2024]
Abstract
As part of its pathogenesis, Salmonella enterica serovar Typhimurium delivers effector proteins into host cells. One effector is SspH2, a member of the so-called novel E3 ubiquitin ligase family, that interacts with and enhances, NOD1 pro-inflammatory signaling, though the underlying mechanisms are unclear. Here, we report that SspH2 interacts with multiple members of the NLRC family to enhance pro-inflammatory signaling by targeted ubiquitination. We show that SspH2 modulates host innate immunity by interacting with both NOD1 and NOD2 in mammalian epithelial cell culture via the NF-κB pathway. Moreover, purified SspH2 and NOD1 directly interact, where NOD1 potentiates SspH2 E3 ubiquitin ligase activity. Mass spectrometry and mutational analyses identified four key lysine residues in NOD1 that are required for its enhanced activation by SspH2, but not its basal activity. These critical lysine residues are positioned in the same region of NOD1 and define a surface on the receptor that appears to be targeted by SspH2. Overall, this work provides evidence for post-translational modification of NOD1 by ubiquitin and uncovers a unique mechanism of spatially selective ubiquitination to enhance the activation of an archetypal NLR.
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Affiliation(s)
- Cole J. Delyea
- Department
of Medical Microbiology and Immunology, Faculty of Medicine &
Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Malcolm D. Forster
- Department
of Medical Microbiology and Immunology, Faculty of Medicine &
Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Shu Luo
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Bradley E. Dubrule
- Department
of Medical Microbiology and Immunology, Faculty of Medicine &
Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Olivier Julien
- Department
of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Amit P. Bhavsar
- Department
of Medical Microbiology and Immunology, Faculty of Medicine &
Dentistry, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
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2
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Xu Y, Lin F, Liao G, Sun J, Chen W, Zhang L. Ripks and Neuroinflammation. Mol Neurobiol 2024; 61:6771-6787. [PMID: 38349514 DOI: 10.1007/s12035-024-03981-4] [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: 08/23/2023] [Accepted: 01/20/2024] [Indexed: 08/22/2024]
Abstract
Neuroinflammation is an immune response in the central nervous system and poses a significant threat to human health. Studies have shown that the receptor serine/threonine protein kinase family (RIPK) family, a popular research target in inflammation, has been shown to play an essential role in neuroinflammation. It is significant to note that the previous reviews have only examined the link between RIPK1 and neuroinflammation. However, it has yet to systematically analyze the relationship between the RIPK family and neuroinflammation. Activation of RIPK1 promotes neuroinflammation. RIPK1 and RIPK3 are responsible for the control of cell death, including apoptosis, necrosis, and inflammation. RIPK1 and RIPK3 regulate inflammatory responses through the release of damage in necroptosis. RIPK1 and RIPK3 regulate inflammatory responses by releasing damage-associated molecular patterns (DAMPs) during necrosis. In addition, activated RIPK1 nuclear translocation and its interaction with the BAF complex leads to upregulation of chromatin modification and inflammatory gene expression, thereby triggering inflammation. Although RIPK2 is not directly involved in regulating cell death, it is considered an essential target for treating neurological inflammation. When the peptidoglycan receptor detects peptidoglycan IE-DAP or MDP in bacteria, it prompts NOD1 and NOD2 to recruit RIPK2 and activate the XIAP E3 ligase. This leads to the K63 ubiquitination of RIPK2. This is followed by LUBAC-mediated linear ubiquitination, which activates NF-KB and MAPK pathways to produce cytokines and chemokines. In conclusion, there are seven known members of the RIPK family, but RIPK4, RIPK5, RIPK6, and RIPK7 have not been linked to neuroinflammation. This article seeks to explore the potential of RIPK1, RIPK2, and RIPK3 kinases as therapeutic interventions for neuroinflammation, which is associated with Alzheimer's disease (AD), amyotrophic lateral sclerosis (ALS), ischemic stroke, Parkinson's disease (PD), multiple sclerosis (MS), and traumatic brain injury (TBI).
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Affiliation(s)
- Yue Xu
- Department of Cerebrovascular Disease, Sun Yat-Sen University, The Fifth Affiliated Hospital, Zhuhai, 519000, Guangdong, People's Republic of China
| | - Feng Lin
- Department of Cerebrovascular Disease, Sun Yat-Sen University, The Fifth Affiliated Hospital, Zhuhai, 519000, Guangdong, People's Republic of China
| | - Guolei Liao
- Department of Cerebrovascular Disease, Sun Yat-Sen University, The Fifth Affiliated Hospital, Zhuhai, 519000, Guangdong, People's Republic of China
| | - Jiaxing Sun
- Department of Cerebrovascular Disease, Sun Yat-Sen University, The Fifth Affiliated Hospital, Zhuhai, 519000, Guangdong, People's Republic of China
| | - Wenli Chen
- Department of Pharmacy, Sun Yat-Sen University, The Fifth Affiliated Hospital, Zhuhai, 519000, Guangdong, People's Republic of China.
| | - Lei Zhang
- Department of Cerebrovascular Disease, Sun Yat-Sen University, The Fifth Affiliated Hospital, Zhuhai, 519000, Guangdong, People's Republic of China.
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3
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Rinotas V, Iliaki K, Pavlidi L, Meletakos T, Mosialos G, Armaka M. Cyld restrains the hyperactivation of synovial fibroblasts in inflammatory arthritis by regulating the TAK1/IKK2 signaling axis. Cell Death Dis 2024; 15:584. [PMID: 39122678 PMCID: PMC11316070 DOI: 10.1038/s41419-024-06966-2] [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: 02/07/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024]
Abstract
TNF is a potent cytokine known for its involvement in physiology and pathology. In Rheumatoid Arthritis (RA), persistent TNF signals cause aberrant activation of synovial fibroblasts (SFs), the resident cells crucially involved in the inflammatory and destructive responses of the affected synovial membrane. However, the molecular switches that control the pathogenic activation of SFs remain poorly defined. Cyld is a major component of deubiquitination (DUB) machinery regulating the signaling responses towards survival/inflammation and programmed necrosis that induced by cytokines, growth factors and microbial products. Herein, we follow functional genetic approaches to understand how Cyld affects arthritogenic TNF signaling in SFs. We demonstrate that in spontaneous and induced RA models, SF-Cyld DUB deficiency deteriorates arthritic phenotypes due to increased levels of chemokines, adhesion receptors and bone-degrading enzymes generated by mutant SFs. Mechanistically, Cyld serves to restrict the TNF-induced hyperactivation of SFs by limiting Tak1-mediated signaling, and, therefore, leading to supervised NF-κB and JNK activity. However, Cyld is not critically involved in the regulation of TNF-induced death of SFs. Our results identify SF-Cyld as a regulator of TNF-mediated arthritis and inform the signaling landscape underpinning the SF responses.
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Affiliation(s)
- Vagelis Rinotas
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center (BSRC) "Alexander Fleming", Vari, Greece
| | - Kalliopi Iliaki
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center (BSRC) "Alexander Fleming", Vari, Greece
| | - Lydia Pavlidi
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center (BSRC) "Alexander Fleming", Vari, Greece
| | - Theodore Meletakos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center (BSRC) "Alexander Fleming", Vari, Greece
| | - George Mosialos
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Macedonia, Greece
| | - Marietta Armaka
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center (BSRC) "Alexander Fleming", Vari, Greece.
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4
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Davidson S, Shibata Y, Collard S, Zheng H, Kong K, Sun JM, Laohamonthonkul P, Cerra A, Kratina T, Li MW, Russell C, van Beek A, Kirk EP, Walsh R, Alqanatish J, Almojali A, Alsuwairi W, Alrasheed A, Lalaoui N, Gray PE, Komander D, Masters SL. Dominant negative OTULIN-related autoinflammatory syndrome. J Exp Med 2024; 221:e20222171. [PMID: 38630025 PMCID: PMC11022884 DOI: 10.1084/jem.20222171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 11/19/2023] [Accepted: 02/21/2024] [Indexed: 04/19/2024] Open
Abstract
OTU deubiquitinase with linear linkage specificity (OTULIN) regulates inflammation and cell death by deubiquitinating linear ubiquitin chains generated by the linear ubiquitin chain assembly complex (LUBAC). Biallelic loss-of-function mutations causes OTULIN-related autoinflammatory syndrome (ORAS), while OTULIN haploinsuffiency has not been associated with spontaneous inflammation. However, herein, we identify two patients with the heterozygous mutation p.Cys129Ser in OTULIN. Consistent with ORAS, we observed accumulation of linear ubiquitin chains, increased sensitivity to TNF-induced death, and dysregulation of inflammatory signaling in patient cells. While the C129S mutation did not affect OTULIN protein stability or binding capacity to LUBAC and linear ubiquitin chains, it did ablate OTULIN deubiquitinase activity. Loss of activity facilitated the accumulation of autoubiquitin chains on LUBAC. Altered ubiquitination of LUBAC inhibits its recruitment to the TNF receptor signaling complex, promoting TNF-induced cell death and disease pathology. By reporting the first dominant negative mutation driving ORAS, this study expands our clinical understanding of OTULIN-associated pathology.
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Affiliation(s)
- Sophia Davidson
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Yuri Shibata
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Sophie Collard
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Hongyu Zheng
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Klara Kong
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - June M. Sun
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Pawat Laohamonthonkul
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Anthony Cerra
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Tobias Kratina
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | | | | | - Margaret W.Y. Li
- School of Clinical Medicine, University of New South Wales, Randwick, Australia
- Department of Immunology and Infectious Diseases, Sydney Children’s Hospital, Randwick, Australia
| | - Carolyn Russell
- Department of Paediatric Surgery, Sydney Children’s Hospital, Randwick, Australia
| | - Anna van Beek
- Department of General Paediatrics, Sydney Children’s Hospital, Randwick, Australia
| | - Edwin P. Kirk
- School of Clinical Medicine, University of New South Wales, Randwick, Australia
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Australia
- New South Wales Health Pathology Randwick Genomics Laboratory, Randwick, Australia
| | - Rebecca Walsh
- New South Wales Health Pathology Randwick Genomics Laboratory, Randwick, Australia
| | - Jubran Alqanatish
- Pediatric Rheumatology, King Abdullah Specialist Children’s Hospital, National Guard Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdullah Almojali
- Pediatric Rheumatology, King Abdullah Specialist Children’s Hospital, National Guard Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Wafaa Alsuwairi
- Pediatric Rheumatology, King Abdullah Specialist Children’s Hospital, National Guard Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman Alrasheed
- Pediatric Rheumatology, King Abdullah Specialist Children’s Hospital, National Guard Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Najoua Lalaoui
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Paul E. Gray
- Department of Immunology and Infectious Diseases, Sydney Children’s Hospital, Randwick, Australia
- University of Western Sydney, Sydney, Australia
| | - David Komander
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | - Seth L. Masters
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Australia
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Australia
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5
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Dou B, Jiang G, Peng W, Liu C. OTULIN deficiency: focus on innate immune system impairment. Front Immunol 2024; 15:1371564. [PMID: 38774872 PMCID: PMC11106414 DOI: 10.3389/fimmu.2024.1371564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/04/2024] [Indexed: 05/24/2024] Open
Abstract
OTULIN deficiency is a complex disease characterized by a wide range of clinical manifestations, including skin rash, joint welling, lipodystrophy to pulmonary abscess, and sepsis shock. This disease is mechanistically linked to mutations in the OTULIN gene, resulting in an immune disorder that compromises the body's ability to effectively combat pathogens and foreign stimuli. The OTULIN gene is responsible for encoding a deubiquitinating enzyme crucial for hydrolyzing Met1-poly Ub chains, and its dysfunction leads to dysregulated immune responses. Patients with OTULIN deficiency often exhibit an increase in monocytes, including neutrophils and macrophages, along with inflammatory clinical features. The onset of symptoms typically occurs at an early age. However, individuals with OTULIN haploinsufficiency are particularly susceptible to life-threatening staphylococcal infections. Currently, the most effective treatment for patients with OTULIN biallelic mutations involves the use of TNF-blocking agents, which target the dysregulated immune response. In conclusion, OTULIN deficiency presents a complex clinical picture with diverse manifestations, attributed to mutations in the OTULIN gene. Understanding the underlying mechanisms is crucial for developing targeted therapeutic interventions to address this challenging condition. Further research into the pathophysiology of OTULIN deficiency is essential for improving clinical management and outcomes for affected individuals.
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Affiliation(s)
- Bo Dou
- Central South University, Xiangya Hospital, Pediatric Department, Changsha, Hunan, China
| | - Gang Jiang
- Hunan Normal University, Hunan Provincial People's Hospital, Department of Respiratory Medicine, Changsha, Hunan, China
| | - Wang Peng
- Central South University, Xiangya Hospital, Pediatric Department, Changsha, Hunan, China
| | - Chentao Liu
- Central South University, Xiangya Hospital, Pediatric Department, Changsha, Hunan, China
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6
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Vringer E, Heilig R, Riley JS, Black A, Cloix C, Skalka G, Montes-Gómez AE, Aguado A, Lilla S, Walczak H, Gyrd-Hansen M, Murphy DJ, Huang DT, Zanivan S, Tait SW. Mitochondrial outer membrane integrity regulates a ubiquitin-dependent and NF-κB-mediated inflammatory response. EMBO J 2024; 43:904-930. [PMID: 38337057 PMCID: PMC10943237 DOI: 10.1038/s44318-024-00044-1] [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: 02/20/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/12/2024] Open
Abstract
Mitochondrial outer membrane permeabilisation (MOMP) is often essential for apoptosis, by enabling cytochrome c release that leads to caspase activation and rapid cell death. Recently, MOMP has been shown to be inherently pro-inflammatory with emerging cellular roles, including its ability to elicit anti-tumour immunity. Nonetheless, how MOMP triggers inflammation and how the cell regulates this remains poorly defined. We find that upon MOMP, many proteins localised either to inner or outer mitochondrial membranes are ubiquitylated in a promiscuous manner. This extensive ubiquitylation serves to recruit the essential adaptor molecule NEMO, leading to the activation of pro-inflammatory NF-κB signalling. We show that disruption of mitochondrial outer membrane integrity through different means leads to the engagement of a similar pro-inflammatory signalling platform. Therefore, mitochondrial integrity directly controls inflammation, such that permeabilised mitochondria initiate NF-κB signalling.
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Affiliation(s)
- Esmee Vringer
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Rosalie Heilig
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Joel S Riley
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Annabel Black
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Catherine Cloix
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - George Skalka
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Alfredo E Montes-Gómez
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Aurore Aguado
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Sergio Lilla
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Henning Walczak
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, UK
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Mads Gyrd-Hansen
- Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research Center, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Murphy
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Danny T Huang
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Sara Zanivan
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK
| | - Stephen Wg Tait
- Cancer Research UK Scotland Institute, Switchback Road, Glasgow, G61 1BD, UK.
- School of Cancer Sciences, University of Glasgow, Switchback Road, Glasgow, G61 1BD, UK.
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7
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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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8
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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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9
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Rivoal M, Dubuquoy L, Millet R, Leleu-Chavain N. Receptor Interacting Ser/Thr-Protein Kinase 2 as a New Therapeutic Target. J Med Chem 2023; 66:14391-14410. [PMID: 37857324 DOI: 10.1021/acs.jmedchem.3c00593] [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] [Indexed: 10/21/2023]
Abstract
Receptor interacting serine/threonine protein kinase 2 (RIPK2) is a downstream signaling molecule essential for the activation of several innate immune receptors, including the NOD-like receptors (NOD1 and NOD2). Recognition of pathogen-associated molecular pattern proteins by NOD1/2 leads to their interaction with RIPK2, which induces release of pro-inflammatory cytokines through the activation of NF-κB and MAPK pathways, among others. Thus, RIPK2 has emerged as a key mediator of intracellular signal transduction and represents a new potential therapeutic target for the treatment of various conditions, including inflammatory diseases and cancer. In this Perspective, first, an overview of the mechanisms that underlie RIPK2 function will be presented along with its role in several diseases. Then, the existing inhibitors that target RIPK2 and different therapeutic strategies will be reviewed, followed by a discussion on current challenges and outlook.
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Affiliation(s)
- Morgane Rivoal
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
| | - Laurent Dubuquoy
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
| | - Régis Millet
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
| | - Natascha Leleu-Chavain
- Inserm, U1286 - INFINITE - Institute for Translational Research in Inflammation, University of Lille, F-59000 Lille, France
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10
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Lee J, Huh J, Lee Y, Jin Y, Bai F, Ha UH. DnaJ-induced miRNA-146a negatively regulates the expression of IL-8 in macrophages. Microb Pathog 2023; 184:106357. [PMID: 37716625 DOI: 10.1016/j.micpath.2023.106357] [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: 07/15/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 09/18/2023]
Abstract
As a member of the damage-associated molecular patterns, heat shock proteins (HSPs) are widely recognized for their role in initiating innate immune responses. These highly conserved proteins are expressed ubiquitously in both prokaryotes and eukaryotes. In this study, our aim was to investigate how DnaJ, a HSP40 homolog derived from Pseudomonas aeruginosa (P. aeruginosa), influences the regulation of IL-8 expression in macrophages. Treatment with DnaJ served as a stimulus, inducing a more robust expression of IL-8 compared to other HSP homologs, including DnaK, GroEL, and HtpG. This effect was achieved through the activation of the NF-κB signaling pathway. Interestingly, DnaJ treatment also significantly increased the expression of microRNA-146a (miR-146a), which appears to play a role in modulating the expression of innate defense genes. As a consequence, pre-treatment with DnaJ led to a reduction in the extent of IL-8 induction in response to P. aeruginosa treatment. Notably, this reduction was counteracted by transfection of a miR-146a inhibitor, highlighting the involvement of miR-146a in P. aeruginosa-mediated induction of IL-8 expression. Therefore, this study uncovers the role of DnaJ in triggering the expression of miR-146a, which, in turn, modulates the excessive expression of IL-8 induced by P. aeruginosa infection.
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Affiliation(s)
- Jaehoo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, Republic of Korea
| | - Jinwon Huh
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
| | - Yeji Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea
| | - Yongxin Jin
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, Nankai University, Tianjin, 300071, China
| | - Fang Bai
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, Nankai University, Tianjin, 300071, China
| | - Un-Hwan Ha
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, 30019, Republic of Korea; Interdisciplinary Graduate Program for Artificial Intelligence Smart Convergence Technology, Korea University, Sejong, 30019, Republic of Korea.
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11
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Li Y, Zhu J, Yu Z, Zhai F, Li H, Jin X. Regulation of apoptosis by ubiquitination in liver cancer. Am J Cancer Res 2023; 13:4832-4871. [PMID: 37970337 PMCID: PMC10636691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/04/2023] [Indexed: 11/17/2023] Open
Abstract
Apoptosis is a programmed cell death process critical to cell development and tissue homeostasis in multicellular organisms. Defective apoptosis is a crucial step in the malignant transformation of cells, including hepatocellular carcinoma (HCC), where the apoptosis rate is higher than in normal liver tissues. Ubiquitination, a post-translational modification process, plays a precise role in regulating the formation and function of different death-signaling complexes, including those involved in apoptosis. Aberrant expression of E3 ubiquitin ligases (E3s) in liver cancer (LC), such as cellular inhibitors of apoptosis proteins (cIAPs), X chromosome-linked IAP (XIAP), and linear ubiquitin chain assembly complex (LUBAC), can contribute to HCC development by promoting cell survival and inhibiting apoptosis. Therefore, the review introduces the main apoptosis pathways and the regulation of proteins in these pathways by E3s and deubiquitinating enzymes (DUBs). It summarizes the abnormal expression of these regulators in HCC and their effects on cancer inhibition or promotion. Understanding the role of ubiquitination in apoptosis and LC can provide insights into potential targets for therapeutic intervention.
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Affiliation(s)
- Yuxuan Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo UniversityNingbo 315040, Zhejiang, P. R. China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo UniversityNingbo 315040, Zhejiang, P. R. China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Zongdong Yu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo UniversityNingbo 315040, Zhejiang, P. R. China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Fengguang Zhai
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Hong Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo UniversityNingbo 315040, Zhejiang, P. R. China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
| | - Xiaofeng Jin
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo UniversityNingbo 315040, Zhejiang, P. R. China
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo UniversityNingbo 315211, Zhejiang, P. R. China
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12
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Hadian K, Stockwell BR. The therapeutic potential of targeting regulated non-apoptotic cell death. Nat Rev Drug Discov 2023; 22:723-742. [PMID: 37550363 DOI: 10.1038/s41573-023-00749-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2023] [Indexed: 08/09/2023]
Abstract
Cell death is critical for the development and homeostasis of almost all multicellular organisms. Moreover, its dysregulation leads to diverse disease states. Historically, apoptosis was thought to be the major regulated cell death pathway, whereas necrosis was considered to be an unregulated form of cell death. However, research in recent decades has uncovered several forms of regulated necrosis that are implicated in degenerative diseases, inflammatory conditions and cancer. The growing insight into these regulated, non-apoptotic cell death pathways has opened new avenues for therapeutic targeting. Here, we describe the regulatory pathways of necroptosis, pyroptosis, parthanatos, ferroptosis, cuproptosis, lysozincrosis and disulfidptosis. We discuss small-molecule inhibitors of the pathways and prospects for future drug discovery. Together, the complex mechanisms governing these pathways offer strategies to develop therapeutics that control non-apoptotic cell death.
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Affiliation(s)
- Kamyar Hadian
- Research Unit Signaling and Translation, Helmholtz Zentrum München, Neuherberg, Germany.
| | - Brent R Stockwell
- Department of Biological Sciences and Department of Chemistry, Columbia University, New York, NY, USA.
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13
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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: 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: 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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14
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Zhao W, Leng RX, Ye DQ. RIPK2 as a promising druggable target for autoimmune diseases. Int Immunopharmacol 2023; 118:110128. [PMID: 37023697 DOI: 10.1016/j.intimp.2023.110128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023]
Abstract
Receptor Interacting Serine/Threonine Kinase 2 (RIPK2) is an essential regulator of the inflammatory process and immune response. In innate immunity, the NOD-RIPK2 signaling axis is an important pathway that directly mediates inflammation and immune response. In adaptive immunity, RIPK2 may affect T cell proliferation, differentiation and cellular homeostasis thereby involving T cell-driven autoimmunity, but the exact mechanism remains unclear. Recent advances suggest a key role of RIPK2 in diverse autoimmune diseases (ADs) such as inflammatory bowel diseases, rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, and Behcet's disease. This review aims to provide valuable therapeutic direction for ADs by focusing on the function and modulation of RIPK2 in innate and adaptive immunity, its involvement with various ADs and the application of RIPK2-related drugs in ADs. We raise the notion that drug targeting RIPK2 could be a promising therapeutic strategy for the treatment of ADs, though much work remains to be done for clinical application.
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15
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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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16
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SPATA2 restricts OTULIN-dependent LUBAC activity independently of CYLD. Cell Rep 2023; 42:111961. [PMID: 36640323 DOI: 10.1016/j.celrep.2022.111961] [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: 07/08/2022] [Revised: 11/10/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
SPATA2 mediates the recruitment of CYLD to immune receptor complexes by bridging the interaction of CYLD with the linear ubiquitylation assembly complex (LUBAC) component HOIP. Whether SPATA2 exhibits functions independently of CYLD is unclear. Here, we show that, while Cyld-/- and Spata2-/- mice are viable, double mutants exhibit highly penetrant perinatal lethality, indicating independent functions of SPATA2 and CYLD. Cyld-/-Spata2-/- fibroblasts show increased M1-linked TNFR1-SC ubiquitylation and, similar to Cyld-/-Spata2-/- macrophages and intestinal epithelial cells, elevated pro-inflammatory gene expression compared with Cyld-/- or Spata2-/- cells. We show that SPATA2 competes with OTULIN for binding to HOIP via its PUB-interacting motif (PIM) and its zinc finger domain, thereby promoting autoubiquitylation of LUBAC. Consistently, increased pro-inflammatory signaling in Cyld-/-Spata2-/- cells depends on the presence of OTULIN. Our data therefore indicate that SPATA2 counteracts, independently of CYLD, the deubiquitylation of LUBAC by OTULIN and thereby attenuates LUBAC activity and pro-inflammatory signaling.
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17
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Yuan H, Wei S, Ren Z, Li F, Liu B, Liu R, Zhang X. KLHL21/CYLD signaling confers aggressiveness in bladder cancer through inactivating NF-κB signaling. Int Immunopharmacol 2023; 114:109202. [PMID: 36538852 DOI: 10.1016/j.intimp.2022.109202] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 12/23/2022]
Abstract
Bladder carcinoma (BC) is one of the most commonly diagnosed malignant cancers worldwide. Kelch-like protein 21 (KLHL21) has been shown to be involved in a number of human tumors. The study aimed to investigate the effects and mechanism of KLHL21 on BC progression. We found that KLHL21 expression was significantly decreased in human BC tissues and cell lines compared with the paired normal samples, and patients with lower KLHL21 expression exhibited poorer overall survival. In vitro studies then showed that KLHL21 over-expression significantly reduced the proliferation, migration and invasion in BC cells, while KLHL21 knockdown markedly accelerated the proliferative, migratory and invasive properties of BC cells. Animal studies confirmed that KLHL21 exhibited anti-tumor function in the xenograft mouse models, as indicated by the reduced tumor growth rates, and mice with KLHL21 knockdown showed the opposite tumor growth profile. Additionally, we found that KLHL21 negatively mediated the nuclear factor-κB (NF-κB) signaling activation, as well as its down-streaming molecules involved in the biological regulation of cell survival, death and migratory processes. Mechanistically, cylindromatosis (CYLD) expression levels were significantly up-regulated in BC cells over-expressing KLHL21, but were down-regulated upon KLHL21 knockdown. We further uncovered that KLHL21 directly interacted with CYLD in BC cells. Of note, we found that KLHL21 mainly in cytoplasm could restrain CYLD degradation by prohibiting its ubiquitination in BC cells. More importantly, our in vitro experiments displayed that KLHL21-inhibited progression and NF-κB/p65 activation in BC cells were completely abolished by CYLD deletion, revealing that CYLD expression was required for KLHL21 to perform its anti-tumor function in BC. Collectively, all these findings uncovered that KLHL21/CYLD axis may be a promising therapeutic target for BC treatment.
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Affiliation(s)
- Hongyi Yuan
- Department of Urology Surgery, The Second Affiliated Hospital of Xingtai Medical College, Xingtai, Hebei Province 054000, China
| | - Shufei Wei
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province 050000, China
| | - Zongtao Ren
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province 050000, China
| | - Feng Li
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province 050000, China
| | - Bin Liu
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province 050000, China
| | - Rui Liu
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province 050000, China
| | - Xiaoyu Zhang
- Department of Urology Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei Province 050000, China.
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18
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Wu Z, Berlemann LA, Bader V, Sehr DA, Dawin E, Covallero A, Meschede J, Angersbach L, Showkat C, Michaelis JB, Münch C, Rieger B, Namgaladze D, Herrera MG, Fiesel FC, Springer W, Mendes M, Stepien J, Barkovits K, Marcus K, Sickmann A, Dittmar G, Busch KB, Riedel D, Brini M, Tatzelt J, Cali T, Winklhofer KF. LUBAC assembles a ubiquitin signaling platform at mitochondria for signal amplification and transport of NF-κB to the nucleus. EMBO J 2022; 41:e112006. [PMID: 36398858 PMCID: PMC9753471 DOI: 10.15252/embj.2022112006] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Mitochondria are increasingly recognized as cellular hubs to orchestrate signaling pathways that regulate metabolism, redox homeostasis, and cell fate decisions. Recent research revealed a role of mitochondria also in innate immune signaling; however, the mechanisms of how mitochondria affect signal transduction are poorly understood. Here, we show that the NF-κB pathway activated by TNF employs mitochondria as a platform for signal amplification and shuttling of activated NF-κB to the nucleus. TNF treatment induces the recruitment of HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), and its substrate NEMO to the outer mitochondrial membrane, where M1- and K63-linked ubiquitin chains are generated. NF-κB is locally activated and transported to the nucleus by mitochondria, leading to an increase in mitochondria-nucleus contact sites in a HOIP-dependent manner. Notably, TNF-induced stabilization of the mitochondrial kinase PINK1 furthermore contributes to signal amplification by antagonizing the M1-ubiquitin-specific deubiquitinase OTULIN. Overall, our study reveals a role for mitochondria in amplifying TNF-mediated NF-κB activation, both serving as a signaling platform, as well as a transport mode for activated NF-κB to the nuclear.
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Affiliation(s)
- Zhixiao Wu
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena A Berlemann
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Verian Bader
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Dominik A Sehr
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Eva Dawin
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | | | - Jens Meschede
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Lena Angersbach
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Cathrin Showkat
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Jonas B Michaelis
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Christian Münch
- Faculty of Medicine, Institute of Biochemistry IIGoethe University FrankfurtFrankfurt am MainGermany
| | - Bettina Rieger
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dmitry Namgaladze
- Institute of Biochemistry I, Faculty of MedicineGoethe‐University FrankfurtFrankfurtGermany
| | - Maria Georgina Herrera
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
| | - Fabienne C Fiesel
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Wolfdieter Springer
- Department of NeuroscienceMayo ClinicJacksonvilleFLUSA
- Neuroscience PhD ProgramMayo Clinic Graduate School of Biomedical SciencesJacksonvilleFLUSA
| | - Marta Mendes
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
| | - Jennifer Stepien
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katalin Barkovits
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Katrin Marcus
- Medizinisches Proteom‐CenterRuhr‐Universität BochumBochumGermany
- Medical Proteome Analysis, Center for Protein Diagnostics (PRODI)Ruhr‐University BochumBochumGermany
| | - Albert Sickmann
- Leibniz‐Institut für Analytische Wissenschaften—ISAS—e.VDortmundGermany
| | - Gunnar Dittmar
- Proteomics of Cellular Signaling, Department of Infection and ImmunityLuxembourg Institute of HealthStrassenLuxembourg
- Department of Life Sciences and MedicineUniversity of LuxembourgBelvauxLuxembourg
| | - Karin B Busch
- Institute for Integrative Cell Biology and Physiology, Faculty of BiologyUniversity of MünsterMünsterGermany
| | - Dietmar Riedel
- Laboratory for Electron MicroscopyMax Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Marisa Brini
- Department of BiologyUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
| | - Jörg Tatzelt
- Department Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
| | - Tito Cali
- Department of Biomedical SciencesUniversity of PaduaPaduaItaly
- Centro Studi per la Neurodegenerazione (CESNE)University of PadovaPaduaItaly
- Padua Neuroscience Center (PNC)University of PaduaPaduaItaly
| | - Konstanze F Winklhofer
- Department Molecular Cell Biology, Institute of Biochemistry and PathobiochemistryRuhr University BochumBochumGermany
- RESOLV Cluster of ExcellenceRuhr University BochumBochumGermany
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19
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Usher JL, Sanchez‐Martinez A, Terriente‐Felix A, Chen P, Lee JJ, Chen C, Whitworth AJ. Parkin drives pS65-Ub turnover independently of canonical autophagy in Drosophila. EMBO Rep 2022; 23:e53552. [PMID: 36250243 PMCID: PMC9724668 DOI: 10.15252/embr.202153552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/05/2022] [Accepted: 09/20/2022] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease-related proteins, PINK1 and Parkin, act in a common pathway to maintain mitochondrial quality control. While the PINK1-Parkin pathway can promote autophagic mitochondrial turnover (mitophagy) following mitochondrial toxification in cell culture, alternative quality control pathways are suggested. To analyse the mechanisms by which the PINK1-Parkin pathway operates in vivo, we developed methods to detect Ser65-phosphorylated ubiquitin (pS65-Ub) in Drosophila. Exposure to the oxidant paraquat led to robust, Pink1-dependent pS65-Ub production, while pS65-Ub accumulates in unstimulated parkin-null flies, consistent with blocked degradation. Additionally, we show that pS65-Ub specifically accumulates on disrupted mitochondria in vivo. Depletion of the core autophagy proteins Atg1, Atg5 and Atg8a did not cause pS65-Ub accumulation to the same extent as loss of parkin, and overexpression of parkin promoted turnover of both basal and paraquat-induced pS65-Ub in an Atg5-null background. Thus, we have established that pS65-Ub immunodetection can be used to analyse Pink1-Parkin function in vivo as an alternative to reporter constructs. Moreover, our findings suggest that the Pink1-Parkin pathway can promote mitochondrial turnover independently of canonical autophagy in vivo.
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Affiliation(s)
- Joanne L Usher
- MRC Mitochondrial Biology UnitCambridgeUK
- PNAC Division, MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
MSD R&D Innovation CentreLondonUK
| | | | | | - Po‐Lin Chen
- National Institute of Infectious Diseases and VaccinologyNational Health Research InstitutesZhunanTaiwan
| | | | - Chun‐Hong Chen
- National Institute of Infectious Diseases and VaccinologyNational Health Research InstitutesZhunanTaiwan
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20
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Peng R, Wang CK, Wang‐Kan X, Idorn M, Kjær M, Zhou FY, Fiil BK, Timmermann F, Orozco SL, McCarthy J, Leung CS, Lu X, Bagola K, Rehwinkel J, Oberst A, Maelfait J, Paludan SR, Gyrd‐Hansen M. Human ZBP1 induces cell death-independent inflammatory signaling via RIPK3 and RIPK1. EMBO Rep 2022; 23:e55839. [PMID: 36268590 PMCID: PMC9724671 DOI: 10.15252/embr.202255839] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
ZBP1 is an interferon-induced cytosolic nucleic acid sensor that facilitates antiviral responses via RIPK3. Although ZBP1-mediated programmed cell death is widely described, whether and how it promotes inflammatory signaling is unclear. Here, we report a ZBP1-induced inflammatory signaling pathway mediated by K63- and M1-linked ubiquitin chains, which depends on RIPK1 and RIPK3 as scaffolds independently of cell death. In human HT29 cells, ZBP1 associated with RIPK1 and RIPK3 as well as ubiquitin ligases cIAP1 and LUBAC. ZBP1-induced K63- and M1-linked ubiquitination of RIPK1 and ZBP1 to promote TAK1- and IKK-mediated inflammatory signaling and cytokine production. Inhibition of caspase activity suppressed ZBP1-induced cell death but enhanced cytokine production in a RIPK1- and RIPK3 kinase activity-dependent manner. Lastly, we provide evidence that ZBP1 signaling contributes to SARS-CoV-2-induced cytokine production. Taken together, we describe a ZBP1-RIPK3-RIPK1-mediated inflammatory signaling pathway relayed by the scaffolding role of RIPKs and regulated by caspases, which may induce inflammation when ZBP1 is activated below the threshold needed to trigger a cell death response.
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Affiliation(s)
- Ruoshi Peng
- Nuffield Department of Medicine, Ludwig Institute for Cancer ResearchUniversity of OxfordOxfordUK
| | - Chris Kedong Wang
- Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research CenterUniversity of CopenhagenCopenhagenDenmark
| | - Xuan Wang‐Kan
- Nuffield Department of Medicine, Ludwig Institute for Cancer ResearchUniversity of OxfordOxfordUK
| | - Manja Idorn
- Department of BiomedicineAarhus UniversityAarhus CDenmark
| | - Majken Kjær
- Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research CenterUniversity of CopenhagenCopenhagenDenmark
| | - Felix Y Zhou
- Nuffield Department of Medicine, Ludwig Institute for Cancer ResearchUniversity of OxfordOxfordUK
| | - Berthe Katrine Fiil
- Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research CenterUniversity of CopenhagenCopenhagenDenmark
| | - Frederik Timmermann
- Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research CenterUniversity of CopenhagenCopenhagenDenmark
| | - Susana L Orozco
- Department of ImmunologyUniversity of WashingtonSeattleWAUSA
| | - Julia McCarthy
- Nuffield Department of Medicine, Ludwig Institute for Cancer ResearchUniversity of OxfordOxfordUK
| | - Carol S Leung
- Nuffield Department of Medicine, Ludwig Institute for Cancer ResearchUniversity of OxfordOxfordUK
| | - Xin Lu
- Nuffield Department of Medicine, Ludwig Institute for Cancer ResearchUniversity of OxfordOxfordUK
| | - Katrin Bagola
- Nuffield Department of Medicine, Ludwig Institute for Cancer ResearchUniversity of OxfordOxfordUK
- Division of ImmunologyFederal Institute for Vaccines and Biomedicines, Paul‐Ehrlich‐InstitutLangenGermany
| | - Jan Rehwinkel
- MRC Human Immunology Unit, Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Andrew Oberst
- Department of ImmunologyUniversity of WashingtonSeattleWAUSA
| | - Jonathan Maelfait
- VIB‐UGent Center for Inflammation ResearchGhentBelgium
- Department of Biomedical Molecular BiologyGhent UniversityGhentBelgium
| | | | - Mads Gyrd‐Hansen
- Nuffield Department of Medicine, Ludwig Institute for Cancer ResearchUniversity of OxfordOxfordUK
- Department of Immunology and Microbiology, LEO Foundation Skin Immunology Research CenterUniversity of CopenhagenCopenhagenDenmark
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21
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Gonzalez-Santamarta M, Bouvier C, Rodriguez MS, Xolalpa W. Ubiquitin-chains dynamics and its role regulating crucial cellular processes. Semin Cell Dev Biol 2022; 132:155-170. [PMID: 34895814 DOI: 10.1016/j.semcdb.2021.11.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/19/2021] [Accepted: 11/23/2021] [Indexed: 12/15/2022]
Abstract
The proteome adapts to multiple situations occurring along the life of the cell. To face these continuous changes, the cell uses posttranslational modifications (PTMs) to control the localization, association with multiple partners, stability, and activity of protein targets. One of the most dynamic protein involved in PTMs is Ubiquitin (Ub). Together with other members of the same family, known as Ubiquitin-like (UbL) proteins, Ub rebuilds the architecture of a protein in a few minutes to change its properties in a very efficient way. This capacity of Ub and UbL is in part due to their potential to form complex architectures when attached to target proteins or when forming Ub chains. The highly dynamic formation and remodeling of Ub chains is regulated by the action of conjugating and deconjugating enzymes that determine, in due time, the correct chain architecture for a particular cellular function. Chain remodeling occurs in response to physiologic stimuli but also in pathologic situations. Here, we illustrate well-documented cases of chain remodeling during DNA repair, activation of the NF-κB pathway and autophagy, as examples of this dynamic regulation. The crucial role of enzymes and cofactors regulating chain remodeling is discussed.
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Affiliation(s)
- Maria Gonzalez-Santamarta
- Laboratoire de Chimie de Coordination (LCC) - UPR 8241 CNRS, and UMR 152 Pharma-Dev, Université de Toulouse, IRD, UPS, 31400 Toulouse, France.
| | - Corentin Bouvier
- Laboratoire de Chimie de Coordination (LCC) - UPR 8241 CNRS, and UMR 152 Pharma-Dev, Université de Toulouse, IRD, UPS, 31400 Toulouse, France.
| | - Manuel S Rodriguez
- Laboratoire de Chimie de Coordination (LCC) - UPR 8241 CNRS, and UMR 152 Pharma-Dev, Université de Toulouse, IRD, UPS, 31400 Toulouse, France.
| | - Wendy Xolalpa
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62250 Cuernavaca, Morelos, Mexico.
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22
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Chen Z, Ioris RM, Richardson S, Van Ess AN, Vendrell I, Kessler BM, Buffa FM, Busino L, Clifford SC, Bullock AN, D'Angiolella V. Disease-associated KBTBD4 mutations in medulloblastoma elicit neomorphic ubiquitylation activity to promote CoREST degradation. Cell Death Differ 2022; 29:1955-1969. [PMID: 35379950 PMCID: PMC9525703 DOI: 10.1038/s41418-022-00983-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/30/2022] Open
Abstract
Medulloblastoma is the most common malignant brain tumour in children. Genomic studies have identified distinct disease subgroups: wnt/wingless (WNT), sonic hedgehog (SHH), and non-WNT/non-SHH, comprising group 3 and group 4. Alterations in WNT and SHH signalling form the pathogenetic basis for their subgroups, whereas those for non-WNT/non-SHH tumours remain largely elusive. Recent analyses have revealed recurrent in-frame insertions in the E3 ubiquitin ligase adaptor Kelch Repeat and BTB Domain Containing 4 (KBTBD4) in cases of group 3/4 medulloblastoma. Critically, group 3/4 tumours with KBTBD4 mutations typically lack other gene-specific alterations, such as MYC amplification, indicating KBTBD4 insertion mutations as the primary genetic driver. Delineating the role of KBTBD4 mutations thus offers significant opportunities to understand tumour pathogenesis and to exploit the underpinning mechanisms therapeutically. Here, we show a novel mechanism in cancer pathogenesis whereby indel mutations in KBTBD4 drive its recognition of neo-substrates for degradation. We observe that KBTBD4 mutants promote the recruitment and ubiquitylation of the REST Corepressor (CoREST), which forms a complex to modulate chromatin accessibility and transcriptional programmes. The degradation of CoREST promoted by KBTBD4 mutation diverts epigenetic programmes inducing significant alterations in transcription to promote increased stemness of cancer cells. Transcriptional analysis of >200 human group 3 and 4 medulloblastomas by RNA-seq, highlights the presence of CoREST and stem-like signatures in tumours with KBTBD4 mutations, which extend to a further sub-set of non-mutant tumours, suggesting CoREST alterations as a novel pathogenetic mechanism of wide relevance in groups 3 and 4. Our findings uncover KBTBD4 mutation as a novel driver of epigenetic reprogramming in non-WNT/non-SHH medulloblastoma, establish a novel mode of tumorigenesis through gain-of-function mutations in ubiquitin ligases (neo-substrate recruitment) and identify both mutant KBTBD4 and CoREST complexes as new druggable targets for improved tumour-specific therapies.
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Affiliation(s)
- Zhuoyao Chen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Rafael M Ioris
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Stacey Richardson
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, NE1 7RU, UK
| | - Ava N Van Ess
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Iolanda Vendrell
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Francesca M Buffa
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Luca Busino
- Department of Cancer Biology and Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven C Clifford
- Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle upon Tyne, NE1 7RU, UK
| | - Alex N Bullock
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Vincenzo D'Angiolella
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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23
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Yin X, Liu Q, Liu F, Tian X, Yan T, Han J, Jiang S. Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis. Front Cell Dev Biol 2022; 10:944460. [PMID: 35874839 PMCID: PMC9298949 DOI: 10.3389/fcell.2022.944460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.
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Affiliation(s)
- Xiu Yin
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Han
- Department of Thyroid and Breast Surgery, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
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24
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Yuan L, Li P, Zheng Q, Wang H, Xiao H. The Ubiquitin-Proteasome System in Apoptosis and Apoptotic Cell Clearance. Front Cell Dev Biol 2022; 10:914288. [PMID: 35874820 PMCID: PMC9300945 DOI: 10.3389/fcell.2022.914288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/16/2022] [Indexed: 12/30/2022] Open
Abstract
Ubiquitination, a critical post-translational modification of proteins, refers to the covalent attachment of ubiquitin to the substrate and is involved in various biological processes such as protein stability regulation, DNA damage repair, and apoptosis, among others. E3 ubiquitin ligases are essential enzymes of the ubiquitin pathway with high substrate specificity and precisely regulate specific proteins’ turnover. As one of the most well-studied forms of programmed cell death, apoptosis is substantially conserved across the evolutionary tree. The final critical stage in apoptosis is the removal of apoptotic cells by professional and non-professional phagocytes. Apoptosis and apoptotic cell clearance are crucial for the normal development, differentiation, and growth of multicellular organisms, as well as their association with a variety of inflammatory and immune diseases. In this review, we discuss the role of ubiquitination and deubiquitination in apoptosis and apoptotic cell clearance.
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Affiliation(s)
- Lei Yuan
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Peiyao Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Qian Zheng
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Hui Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Hui Xiao
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
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25
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Estavoyer B, Messmer C, Echbicheb M, Rudd CE, Milot E, Affar EB. Mechanisms orchestrating the enzymatic activity and cellular functions of deubiquitinases. J Biol Chem 2022; 298:102198. [PMID: 35764170 PMCID: PMC9356280 DOI: 10.1016/j.jbc.2022.102198] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
Deubiquitinases (DUBs) are required for the reverse reaction of ubiquitination and act as major regulators of ubiquitin signaling processes. Emerging evidence suggests that these enzymes are regulated at multiple levels in order to ensure proper and timely substrate targeting and to prevent the adverse consequences of promiscuous deubiquitination. The importance of DUB regulation is highlighted by disease-associated mutations that inhibit or activate DUBs, deregulating their ability to coordinate cellular processes. Here, we describe the diverse mechanisms governing protein stability, enzymatic activity, and function of DUBs. In particular, we outline how DUBs are regulated by their protein domains and interacting partners. Intramolecular interactions can promote protein stability of DUBs, influence their subcellular localization, and/or modulate their enzymatic activity. Remarkably, these intramolecular interactions can induce self-deubiquitination to counteract DUB ubiquitination by cognate E3 ubiquitin ligases. In addition to intramolecular interactions, DUBs can also oligomerize and interact with a wide variety of cellular proteins, thereby forming obligate or facultative complexes that regulate their enzymatic activity and function. The importance of signaling and post-translational modifications in the integrated control of DUB function will also be discussed. While several DUBs are described with respect to the multiple layers of their regulation, the tumor suppressor BAP1 will be outlined as a model enzyme whose localization, stability, enzymatic activity, and substrate recognition are highly orchestrated by interacting partners and post-translational modifications.
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Affiliation(s)
- Benjamin Estavoyer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Clémence Messmer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Mohamed Echbicheb
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Christopher E Rudd
- Laboratory for Cell Signaling in Immunotherapy, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Eric Milot
- Laboratory for Malignant Hematopoiesis and Epigenetic Regulation of Gene Expression, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - El Bachir Affar
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada.
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26
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Mechanistic insights into the subversion of the linear ubiquitin chain assembly complex by the E3 ligase IpaH1.4 of Shigella flexneri. Proc Natl Acad Sci U S A 2022; 119:e2116776119. [PMID: 35294289 PMCID: PMC8944867 DOI: 10.1073/pnas.2116776119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
SignificanceShigella flexneri, a deleterious bacterium, causes massive human infection cases and deaths worldwide. To facilitate survival and replication in infected host cells, S. flexneri can secrete two highly similar E3 ligase effectors, IpaH1.4 and IpaH2.5, to subvert the linear ubiquitin chain assembly complex (LUBAC), a key player involved in numerous antibacterial signaling pathways of host cells but with poorly understood mechanisms. In this study, through systematic biochemical and structural characterization, we elucidate the multiple tactics adopted by IpaH1.4/2.5 to disarm the human LUBAC and provide mechanistic insights into the subversion of host LUBAC by IpaH1.4/2.5 of S. flexneri.
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27
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Zinngrebe J, Moepps B, Monecke T, Gierschik P, Schlichtig F, Barth TFE, Strauß G, Boldrin E, Posovszky C, Schulz A, Beringer O, Rieser E, Jacobsen E, Lorenz MR, Schwarz K, Pannicke U, Walczak H, Niessing D, Schuetz C, Fischer‐Posovszky P, Debatin K. Compound heterozygous variants in OTULIN are associated with fulminant atypical late-onset ORAS. EMBO Mol Med 2022; 14:e14901. [PMID: 35170849 PMCID: PMC8899767 DOI: 10.15252/emmm.202114901] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 01/11/2023] Open
Abstract
Autoinflammatory diseases are a heterogenous group of disorders defined by fever and systemic inflammation suggesting involvement of genes regulating innate immune responses. Patients with homozygous loss-of-function variants in the OTU-deubiquitinase OTULIN suffer from neonatal-onset OTULIN-related autoinflammatory syndrome (ORAS) characterized by fever, panniculitis, diarrhea, and arthritis. Here, we describe an atypical form of ORAS with distinct clinical manifestation of the disease caused by two new compound heterozygous variants (c.258G>A (p.M86I)/c.500G>C (p.W167S)) in the OTULIN gene in a 7-year-old affected by a life-threatening autoinflammatory episode with sterile abscess formation. On the molecular level, we find binding of OTULIN to linear ubiquitin to be compromised by both variants; however, protein stability and catalytic activity is most affected by OTULIN variant p.W167S. These molecular changes together lead to increased levels of linear ubiquitin linkages in patient-derived cells triggering the disease. Our data indicate that the spectrum of ORAS patients is more diverse than previously thought and, thus, supposedly asymptomatic individuals might also be affected. Based on our results, we propose to subdivide the ORAS into classical and atypical entities.
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Affiliation(s)
- Julia Zinngrebe
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Barbara Moepps
- Institute of Pharmacology and ToxicologyUlm UniversityUlmGermany
| | - Thomas Monecke
- Institute of Pharmaceutical BiotechnologyUlm UniversityUlmGermany
| | - Peter Gierschik
- Institute of Pharmacology and ToxicologyUlm UniversityUlmGermany
| | - Ferdinand Schlichtig
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | | | - Gudrun Strauß
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Elena Boldrin
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Carsten Posovszky
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Ansgar Schulz
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Ortraud Beringer
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Eva Rieser
- Institute of Biochemistry I & CECAD Research CenterUniversity of CologneCologneGermany
| | - Eva‐Maria Jacobsen
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | | | - Klaus Schwarz
- Institute for Transfusion MedicineUlm UniversityUlmGermany
- Institute for Clinical Transfusion Medicine and Immunogenetics UlmGerman Red Cross Blood Service Baden‐Wuerttemberg – HessenUlmGermany
| | | | - Henning Walczak
- Institute of Biochemistry I & CECAD Research CenterUniversity of CologneCologneGermany
- UCL Cancer InstituteLondonUK
| | - Dierk Niessing
- Institute of Pharmaceutical BiotechnologyUlm UniversityUlmGermany
| | | | | | - Klaus‐Michael Debatin
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
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28
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Tripathi-Giesgen I, Behrends C, Alpi AF. The ubiquitin ligation machinery in the defense against bacterial pathogens. EMBO Rep 2021; 22:e52864. [PMID: 34515402 PMCID: PMC8567218 DOI: 10.15252/embr.202152864] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/21/2021] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin system is an important part of the host cellular defense program during bacterial infection. This is in particular evident for a number of bacteria including Salmonella Typhimurium and Mycobacterium tuberculosis which—inventively as part of their invasion strategy or accidentally upon rupture of seized host endomembranes—become exposed to the host cytosol. Ubiquitylation is involved in the detection and clearance of these bacteria as well as in the activation of innate immune and inflammatory signaling. Remarkably, all these defense responses seem to emanate from a dense layer of ubiquitin which coats the invading pathogens. In this review, we focus on the diverse group of host cell E3 ubiquitin ligases that help to tailor this ubiquitin coat. In particular, we address how the divergent ubiquitin conjugation mechanisms of these ligases contribute to the complexity of the anti‐bacterial coating and the recruitment of different ubiquitin‐binding effectors. We also discuss the activation and coordination of the different E3 ligases and which strategies bacteria evolved to evade the activities of the host ubiquitin system.
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Affiliation(s)
- Ishita Tripathi-Giesgen
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Behrends
- Munich Cluster for Systems Neurology (SyNergy), Medical Faculty, Ludwig-Maximilians-University München, München, Germany
| | - Arno F Alpi
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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29
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Fung SY, Lu HY, Sharma M, Sharma AA, Saferali A, Jia A, Abraham L, Klein T, Gold MR, Noterangelo LD, Overall CM, Turvey SE. MALT1-Dependent Cleavage of HOIL1 Modulates Canonical NF-κB Signaling and Inflammatory Responsiveness. Front Immunol 2021; 12:749794. [PMID: 34721419 PMCID: PMC8552041 DOI: 10.3389/fimmu.2021.749794] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Nuclear factor kappa B (NF-κB) is a critical transcription factor involved in regulating cell activation, inflammation, and survival. The linear ubiquitin chain assembly complex (LUBAC) which consists of HOIL1, HOIP, and SHARPIN, catalyzes the linear ubiquitination of target proteins—a post-translational modification that is essential for NF-κB activation. Human germline pathogenic variants that dysregulate linear ubiquitination and NF-κB signaling are associated with immunodeficiency and/or autoinflammation including dermatitis, recurrent fevers, systemic inflammation and enteropathy. We previously identified MALT1 paracaspase as a novel negative regulator of LUBAC by proteolytic cleavage of HOIL1. To directly investigate the impact of HOIL1 cleavage activity on the inflammatory response, we employed a stable transduction system to express and directly compare non-cleavable HOIL1 with wild-type HOIL1 in primary HOIL1-deficient patient skin fibroblasts. We discovered that non-cleavable HOIL1 resulted in enhanced NF-κB signaling in response to innate stimuli. Transcriptomics revealed enrichment of inflammation and proinflammatory cytokine-related pathways after stimulation. Multiplexed cytokine assays confirmed a ‘hyperinflammatory’ phenotype in these cells. This work highlights the physiological importance of MALT1-dependent cleavage and modulation of HOIL1 on NF-κB signaling and inflammation, provides a mechanism for the autoinflammation observed in MALT1-deficient patients, and will inform the development of therapeutics that target MALT1 paracaspase and LUBAC function in treating autoinflammatory skin diseases.
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Affiliation(s)
- Shan-Yu Fung
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Province and Ministry Co-Sponsored Collaborative Innovation Center for Medical Epigenetics and Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Henry Y Lu
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Mehul Sharma
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Ashish A Sharma
- Department of Pathology, Case Western Reserve University, Cleveland, OH, United States
| | - Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, United States
| | - Alicia Jia
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Libin Abraham
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Theo Klein
- Department of Analytical Solutions, Ducares/Triskelion BV, Utrecht, Netherlands
| | - Michael R Gold
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Luigi D Noterangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, Department of Oral Biological and Medical Science, Center for Blood Research, The University of British Columbia, Vancouver, BC, Canada
| | - Stuart E Turvey
- Department of Pediatrics, British Columbia Children's Hospital and The University of British Columbia, Vancouver, BC, Canada.,Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada.,Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
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30
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LUBAC: a new player in polyglucosan body disease. Biochem Soc Trans 2021; 49:2443-2454. [PMID: 34709403 PMCID: PMC8589444 DOI: 10.1042/bst20210838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/13/2022]
Abstract
Altered protein ubiquitination is associated with the pathobiology of numerous diseases; however, its involvement in glycogen metabolism and associated polyglucosan body (PB) disease has not been investigated in depth. In PB disease, excessively long and less branched glycogen chains (polyglucosan bodies, PBs) are formed, which precipitate in different tissues causing myopathy, cardiomyopathy and/or neurodegeneration. Linear ubiquitin chain assembly complex (LUBAC) is a multi-protein complex composed of two E3 ubiquitin ligases HOIL-1L and HOIP and an adaptor protein SHARPIN. Together they are responsible for M1-linked ubiquitination of substrates primarily related to immune signaling and cell death pathways. Consequently, severe immunodeficiency is a hallmark of many LUBAC deficient patients. Remarkably, all HOIL-1L deficient patients exhibit accumulation of PBs in different organs especially skeletal and cardiac muscle resulting in myopathy and cardiomyopathy with heart failure. This emphasizes LUBAC's important role in glycogen metabolism. To date, neither a glycogen metabolism-related LUBAC substrate nor the molecular mechanism are known. Hence, current reviews on LUBAC's involvement in glycogen metabolism are lacking. Here, we aim to fill this gap by describing LUBAC's involvement in PB disease. We present a comprehensive review of LUBAC structure, its role in M1-linked and other types of atypical ubiquitination, PB pathology in human patients and findings in new mouse models to study the disease. We conclude the review with recent drug developments and near-future gene-based therapeutic approaches to treat LUBAC related PB disease.
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31
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Elliott PR, Leske D, Wagstaff J, Schlicher L, Berridge G, Maslen S, Timmermann F, Ma B, Fischer R, Freund SMV, Komander D, Gyrd-Hansen M. Regulation of CYLD activity and specificity by phosphorylation and ubiquitin-binding CAP-Gly domains. Cell Rep 2021; 37:109777. [PMID: 34610306 PMCID: PMC8511506 DOI: 10.1016/j.celrep.2021.109777] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
Non-degradative ubiquitin chains and phosphorylation events govern signaling responses by innate immune receptors. The deubiquitinase CYLD in complex with SPATA2 is recruited to receptor signaling complexes by the ubiquitin ligase LUBAC and regulates Met1- and Lys63-linked polyubiquitin and receptor signaling outcomes. Here, we investigate the molecular determinants of CYLD activity. We reveal that two CAP-Gly domains in CYLD are ubiquitin-binding domains and demonstrate a requirement of CAP-Gly3 for CYLD activity and regulation of immune receptor signaling. Moreover, we identify a phosphorylation switch outside of the catalytic USP domain, which activates CYLD toward Lys63-linked polyubiquitin. The phosphorylated residue Ser568 is a novel tumor necrosis factor (TNF)-regulated phosphorylation site in CYLD and works in concert with Ser418 to enable CYLD-mediated deubiquitination and immune receptor signaling. We propose that phosphorylated CYLD, together with SPATA2 and LUBAC, functions as a ubiquitin-editing complex that balances Lys63- and Met1-linked polyubiquitin at receptor signaling complexes to promote LUBAC signaling.
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Affiliation(s)
- Paul R Elliott
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Derek Leske
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jane Wagstaff
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Lisa Schlicher
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Georgina Berridge
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Sarah Maslen
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Frederik Timmermann
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Biao Ma
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Roman Fischer
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Stefan M V Freund
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, 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.
| | - Mads Gyrd-Hansen
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK; LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Maersk Tower, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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Zhang H, Zhao X, Guo Y, Chen R, He J, Li L, Qiang Z, Yang Q, Liu X, Huang C, Lu R, Fang J, Cao Y, Huang J, Wang Y, Huang J, Chen GQ, Cheng J, Yu J. Hypoxia regulates overall mRNA homeostasis by inducing Met 1-linked linear ubiquitination of AGO2 in cancer cells. Nat Commun 2021; 12:5416. [PMID: 34518544 PMCID: PMC8438024 DOI: 10.1038/s41467-021-25739-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 08/26/2021] [Indexed: 11/30/2022] Open
Abstract
Hypoxia is the most prominent feature in human solid tumors and induces activation of hypoxia-inducible factors and their downstream genes to promote cancer progression. However, whether and how hypoxia regulates overall mRNA homeostasis is unclear. Here we show that hypoxia inhibits global-mRNA decay in cancer cells. Mechanistically, hypoxia induces the interaction of AGO2 with LUBAC, the linear ubiquitin chain assembly complex, which co-localizes with miRNA-induced silencing complex and in turn catalyzes AGO2 occurring Met1-linked linear ubiquitination (M1-Ubi). A series of biochemical experiments reveal that M1-Ubi of AGO2 restrains miRNA-mediated gene silencing. Moreover, combination analyses of the AGO2-associated mRNA transcriptome by RIP-Seq and the mRNA transcriptome by RNA-Seq confirm that AGO2 M1-Ubi interferes miRNA-targeted mRNA recruiting to AGO2, and thereby facilitates accumulation of global mRNAs. By this mechanism, short-term hypoxia may protect overall mRNAs and enhances stress tolerance, whereas long-term hypoxia in tumor cells results in seriously changing the entire gene expression profile to drive cell malignant evolution. Met1-linked linear ubiquitination (M1-Ubi) is catalyzed by linear ubiquitin chain assembly complex (LUBAC). Here the authors show that Ago2 protein is M1-Ubi modified by LUBAC complex under hypoxia condition leading to less association of miRNA target mRNAs to Ago2 protein and de-repression of miRNA targets.
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Affiliation(s)
- Hailong Zhang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xian Zhao
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yanmin Guo
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ran Chen
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jianfeng He
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lian Li
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zhe Qiang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Qianqian Yang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaojia Liu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Caihu Huang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Runhui Lu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiayu Fang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yingting Cao
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jiayi Huang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yanli Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jian Huang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Guo-Qiang Chen
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jinke Cheng
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Jianxiu Yu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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33
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Zhou Y, Bu Z, Qian J, Cheng Y, Qiao L, Yang S, Cheng S, Wang X, Ren L, Yang Y. Brucella melitensis UGPase inhibits the activation of NF-κB by modulating the ubiquitination of NEMO. BMC Vet Res 2021; 17:289. [PMID: 34461896 PMCID: PMC8404259 DOI: 10.1186/s12917-021-02993-9] [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: 06/19/2020] [Accepted: 08/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND UTP-glucose-1-phosphoryl transferase (UGPase) catalyzes the synthesis of UDP-glucose, which is essential for generating the glycogen needed for the synthesis of bacterial lipopolysaccharide (LPS) and capsular polysaccharide, which play important roles in bacterial virulence. However, the molecular function of UGPase in Brucella is still unknown. RESULTS In this study, the ubiquitination modification of host immune-related protein in cells infected with UGPase-deleted or wild-type Brucella was analyzed using ubiquitination proteomics technology. The ubiquitination modification level and type of NF-κB Essential Modulator (NEMO or Ikbkg), a molecule necessary for NF-κB signal activation, was evaluated using Coimmunoprecipitation, Western blot, and dual-Luciferase Assay. We found 80 ubiquitin proteins were upregulated and 203 ubiquitin proteins were downregulated in cells infected with B. melitensis 16 M compared with those of B. melitensis UGPase-deleted strain (16 M-UGPase-). Moreover, the ubiquitin-modified proteins were mostly enriched in the categories of regulation of kinase/NF-κB signaling and response to a bacterium, suggesting Brucella UGPase inhibits ubiquitin modification of related proteins in the host NF-κB signaling pathway. Further analysis showed that the ubiquitination levels of NEMO K63 (K63-Ub) and Met1 (Met1-Ub) were significantly increased in the 16 M-UGPase--infected cells compared with that of the 16 M-infected cells, further confirming that the ubiquitination levels of NF-κB signaling-related proteins were regulated by the bacterial UGPase. Besides, the expression level of IκBα was decreased, but the level of p-P65 was significantly increased in the 16 M-UGPase--infected cells compared with that of the 16 M- and mock-infected cells, demonstrating that B. melitensis UGPase can significantly inhibit the degradation of IκBα and the phosphorylation of p65, and thus suppressing the NF-κB pathway. CONCLUSIONS The results of this study showed that Brucella melitensis UGPase inhibits the activation of NF-κB by modulating the ubiquitination of NEMO, which will provide a new scientific basis for the study of immune mechanisms induced by Brucella.
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Affiliation(s)
- Yucheng Zhou
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 130112, Changchun, China
| | - Zhaoyang Bu
- Military Veterinary Institute, Academy of Military Medical Sciences, 130112, Changchun, China
| | - Jing Qian
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, China
| | - Yuening Cheng
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 130112, Changchun, China
| | - Lianjiang Qiao
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 130112, Changchun, China
| | - Sen Yang
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 130112, Changchun, China
| | - Shipeng Cheng
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 130112, Changchun, China
| | - Xinglong Wang
- Military Veterinary Institute, Academy of Military Medical Sciences, 130112, Changchun, China
| | - Linzhu Ren
- College of Animal Sciences, Jilin University, 130062, Changchun, China.
| | - Yanling Yang
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 130112, Changchun, China.
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34
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The Role of microRNAs in NK Cell Development and Function. Cells 2021; 10:cells10082020. [PMID: 34440789 PMCID: PMC8391642 DOI: 10.3390/cells10082020] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/29/2021] [Accepted: 08/04/2021] [Indexed: 12/24/2022] Open
Abstract
The clinical use of natural killer (NK) cells is at the forefront of cellular therapy. NK cells possess exceptional antitumor cytotoxic potentials and can generate significant levels of proinflammatory cytokines. Multiple genetic manipulations are being tested to augment the anti-tumor functions of NK cells. One such method involves identifying and altering microRNAs (miRNAs) that play essential roles in the development and effector functions of NK cells. Unique miRNAs can bind and inactivate mRNAs that code for cytotoxic proteins. MicroRNAs, such as the members of the Mirc11 cistron, downmodulate ubiquitin ligases that are central to the activation of the obligatory transcription factors responsible for the production of inflammatory cytokines. These studies reveal potential opportunities to post-translationally enhance the effector functions of human NK cells while reducing unwanted outcomes. Here, we summarize the recent advances made on miRNAs in murine and human NK cells and their relevance to NK cell development and functions.
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35
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Tonnus W, Belavgeni A, Beuschlein F, Eisenhofer G, Fassnacht M, Kroiss M, Krone NP, Reincke M, Bornstein SR, Linkermann A. The role of regulated necrosis in endocrine diseases. Nat Rev Endocrinol 2021; 17:497-510. [PMID: 34135504 PMCID: PMC8207819 DOI: 10.1038/s41574-021-00499-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/22/2021] [Indexed: 12/13/2022]
Abstract
The death of endocrine cells is involved in type 1 diabetes mellitus, autoimmunity, adrenopause and hypogonadotropism. Insights from research on basic cell death have revealed that most pathophysiologically important cell death is necrotic in nature, whereas regular metabolism is maintained by apoptosis programmes. Necrosis is defined as cell death by plasma membrane rupture, which allows the release of damage-associated molecular patterns that trigger an immune response referred to as necroinflammation. Regulated necrosis comes in different forms, such as necroptosis, pyroptosis and ferroptosis. In this Perspective, with a focus on the endocrine environment, we introduce these cell death pathways and discuss the specific consequences of regulated necrosis. Given that clinical trials of necrostatins for the treatment of autoimmune conditions have already been initiated, we highlight the therapeutic potential of such novel therapeutic approaches that, in our opinion, should be tested in endocrine disorders in the future.
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Affiliation(s)
- Wulf Tonnus
- Clinic of Internal Medicine III, Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Alexia Belavgeni
- Clinic of Internal Medicine III, Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Felix Beuschlein
- Medizinische Klinik und Poliklinik IV, Hospital of the Ludwig-Maximilian-University Munich, Munich, Germany
- Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, Universitätsspital Zürich, Zürich, Switzerland
| | - Graeme Eisenhofer
- Clinic of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Martin Fassnacht
- Clinic of Internal Medicine I, Division of Endocrinology and Diabetology, University Hospital, University of Würzburg, Würzburg, Germany
| | - Matthias Kroiss
- Clinic of Internal Medicine I, Division of Endocrinology and Diabetology, University Hospital, University of Würzburg, Würzburg, Germany
| | - Nils P Krone
- Clinic of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- Academic Unit of Child Health, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Martin Reincke
- Medizinische Klinik und Poliklinik IV, Hospital of the Ludwig-Maximilian-University Munich, Munich, Germany
| | - Stefan R Bornstein
- Klinik für Endokrinologie, Diabetologie und Klinische Ernährung, Universitätsspital Zürich, Zürich, Switzerland
- Clinic of Internal Medicine III, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- Diabetes and Nutritional Sciences, King's College London, London, UK
| | - Andreas Linkermann
- Clinic of Internal Medicine III, Division of Nephrology, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany.
- Biotechnology Center, Technische Universität Dresden, Dresden, Germany.
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36
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Hong JY, Lin SC, Kuo BJ, Lo YC. Structural and Biochemical Basis for Higher-Order Assembly between A20-Binding Inhibitor of NF-κB 1 (ABIN1) and M1-Linked Ubiquitins. J Mol Biol 2021; 433:167116. [PMID: 34161781 DOI: 10.1016/j.jmb.2021.167116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 06/03/2021] [Accepted: 06/17/2021] [Indexed: 10/21/2022]
Abstract
Polyubiquitination is important in controlling NF-κB signaling. Excessive NF-κB activity has been linked to inflammatory disorders and autoimmune diseases, while ABIN1 could attenuate NF-κB activation to maintain immune homeostasis by utilizing UBAN to recognize linear (M1)-linked polyubiquitinated NF-κB activation mediators, including NEMO, IRAK1 and RIP1. PolyUb-mediated UBAN recruitment remains undetermined, since the recognition studies focused mostly on di-ubiquitin (diUb). Here we report three crystal structures of human ABIN1 UBAN (hABIN1UBAN) in complex with M1-linked diUb, triUb, and tetraUb, respectively. Notably, the hABIN1UBAN:diUb structure reveals that a diUb randomly binds one of the Ub-binding sites of the hABIN1UBAN dimer and leaves the other site vacant. Together with the ITC and gel-filtration analyses, we found that M1-triUb and M1-tetraUb adopt two unique conformations, instead of an elongated one, and they preferentially use the N-terminal two-Ub unit to bind the primary Ub-binding site of a hABIN1UBAN dimer and the C-terminal two-Ub unit to bind the secondary Ub-binding site of another hABIN1UBAN dimer. Especially, our results suggest that two ABIN1UBAN dimers cooperatively bind two UBAN-binding units of a tetraUb or vice versa. Since the UBAN family members share a conserved diUb-binding mode, our results suggest that M1-polyUb modification allows multiple copies of the two-tandem Ub unit to simultaneously coordinate multiple and/or different binding partners to increase their local concentrations and to facilitate the formation of a large signaling complex. Our study provides a structural-functional glimpse of M1-polyUb as a multiple-molecule binding platform to exert its intrinsic structural plasticity in mediating cellular signaling.
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Affiliation(s)
- Jhen-Yi Hong
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Su-Chang Lin
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Bai-Jiun Kuo
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yu-Chih Lo
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 70101, Taiwan.
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37
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Tryptophanemia is controlled by a tryptophan-sensing mechanism ubiquitinating tryptophan 2,3-dioxygenase. Proc Natl Acad Sci U S A 2021; 118:2022447118. [PMID: 34074763 DOI: 10.1073/pnas.2022447118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Maintaining stable tryptophan levels is required to control neuronal and immune activity. We report that tryptophan homeostasis is largely controlled by the stability of tryptophan 2,3-dioxygenase (TDO), the hepatic enzyme responsible for tryptophan catabolism. High tryptophan levels stabilize the active tetrameric conformation of TDO through binding noncatalytic exosites, resulting in rapid catabolism of tryptophan. In low tryptophan, the lack of tryptophan binding in the exosites destabilizes the tetramer into inactive monomers and dimers and unmasks a four-amino acid degron that triggers TDO polyubiquitination by SKP1-CUL1-F-box complexes, resulting in proteasome-mediated degradation of TDO and rapid interruption of tryptophan catabolism. The nonmetabolizable analog alpha-methyl-tryptophan stabilizes tetrameric TDO and thereby stably reduces tryptophanemia. Our results uncover a mechanism allowing a rapid adaptation of tryptophan catabolism to ensure quick degradation of excess tryptophan while preventing further catabolism below physiological levels. This ensures a tight control of tryptophanemia as required for both neurological and immune homeostasis.
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Verboom L, Hoste E, van Loo G. OTULIN in NF-κB signaling, cell death, and disease. Trends Immunol 2021; 42:590-603. [PMID: 34074601 DOI: 10.1016/j.it.2021.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 01/30/2023]
Abstract
Tight control of inflammatory signaling pathways is an absolute requirement to avoid chronic inflammation and disease. One of the proteins responsible for such control is OTU deubiquitinase with linear linkage specificity (OTULIN), the only mammalian deubiquitinating enzyme (DUB) exclusively hydrolyzing linear ubiquitin chains from proteins modified by the linear ubiquitin chain assembly complex (LUBAC) described thus far. Recent findings show that loss-of-function mutations in OTULIN underlie a severe early-onset human autoinflammatory disease and severe pathology in experimental mouse models. Here, we review the molecular and cellular mechanisms by which OTULIN controls inflammation and discuss the involvement of OTULIN in inflammatory disease development. We also highlight several newly identified roles for OTULIN, including a ubiquitin-independent function.
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Affiliation(s)
- Lien Verboom
- VIB Center for Inflammation Research, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Esther Hoste
- VIB Center for Inflammation Research, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Geert van Loo
- VIB Center for Inflammation Research, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.
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Yu H, Hong X, Wu H, Zheng F, Zeng Z, Dai W, Yin L, Liu D, Tang D, Dai Y. The Chromatin Accessibility Landscape of Peripheral Blood Mononuclear Cells in Patients With Systemic Lupus Erythematosus at Single-Cell Resolution. Front Immunol 2021; 12:641886. [PMID: 34084162 PMCID: PMC8168536 DOI: 10.3389/fimmu.2021.641886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 04/14/2021] [Indexed: 12/12/2022] Open
Abstract
Objective Systemic lupus erythematosus (SLE) is a complex autoimmune disease, and various immune cells are involved in the initiation, progression, and regulation of SLE. Our goal was to reveal the chromatin accessibility landscape of peripheral blood mononuclear cells (PBMCs) in SLE patients at single-cell resolution and identify the transcription factors (TFs) that may drive abnormal immune responses. Methods The assay for transposase accessible chromatin in single-cell sequencing (scATAC-seq) method was applied to map the landscape of active regulatory DNA in immune cells from SLE patients at single-cell resolution, followed by clustering, peak annotation and motif analysis of PBMCs in SLE. Results Peripheral blood mononuclear cells were robustly clustered based on their types without using antibodies. We identified twenty patterns of TF activation that drive abnormal immune responses in SLE patients. Then, we observed ten genes that were highly associated with SLE pathogenesis by altering T cell activity. Finally, we found 12 key TFs regulating the above six genes (CD83, ELF4, ITPKB, RAB27A, RUNX3, and ZMIZ1) that may be related to SLE disease pathogenesis and were significantly enriched in SLE patients (p <0.05, FC >2). With qPCR experiments on CD83, ELF4, RUNX3, and ZMIZ1 in B cells, we observed a significant difference in the expression of genes (ELF4, RUNX3, and ZMIZ1), which were regulated by seven TFs (EWSR1-FLI1, MAF, MAFA, NFIB, NR2C2 (var. 2), TBX4, and TBX5). Meanwhile, the seven TFs showed highly accessible binding sites in SLE patients. Conclusions These results confirm the importance of using single-cell sequencing to uncover the real features of immune cells in SLE patients, reveal key TFs in SLE-PBMCs, and provide foundational insights relevant for epigenetic therapy.
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Affiliation(s)
- Haiyan Yu
- Department of Clinical Medical Research Center, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, China.,The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Xiaoping Hong
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Hongwei Wu
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Fengping Zheng
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Zhipeng Zeng
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, United States
| | - Lianghong Yin
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Dongzhou Liu
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Donge Tang
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
| | - Yong Dai
- Department of Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, China
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Honjo H, Watanabe T, Kamata K, Minaga K, Kudo M. RIPK2 as a New Therapeutic Target in Inflammatory Bowel Diseases. Front Pharmacol 2021; 12:650403. [PMID: 33935757 PMCID: PMC8079979 DOI: 10.3389/fphar.2021.650403] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/26/2021] [Indexed: 12/28/2022] Open
Abstract
Inflammatory bowel diseases (IBDs) are becoming more frequent worldwide. A significant fraction of patients with IBD are refractory to various types of therapeutic biologics and small molecules. Therefore, identification of novel therapeutic targets in IBD is required. Receptor-interacting serine/threonine kinase 2 (RIPK2), also known as receptor-interacting protein 2 (RIP2), is a downstream signaling molecule for nucleotide-binding oligomerization domain 1 (NOD1), NOD2, and Toll-like receptors (TLRs). RIPK2 is expressed in antigen-presenting cells, such as dendritic cells and macrophages. Recognition of microbe-associated molecular patterns by NOD1, NOD2, and TLRs leads to the interaction between RIPK2 and these innate immune receptors, followed by the release of pro-inflammatory cytokines such as TNF-α, IL-6, and IL-12/23p40 through the activation of nuclear factor kappa B and mitogen-activated protein kinases. Thus, activation of RIPK2 plays a critical role in host defense against microbial infections. Recent experimental and clinical studies have provided evidence that activation of RIPK2 is involved in the development of autoimmune diseases, especially IBDs. In addition, the colonic mucosa of patients with IBD exhibits enhanced expression of RIPK2 and associated signaling molecules. Furthermore, the blockage of RIPK2 activation ameliorates the development of experimental murine colitis. Thus, activation of RIPK2 underlies IBD immunopathogenesis. In this review, we attempt to clarify the roles played by RIPK2 in the development of IBD by focusing on its associated signaling pathways. We also discuss the possibility of using RIPK2 as a new therapeutic target in IBD.
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Affiliation(s)
- Hajime Honjo
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Tomohiro Watanabe
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Ken Kamata
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Kosuke Minaga
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Masatoshi Kudo
- Department of Gastroenterology and Hepatology, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
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41
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Budroni V, Versteeg GA. Negative Regulation of the Innate Immune Response through Proteasomal Degradation and Deubiquitination. Viruses 2021; 13:584. [PMID: 33808506 PMCID: PMC8066222 DOI: 10.3390/v13040584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/26/2021] [Accepted: 03/27/2021] [Indexed: 12/25/2022] Open
Abstract
The rapid and dynamic activation of the innate immune system is achieved through complex signaling networks regulated by post-translational modifications modulating the subcellular localization, activity, and abundance of signaling molecules. Many constitutively expressed signaling molecules are present in the cell in inactive forms, and become functionally activated once they are modified with ubiquitin, and, in turn, inactivated by removal of the same post-translational mark. Moreover, upon infection resolution a rapid remodeling of the proteome needs to occur, ensuring the removal of induced response proteins to prevent hyperactivation. This review discusses the current knowledge on the negative regulation of innate immune signaling pathways by deubiquitinating enzymes, and through degradative ubiquitination. It focusses on spatiotemporal regulation of deubiquitinase and E3 ligase activities, mechanisms for re-establishing proteostasis, and degradation through immune-specific feedback mechanisms vs. general protein quality control pathways.
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Affiliation(s)
| | - Gijs A. Versteeg
- Max Perutz Labs, Department of Microbiology, Immunobiology, and Genetics, University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria;
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42
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Roudaire T, Héloir MC, Wendehenne D, Zadoroznyj A, Dubrez L, Poinssot B. Cross Kingdom Immunity: The Role of Immune Receptors and Downstream Signaling in Animal and Plant Cell Death. Front Immunol 2021; 11:612452. [PMID: 33763054 PMCID: PMC7982415 DOI: 10.3389/fimmu.2020.612452] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/29/2020] [Indexed: 12/14/2022] Open
Abstract
Both plants and animals are endowed with sophisticated innate immune systems to combat microbial attack. In these multicellular eukaryotes, innate immunity implies the presence of cell surface receptors and intracellular receptors able to detect danger signal referred as damage-associated molecular patterns (DAMPs) and pathogen-associated molecular patterns (PAMPs). Membrane-associated pattern recognition receptors (PRRs), such as Toll-like receptors (TLRs), C-type lectin receptors (CLRs), receptor-like kinases (RLKs), and receptor-like proteins (RLPs) are employed by these organisms for sensing different invasion patterns before triggering antimicrobial defenses that can be associated with a form of regulated cell death. Intracellularly, animals nucleotide-binding and oligomerization domain (NOD)-like receptors or plants nucleotide-binding domain (NBD)-containing leucine rich repeats (NLRs) immune receptors likely detect effectors injected into the host cell by the pathogen to hijack the immune signaling cascade. Interestingly, during the co-evolution between the hosts and their invaders, key cross-kingdom cell death-signaling macromolecular NLR-complexes have been selected, such as the inflammasome in mammals and the recently discovered resistosome in plants. In both cases, a regulated cell death located at the site of infection constitutes a very effective mean for blocking the pathogen spread and protecting the whole organism from invasion. This review aims to describe the immune mechanisms in animals and plants, mainly focusing on cell death signaling pathways, in order to highlight recent advances that could be used on one side or the other to identify the missing signaling elements between the perception of the invasion pattern by immune receptors, the induction of defenses or the transmission of danger signals to other cells. Although knowledge of plant immunity is less advanced, these organisms have certain advantages allowing easier identification of signaling events, regulators and executors of cell death, which could then be exploited directly for crop protection purposes or by analogy for medical research.
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Affiliation(s)
- Thibault Roudaire
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Marie-Claire Héloir
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - David Wendehenne
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Aymeric Zadoroznyj
- Institut National de la Santé et de la Recherche Médicale (Inserm), LNC UMR1231, Dijon, France.,LNC UMR1231, Université de Bourgogne Franche-Comté, Dijon, France
| | - Laurence Dubrez
- Institut National de la Santé et de la Recherche Médicale (Inserm), LNC UMR1231, Dijon, France.,LNC UMR1231, Université de Bourgogne Franche-Comté, Dijon, France
| | - Benoit Poinssot
- Agroécologie, Agrosup Dijon, CNRS, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
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43
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Design of pyrido[2,3-d]pyrimidin-7-one inhibitors of receptor interacting protein kinase-2 (RIPK2) and nucleotide-binding oligomerization domain (NOD) cell signaling. Eur J Med Chem 2021; 215:113252. [PMID: 33601309 DOI: 10.1016/j.ejmech.2021.113252] [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: 12/11/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 11/23/2022]
Abstract
Receptor interacting protein kinase-2 (RIPK2) is an enzyme involved in the transduction of pro-inflammatory nucleotide-binding oligomerization domain (NOD) cell signaling, a pathway implicated in numerous chronic inflammatory conditions. Herein, a pyrido[2,3-d]pyrimidin-7-one based class of RIPK2 kinase and NOD2 cell signaling inhibitors is described. For example, 33 (e.g. UH15-15) inhibited RIPK2 kinase (IC50 = 8 ± 4 nM) and displayed > 300-fold selectivity versus structurally related activin receptor-like kinase 2 (ALK2). This molecule blocked NOD2-dependent HEKBlue NF-κB activation (IC50 = 20 ± 5 nM) and CXCL8 production (at concentrations > 10 nM). Molecular docking suggests that engagement of Ser25 in the glycine-rich loop may provide increased selectivity versus ALK2 and optimal occupancy of the region between the gatekeeper and the αC-helix may contribute to potent NOD2 cell signaling inhibition. Finally, this compound also demonstrated favorable in vitro ADME and pharmacokinetic properties (e.g. Cmax = 5.7 μM, Tmax = 15 min, t1/2 = 3.4 h and Cl = 45 mL/min/kg following single 10 mg/kg intraperitoneal administration) further supporting the use of pyrido[2,3-d]pyrimidin-7-ones as a new structure class of RIPK2 kinase and NOD cell signaling inhibitors.
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44
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Fiil BK, Gyrd-Hansen M. The Met1-linked ubiquitin machinery in inflammation and infection. Cell Death Differ 2021; 28:557-569. [PMID: 33473179 PMCID: PMC7816137 DOI: 10.1038/s41418-020-00702-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023] Open
Abstract
Ubiquitination is an essential post-translational modification that regulates most cellular processes. The assembly of ubiquitin into polymeric chains by E3 ubiquitin ligases underlies the pleiotropic functions ubiquitin chains regulate. Ubiquitin chains assembled via the N-terminal methionine, termed Met1-linked ubiquitin chains or linear ubiquitin chains, have emerged as essential signalling scaffolds that regulate pro-inflammatory responses, anti-viral interferon responses, cell death and xenophagy of bacterial pathogens downstream of innate immune receptors. Met1-linked ubiquitin chains are exclusively assembled by the linear ubiquitin chain assembly complex, LUBAC, and are disassembled by the deubiquitinases OTULIN and CYLD. Genetic defects that perturb the regulation of Met1-linked ubiquitin chains causes severe immune-related disorders, illustrating their potent signalling capacity. Here, we review the current knowledge about the cellular machinery that conjugates, recognises, and disassembles Met1-linked ubiquitin chains, and discuss the function of this unique posttranslational modification in regulating inflammation, cell death and immunity to pathogens.
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Affiliation(s)
- Berthe Katrine Fiil
- grid.5254.60000 0001 0674 042XLEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Maersk Tower, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Mads Gyrd-Hansen
- grid.5254.60000 0001 0674 042XLEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Maersk Tower, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark ,grid.4991.50000 0004 1936 8948Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ UK
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45
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Jahan AS, Elbæk CR, Damgaard RB. Met1-linked ubiquitin signalling in health and disease: inflammation, immunity, cancer, and beyond. Cell Death Differ 2021; 28:473-492. [PMID: 33441937 DOI: 10.1038/s41418-020-00676-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 12/22/2022] Open
Abstract
Post-translational modification of proteins with ubiquitin (ubiquitination) provides a rapid and versatile mechanism for regulating cellular signalling systems. Met1-linked (or 'linear') ubiquitin chains have emerged as a key regulatory signal that controls cell death, immune signalling, and other vital cellular functions. The molecular machinery that assembles, senses, and disassembles Met1-linked ubiquitin chains is highly specific. In recent years, the thorough biochemical and genetic characterisation of the enzymes and proteins of the Met1-linked ubiquitin signalling machinery has paved the way for substantial advances in our understanding of how Met1-linked ubiquitin chains control cell signalling and biology. Here, we review current knowledge and recent insights into the role of Met1-linked ubiquitin chains in cell signalling with an emphasis on their role in disease biology. Met1-linked ubiquitin has potent regulatory functions in immune signalling, NF-κB transcription factor activation, and cell death. Importantly, mounting evidence shows that dysregulation of Met1-linked ubiquitin signalling is associated with multiple human diseases, including immune disorders, cancer, and neurodegeneration. We discuss the latest evidence on the cellular function of Met1-linked ubiquitin in the context of its associated diseases and highlight new emerging roles of Met1-linked ubiquitin chains in cell signalling, including regulation of protein quality control and metabolism.
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Affiliation(s)
- Akhee Sabiha Jahan
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark
| | - Camilla Reiter Elbæk
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark
| | - Rune Busk Damgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, 2800 Kgs, Lyngby, Denmark.
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46
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Topal Y, Gyrd-Hansen M. RIPK2 NODs to XIAP and IBD. Semin Cell Dev Biol 2021; 109:144-150. [DOI: 10.1016/j.semcdb.2020.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 12/22/2022]
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47
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Oikawa D, Hatanaka N, Suzuki T, Tokunaga F. Cellular and Mathematical Analyses of LUBAC Involvement in T Cell Receptor-Mediated NF-κB Activation Pathway. Front Immunol 2020; 11:601926. [PMID: 33329596 PMCID: PMC7732508 DOI: 10.3389/fimmu.2020.601926] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 10/26/2020] [Indexed: 02/02/2023] Open
Abstract
The LUBAC ubiquitin ligase complex, composed of the HOIP, HOIL-1L, and SHARPIN subunits, stimulates the canonical nuclear factor-κB (NF-κB) activation pathways through its Met1-linked linear ubiquitination activity. Here we performed cellular and mathematical modeling analyses of the LUBAC involvement in the T cell receptor (TCR)-mediated NF-κB activation pathway, using the Jurkat human T cell line. LUBAC is indispensable for TCR-induced NF-κB and T cell activation, and transiently associates with and linearly ubiquitinates the CARMA1-BCL10-MALT1 (CBM) complex, through the catalytic HOIP subunit. In contrast, the linear ubiquitination of NEMO, a substrate of the TNF-α-induced canonical NF-κB activation pathway, was limited during the TCR pathway. Among deubiquitinases, OTULIN, but not CYLD, plays a major role in downregulating LUBAC-mediated TCR signaling. Mathematical modeling indicated that linear ubiquitination of the CBM complex accelerates the activation of IκB kinase (IKK), as compared with the activity induced by linear ubiquitination of NEMO alone. Moreover, simulations of the sequential linear ubiquitination of the CBM complex suggested that the allosteric regulation of linear (de)ubiquitination of CBM subunits is controlled by the ubiquitin-linkage lengths. These results indicated that, unlike the TNF-α-induced NF-κB activation pathway, the TCR-mediated NF-κB activation in T lymphocytes has a characteristic mechanism to induce LUBAC-mediated NF-κB activation.
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Affiliation(s)
- Daisuke Oikawa
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Naoya Hatanaka
- Division of Mathematical Science, Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Takashi Suzuki
- Center for Mathematical Modeling and Data Science, Osaka University, Osaka, Japan
| | - Fuminori Tokunaga
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka, Japan
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Fennell LM, Gomez Diaz C, Deszcz L, Kavirayani A, Hoffmann D, Yanagitani K, Schleiffer A, Mechtler K, Hagelkruys A, Penninger J, Ikeda F. Site-specific ubiquitination of the E3 ligase HOIP regulates apoptosis and immune signaling. EMBO J 2020; 39:e103303. [PMID: 33215740 PMCID: PMC7737615 DOI: 10.15252/embj.2019103303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 09/29/2020] [Accepted: 10/12/2020] [Indexed: 01/01/2023] Open
Abstract
HOIP, the catalytic component of the linear ubiquitin chain assembly complex (LUBAC), is a critical regulator of inflammation. However, how HOIP itself is regulated to control inflammatory responses is unclear. Here, we discover that site-specific ubiquitination of K784 within human HOIP promotes tumor necrosis factor (TNF)-induced inflammatory signaling. A HOIP K784R mutant is catalytically active but shows reduced induction of an NF-κB reporter relative to wild-type HOIP. HOIP K784 is evolutionarily conserved, equivalent to HOIP K778 in mice. We generated HoipK778R/K778R knock-in mice, which show no overt developmental phenotypes; however, in response to TNF, HoipK778R/K778R mouse embryonic fibroblasts display mildly suppressed NF-κB activation and increased apoptotic markers. On the other hand, HOIP K778R enhances the TNF-induced formation of TNFR complex II and an interaction between TNFR complex II and LUBAC. Loss of the LUBAC component SHARPIN leads to embryonic lethality in HoipK778R/K778R mice, which is rescued by knockout of TNFR1. We propose that site-specific ubiquitination of HOIP regulates a LUBAC-dependent switch between survival and apoptosis in TNF signaling.
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Affiliation(s)
- Lilian M Fennell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
| | - Carlos Gomez Diaz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
| | - Luiza Deszcz
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
| | - Anoop Kavirayani
- Vienna Biocenter Core Facilities (VBCF)Vienna Biocenter (VBC)ViennaAustria
| | - David Hoffmann
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
| | - Kota Yanagitani
- Medical Institute of Bioregulation (MIB)Kyushu UniversityFukuokaJapan
| | - Alexander Schleiffer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Karl Mechtler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Research Institute of Molecular Pathology (IMP)Vienna Biocenter (VBC)ViennaAustria
| | - Astrid Hagelkruys
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
| | - Josef Penninger
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Department of Medical GeneticsLife Sciences InstituteUniversity of British ColumbiaVancouverBCCanada
| | - Fumiyo Ikeda
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)Vienna Biocenter (VBC)ViennaAustria
- Medical Institute of Bioregulation (MIB)Kyushu UniversityFukuokaJapan
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Weinelt N, van Wijk SJL. Ubiquitin-dependent and -independent functions of OTULIN in cell fate control and beyond. Cell Death Differ 2020; 28:493-504. [PMID: 33288901 PMCID: PMC7862380 DOI: 10.1038/s41418-020-00675-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/05/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Ubiquitination, and its control by deubiquitinating enzymes (DUBs), mediates protein stability, function, signaling and cell fate. The ovarian tumor (OTU) family DUB OTULIN (FAM105B) exclusively cleaves linear (Met1-linked) poly-ubiquitin chains and plays important roles in auto-immunity, inflammation and infection. OTULIN regulates Met1-linked ubiquitination downstream of tumor necrosis factor receptor 1 (TNFR1), toll-like receptor (TLR) and nucleotide-binding and oligomerization domain-containing protein 2 (NOD2) receptor activation and interacts with the Met1 ubiquitin-specific linear ubiquitin chain assembly complex (LUBAC) E3 ligase. However, despite extensive research efforts, the receptor and cytosolic roles of OTULIN and the distributions of multiple Met1 ubiquitin-associated E3-DUB complexes in the regulation of cell fate still remain controversial and unclear. Apart from that, novel ubiquitin-independent OTULIN functions have emerged highlighting an even more complex role of OTULIN in cellular homeostasis. For example, OTULIN interferes with endosome-to-plasma membrane trafficking and the OTULIN-related pseudo-DUB OTULINL (FAM105A) resides at the endoplasmic reticulum (ER). Here, we discuss how OTULIN contributes to cell fate control and highlight novel ubiquitin-dependent and -independent functions.
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Affiliation(s)
- Nadine Weinelt
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Komturstrasse 3a, 60528, Frankfurt am Main, Germany
| | - Sjoerd J L van Wijk
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Komturstrasse 3a, 60528, Frankfurt am Main, Germany.
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Scholz N, Kurian KM, Siebzehnrubl FA, Licchesi JDF. Targeting the Ubiquitin System in Glioblastoma. Front Oncol 2020; 10:574011. [PMID: 33324551 PMCID: PMC7724090 DOI: 10.3389/fonc.2020.574011] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma is the most common primary brain tumor in adults with poor overall outcome and 5-year survival of less than 5%. Treatment has not changed much in the last decade or so, with surgical resection and radio/chemotherapy being the main options. Glioblastoma is highly heterogeneous and frequently becomes treatment-resistant due to the ability of glioblastoma cells to adopt stem cell states facilitating tumor recurrence. Therefore, there is an urgent need for novel therapeutic strategies. The ubiquitin system, in particular E3 ubiquitin ligases and deubiquitinating enzymes, have emerged as a promising source of novel drug targets. In addition to conventional small molecule drug discovery approaches aimed at modulating enzyme activity, several new and exciting strategies are also being explored. Among these, PROteolysis TArgeting Chimeras (PROTACs) aim to harness the endogenous protein turnover machinery to direct therapeutically relevant targets, including previously considered "undruggable" ones, for proteasomal degradation. PROTAC and other strategies targeting the ubiquitin proteasome system offer new therapeutic avenues which will expand the drug development toolboxes for glioblastoma. This review will provide a comprehensive overview of E3 ubiquitin ligases and deubiquitinating enzymes in the context of glioblastoma and their involvement in core signaling pathways including EGFR, TGF-β, p53 and stemness-related pathways. Finally, we offer new insights into how these ubiquitin-dependent mechanisms could be exploited therapeutically for glioblastoma.
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Affiliation(s)
- Nico Scholz
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Kathreena M. Kurian
- Brain Tumour Research Group, Institute of Clinical Neurosciences, University of Bristol, Bristol, United Kingdom
| | - Florian A. Siebzehnrubl
- Cardiff University School of Biosciences, European Cancer Stem Cell Research Institute, Cardiff, United Kingdom
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