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Liu X, Li Y, Zhang W, Gao N, Chen J, Xiao C, Zhang G. Inhibition of cIAP1/2 reduces RIPK1 phosphorylation in pulmonary endothelial cells and alleviate sepsis-induced lung injury and inflammatory response. Immunol Res 2024:10.1007/s12026-024-09491-8. [PMID: 38748318 DOI: 10.1007/s12026-024-09491-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/08/2024] [Indexed: 06/01/2024]
Abstract
Acute respiratory distress syndrome (ARDS)/acute lung injury (ALI) is a severe complication of sepsis characterized by acute respiratory distress, hypoxemia, and diffuse bilateral pulmonary infiltrates. The regulation of RIPK1 is an important part of the inflammatory response, and cIAP1/2 serves as the E3 ubiquitin ligase for RIPK1. In this study, we investigated the effect and mechanism of cIAP1/2 inhibition on sepsis-induced lung injury. Our results showed that cIAP1/2 inhibition can alleviate sepsis-induced lung injury and reduce the inflammatory response, which is accompanied by downregulation of RIPK1 phosphorylation and ubiquitination. Additionally, cIAP1/2 inhibition led to the up-regulation of programmed cell death, including apoptosis, necroptosis, and pyroptosis, and inhibiting these three cell death pathways can further reduce the inflammatory response, which is similar to the recently discovered programmed cell death pathway PANoptosis. Our findings suggest that cIAP1/2 and PANoptosis inhibition may be a new strategy for treating sepsis-induced lung injury and provide important references for further exploring the mechanism of sepsis-induced lung injury and identifying new therapeutic targets.
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Affiliation(s)
- Xiaoyu Liu
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
| | - Yan Li
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
| | - Weijian Zhang
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
- Peking University, China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Nan Gao
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
| | - Jie Chen
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
| | - Cheng Xiao
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China.
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China.
| | - Guoqiang Zhang
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China.
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2
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Pang J, Vince JE. The role of caspase-8 in inflammatory signalling and pyroptotic cell death. Semin Immunol 2023; 70:101832. [PMID: 37625331 DOI: 10.1016/j.smim.2023.101832] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/20/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
The programmed cell death machinery exhibits surprising flexibility, capable of crosstalk and non-apoptotic roles. Much of this complexity arises from the diverse functions of caspase-8, a cysteine-aspartic acid protease typically associated with activating caspase-3 and - 7 to induce apoptosis. However, recent research has revealed that caspase-8 also plays a role in regulating the lytic gasdermin cell death machinery, contributing to pyroptosis and immune responses in contexts such as infection, autoinflammation, and T-cell signalling. In mice, loss of caspase-8 results in embryonic lethality from unrestrained necroptotic killing, while in humans caspase-8 deficiency can lead to an autoimmune lymphoproliferative syndrome, immunodeficiency, inflammatory bowel disease or, when it can't cleave its substrate RIPK1, early onset periodic fevers. This review focuses on non-canonical caspase-8 signalling that drives immune responses, including its regulation of inflammatory gene transcription, activation within inflammasome complexes, and roles in pyroptotic cell death. Ultimately, a deeper understanding of caspase-8 function will aid in determining whether, and when, targeting caspase-8 pathways could be therapeutically beneficial in human diseases.
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Affiliation(s)
- Jiyi Pang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - James E Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; The Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia.
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3
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Zhang T, Zhang N, Xing J, Zhang S, Chen Y, Xu D, Gu J. UDP-glucuronate metabolism controls RIPK1-driven liver damage in nonalcoholic steatohepatitis. Nat Commun 2023; 14:2715. [PMID: 37169760 PMCID: PMC10175487 DOI: 10.1038/s41467-023-38371-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 04/28/2023] [Indexed: 05/13/2023] Open
Abstract
Hepatocyte apoptosis plays an essential role in the progression of nonalcoholic steatohepatitis (NASH). However, the molecular mechanisms underlying hepatocyte apoptosis remain unclear. Here, we identify UDP-glucose 6-dehydrogenase (UGDH) as a suppressor of NASH-associated liver damage by inhibiting RIPK1 kinase-dependent hepatocyte apoptosis. UGDH is progressively reduced in proportion to NASH severity. UGDH absence from hepatocytes hastens the development of liver damage in male mice with NASH, which is suppressed by RIPK1 kinase-dead knockin mutation. Mechanistically, UGDH suppresses RIPK1 by converting UDP-glucose to UDP-glucuronate, the latter directly binds to the kinase domain of RIPK1 and inhibits its activation. Recovering UDP-glucuronate levels, even after the onset of NASH, improved liver damage. Our findings reveal a role for UGDH and UDP-glucuronate in NASH pathogenesis and uncover a mechanism by which UDP-glucuronate controls hepatocyte apoptosis by targeting RIPK1 kinase, and suggest UDP-glucuronate metabolism as a feasible target for more specific treatment of NASH-associated liver damage.
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Affiliation(s)
- Tao Zhang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, 430022, China
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Na Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Jing Xing
- Lingang Laboratory, Shanghai, 200031, China
| | - Shuhua Zhang
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, 430022, China
| | - Yulu Chen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Daichao Xu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China
- Shanghai Key Laboratory of Aging Studies, Shanghai, 2012010, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jinyang Gu
- Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, 430022, China.
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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4
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Gupta R, Kumari S, Tripathi R, Ambasta RK, Kumar P. Unwinding the modalities of necrosome activation and necroptosis machinery in neurological diseases. Ageing Res Rev 2023; 86:101855. [PMID: 36681250 DOI: 10.1016/j.arr.2023.101855] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/09/2022] [Accepted: 01/15/2023] [Indexed: 01/20/2023]
Abstract
Necroptosis, a regulated form of cell death, is involved in the genesis and development of various life-threatening diseases, including cancer, neurological disorders, cardiac myopathy, and diabetes. Necroptosis initiates with the formation and activation of a necrosome complex, which consists of RIPK1, RIPK2, RIPK3, and MLKL. Emerging studies has demonstrated the regulation of the necroptosis cell death pathway through the implication of numerous post-translational modifications, namely ubiquitination, acetylation, methylation, SUMOylation, hydroxylation, and others. In addition, the negative regulation of the necroptosis pathway has been shown to interfere with brain homeostasis through the regulation of axonal degeneration, mitochondrial dynamics, lysosomal defects, and inflammatory response. Necroptosis is controlled by the activity and expression of signaling molecules, namely VEGF/VEGFR, PI3K/Akt/GSK-3β, c-Jun N-terminal kinases (JNK), ERK/MAPK, and Wnt/β-catenin. Herein, we briefly discussed the implication and potential of necrosome activation in the pathogenesis and progression of neurological manifestations, such as Alzheimer's disease, Parkinson's disease, multiple sclerosis, traumatic brain injury, and others. Further, we present a detailed picture of natural compounds, micro-RNAs, and chemical compounds as therapeutic agents for treating neurological manifestations.
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Affiliation(s)
- Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Rahul Tripathi
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological University (Formerly Delhi College of Engineering), India.
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5
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Ghanavatian P, Salehi-Sedeh H, Ataei F, Hosseinkhani S. Bioluminescent RIPoptosome Assay for FADD/RIPK1 Interaction Based on Split Luciferase Assay in a Human Neuroblastoma Cell Line SH-SY5Y. BIOSENSORS 2023; 13:297. [PMID: 36832063 PMCID: PMC9954477 DOI: 10.3390/bios13020297] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/26/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Different programed cell death (PCD) modalities involve protein-protein interactions in large complexes. Tumor necrosis factor α (TNFα) stimulated assembly of receptor-interacting protein kinase 1 (RIPK1)/Fas-associated death domain (FADD) interaction forms Ripoptosome complex that may cause either apoptosis or necroptosis. The present study addresses the interaction of RIPK1 and FADD in TNFα signaling by fusion of C-terminal (CLuc) and N-terminal (NLuc) luciferase fragments to RIPK1-CLuc (R1C) or FADD-NLuc (FN) in a caspase 8 negative neuroblastic SH-SY5Y cell line, respectively. In addition, based on our findings, an RIPK1 mutant (R1C K612R) had less interaction with FN, resulting in increasing cell viability. Moreover, presence of a caspase inhibitor (zVAD.fmk) increases luciferase activity compared to Smac mimetic BV6 (B), TNFα -induced (T) and non-induced cell. Furthermore, etoposide decreased luciferase activity, but dexamethasone was not effective in SH-SY5Y. This reporter assay might be used to evaluate basic aspects of this interaction as well as for screening of necroptosis and apoptosis targeting drugs with potential therapeutic application.
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6
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Karlowitz R, van Wijk SJL. Surviving death: emerging concepts of RIPK3 and MLKL ubiquitination in the regulation of necroptosis. FEBS J 2023; 290:37-54. [PMID: 34710282 DOI: 10.1111/febs.16255] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/14/2021] [Accepted: 10/27/2021] [Indexed: 01/14/2023]
Abstract
Lytic forms of programmed cell death, like necroptosis, are characterised by cell rupture and the release of cellular contents, often provoking inflammatory responses. In the recent years, necroptosis has been shown to play important roles in human diseases like cancer, infections and ischaemia/reperfusion injury. Coordinated interactions between RIPK1, RIPK3 and MLKL lead to the formation of a dedicated death complex called the necrosome that triggers MLKL-mediated membrane rupture and necroptotic cell death. Necroptotic cell death is tightly controlled by post-translational modifications, among which especially phosphorylation has been characterised in great detail. Although selective ubiquitination is relatively well-explored in the early initiation stages of necroptosis, the mechanisms and functional consequences of RIPK3 and MLKL ubiquitination for necrosome function and necroptosis are only starting to emerge. This review provides an overview on how site-specific ubiquitination of RIPK3 and MLKL regulates, fine-tunes and reverses the execution of necroptotic cell death.
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Affiliation(s)
- Rebekka Karlowitz
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany
| | - Sjoerd J L van Wijk
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University Frankfurt, Germany
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7
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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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8
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Yan L, Zhang T, Wang K, Chen Z, Yang Y, Shan B, Sun Q, Zhang M, Zhang Y, Zhong Y, Liu N, Gu J, Xu D. SENP1 prevents steatohepatitis by suppressing RIPK1-driven apoptosis and inflammation. Nat Commun 2022; 13:7153. [PMID: 36414671 PMCID: PMC9681887 DOI: 10.1038/s41467-022-34993-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022] Open
Abstract
Activation of RIPK1-driven cell death and inflammation play important roles in the progression of nonalcoholic steatohepatitis (NASH). However, the mechanism underlying RIPK1 activation in NASH remains unclear. Here we identified SENP1, a SUMO-specific protease, as a key endogenous inhibitor of RIPK1. SENP1 is progressively reduced in proportion to NASH severity in patients. Hepatocyte-specific SENP1-knockout mice develop spontaneous NASH-related phenotypes in a RIPK1 kinase-dependent manner. We demonstrate that SENP1 deficiency sensitizes cells to RIPK1 kinase-dependent apoptosis by promoting RIPK1 activation following TNFα stimulation. Mechanistically, SENP1 deSUMOylates RIPK1 in TNF-R1 signaling complex (TNF-RSC), keeping RIPK1 in check. Loss of SENP1 leads to SUMOylation of RIPK1, which re-orchestrates TNF-RSC and modulates the ubiquitination patterns and activity of RIPK1. Notably, genetic inhibition of RIPK1 effectively reverses disease progression in hepatocyte-specific SENP1-knockout male mice with high-fat-diet-induced nonalcoholic fatty liver. We propose that deSUMOylation of RIPK1 by SENP1 provides a pathophysiologically relevant cell death-restricting checkpoint that modulates RIPK1 activation in the pathogenesis of nonalcoholic steatohepatitis.
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Affiliation(s)
- Lingjie Yan
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Tao Zhang
- grid.38142.3c000000041936754XDepartment of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215 USA
| | - Kai Wang
- grid.13402.340000 0004 1759 700XDepartment of Hepatobiliary and Pancreatic Surgery, Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang Province, Hangzhou First People’s Hospital Affiliated Zhejiang University School of Medicine, Hangzhou, 310006 China ,grid.13402.340000 0004 1759 700XInstitute of Organ Transplantation, Zhejiang University, Hangzhou, 310003 China
| | - Zezhao Chen
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuanxin Yang
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Bing Shan
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Qi Sun
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Mengmeng Zhang
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Yichi Zhang
- grid.412987.10000 0004 0630 1330Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China
| | - Yedan Zhong
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210 China
| | - Nan Liu
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210 China ,Shanghai Key Laboratory of Aging Studies, Shanghai, 201210 China
| | - Jinyang Gu
- grid.412987.10000 0004 0630 1330Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092 China ,grid.33199.310000 0004 0368 7223Center for Liver Transplantation, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Daichao Xu
- grid.9227.e0000000119573309Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210 China ,Shanghai Key Laboratory of Aging Studies, Shanghai, 201210 China
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9
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Distinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19. Proc Natl Acad Sci U S A 2022; 119:e2206610119. [PMID: 35947637 PMCID: PMC9436378 DOI: 10.1073/pnas.2206610119] [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] [Indexed: 12/02/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a coronavirus that spilled over from the bat reservoir. However, the host genetic determinants that drive SARS-CoV-2 susceptibility and COVID-19 severity are largely unknown. Understanding how cellular proteins interacting with SARS-CoV-2 have evolved in primates and bats is of primary importance to decipher differences in the infection outcome between humans and the viral reservoir in bats. Here, we performed comparative functional genetic analyses of hundreds of SARS-CoV-2-interacting proteins to study virus–host interface adaptation over millions of years, pointing to genes similarly—or differentially—engaged in evolutionary arms races and that may be at the basis of in vivo pathogenic differences. The coronavirus disease 19 (COVID-19) pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a coronavirus that spilled over from the bat reservoir. Despite numerous clinical trials and vaccines, the burden remains immense, and the host determinants of SARS-CoV-2 susceptibility and COVID-19 severity remain largely unknown. Signatures of positive selection detected by comparative functional genetic analyses in primate and bat genomes can uncover important and specific adaptations that occurred at virus–host interfaces. We performed high-throughput evolutionary analyses of 334 SARS-CoV-2-interacting proteins to identify SARS-CoV adaptive loci and uncover functional differences between modern humans, primates, and bats. Using DGINN (Detection of Genetic INNovation), we identified 38 bat and 81 primate proteins with marks of positive selection. Seventeen genes, including the ACE2 receptor, present adaptive marks in both mammalian orders, suggesting common virus–host interfaces and past epidemics of coronaviruses shaping their genomes. Yet, 84 genes presented distinct adaptations in bats and primates. Notably, residues involved in ubiquitination and phosphorylation of the inflammatory RIPK1 have rapidly evolved in bats but not primates, suggesting different inflammation regulation versus humans. Furthermore, we discovered residues with typical virus–host arms race marks in primates, such as in the entry factor TMPRSS2 or the autophagy adaptor FYCO1, pointing to host-specific in vivo interfaces that may be drug targets. Finally, we found that FYCO1 sites under adaptation in primates are those associated with severe COVID-19, supporting their importance in pathogenesis and replication. Overall, we identified adaptations involved in SARS-CoV-2 infection in bats and primates, enlightening modern genetic determinants of virus susceptibility and severity.
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10
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No longer married to inflammasome signaling: the diverse interacting pathways leading to pyroptotic cell death. Biochem J 2022; 479:1083-1102. [PMID: 35608339 PMCID: PMC9162454 DOI: 10.1042/bcj20210711] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 02/07/2023]
Abstract
For over 15 years the lytic cell death termed pyroptosis was defined by its dependency on the inflammatory caspase, caspase-1, which, upon pathogen sensing, is activated by innate immune cytoplasmic protein complexes known as inflammasomes. However, this definition of pyroptosis changed when the pore-forming protein gasdermin D (GSDMD) was identified as the caspase-1 (and caspase-11) substrate required to mediate pyroptotic cell death. Consequently, pyroptosis has been redefined as a gasdermin-dependent cell death. Studies now show that, upon liberation of the N-terminal domain, five gasdermin family members, GSDMA, GSDMB, GSDMC, GSDMD and GSDME can all form plasma membrane pores to induce pyroptosis. Here, we review recent research into the diverse stimuli and cell death signaling pathways involved in the activation of gasdermins; death and toll-like receptor triggered caspase-8 activation of GSDMD or GSMDC, apoptotic caspase-3 activation of GSDME, perforin-granzyme A activation of GSDMB, and bacterial protease activation of GSDMA. We highlight findings that have begun to unravel the physiological situations and disease states that result from gasdermin signaling downstream of inflammasome activation, death receptor and mitochondrial apoptosis, and necroptosis. This new era in cell death research therefore holds significant promise in identifying how distinct, yet often networked, pyroptotic cell death pathways might be manipulated for therapeutic benefit to treat a range of malignant conditions associated with inflammation, infection and cancer.
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11
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RIP1 post-translational modifications. Biochem J 2022; 479:929-951. [PMID: 35522161 DOI: 10.1042/bcj20210725] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/17/2022]
Abstract
Receptor interacting protein 1 (RIP1) kinase is a critical regulator of inflammation and cell death signaling, and plays a crucial role in maintaining immune responses and proper tissue homeostasis. Mounting evidence argues for the importance of RIP1 post-translational modifications in control of its function. Ubiquitination by E3 ligases, such as inhibitors of apoptosis (IAP) proteins and LUBAC, as well as the reversal of these modifications by deubiquitinating enzymes, such as A20 and CYLD, can greatly influence RIP1 mediated signaling. In addition, cleavage by caspase-8, RIP1 autophosphorylation, and phosphorylation by a number of signaling kinases can greatly impact cellular fate. Disruption of the tightly regulated RIP1 modifications can lead to signaling disbalance in TNF and/or TLR controlled and other inflammatory pathways, and result in severe human pathologies. This review will focus on RIP1 and its many modifications with an emphasis on ubiquitination, phosphorylation, and cleavage, and their functional impact on the RIP1's role in signaling pathways.
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12
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Wang Q, Fan D, Xia Y, Ye Q, Xi X, Zhang G, Xiao C. The latest information on the RIPK1 post-translational modifications and functions. Biomed Pharmacother 2021; 142:112082. [PMID: 34449307 DOI: 10.1016/j.biopha.2021.112082] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 12/21/2022] Open
Abstract
RIPK1 is a protein kinase that simultaneously regulates inflammation, apoptosis, and necroptosis. It is thought that RIPK1 has separate functions through its scaffold structure and kinase domains. Moreover, different post-translational modifications in RIPK1 play distinct or even opposing roles. Under different conditions, in different cells and species, and/or upon exposure to different stimuli, infections, and substrates, RIPK1 activation can lead to diverse results. Despite continuous research, many of the conclusions that have been drawn regarding the complex interactions of RIPK1 are controversial. This review is based on an examination and analysis of recent studies on the RIPK1 structure, post-translational modifications, and activation conditions, which can affect its functions. Finally, because of the diverse functions of RIPK1 and their relevance to the pathogenesis of many diseases, we briefly introduce the roles of RIPK1 in inflammatory and autoimmune diseases and the prospects of its use in future diagnostics and treatments.
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Affiliation(s)
- Qiong Wang
- Beijing University of Chinese Medicine, Beijing 100029, China; Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Danping Fan
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing 100029, China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing 100193, China
| | - Ya Xia
- Beijing University of Chinese Medicine, Beijing 100029, China; Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Qinbin Ye
- Beijing University of Chinese Medicine, Beijing 100029, China; Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xiaoyu Xi
- Beijing University of Chinese Medicine, Beijing 100029, China; Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing 100029, China
| | - Guoqiang Zhang
- Department of Emergency, China-Japan Friendship Hospital, Beijing 100029, China.
| | - Cheng Xiao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing 100029, China; Department of Emergency, China-Japan Friendship Hospital, Beijing 100029, China.
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13
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Speir M, Djajawi TM, Conos SA, Tye H, Lawlor KE. Targeting RIP Kinases in Chronic Inflammatory Disease. Biomolecules 2021; 11:biom11050646. [PMID: 33924766 PMCID: PMC8146010 DOI: 10.3390/biom11050646] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/08/2023] Open
Abstract
Chronic inflammatory disorders are characterised by aberrant and exaggerated inflammatory immune cell responses. Modes of extrinsic cell death, apoptosis and necroptosis, have now been shown to be potent drivers of deleterious inflammation, and mutations in core repressors of these pathways underlie many autoinflammatory disorders. The receptor-interacting protein (RIP) kinases, RIPK1 and RIPK3, are integral players in extrinsic cell death signalling by regulating the production of pro-inflammatory cytokines, such as tumour necrosis factor (TNF), and coordinating the activation of the NOD-like receptor protein 3 (NLRP3) inflammasome, which underpin pathological inflammation in numerous chronic inflammatory disorders. In this review, we firstly give an overview of the inflammatory cell death pathways regulated by RIPK1 and RIPK3. We then discuss how dysregulated signalling along these pathways can contribute to chronic inflammatory disorders of the joints, skin, and gastrointestinal tract, and discuss the emerging evidence for targeting these RIP kinases in the clinic.
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Affiliation(s)
- Mary Speir
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; (M.S.); (T.M.D.); (S.A.C.); (H.T.)
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3168, Australia
| | - Tirta M. Djajawi
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; (M.S.); (T.M.D.); (S.A.C.); (H.T.)
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3168, Australia
| | - Stephanie A. Conos
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; (M.S.); (T.M.D.); (S.A.C.); (H.T.)
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3168, Australia
| | - Hazel Tye
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; (M.S.); (T.M.D.); (S.A.C.); (H.T.)
| | - Kate E. Lawlor
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC 3168, Australia; (M.S.); (T.M.D.); (S.A.C.); (H.T.)
- Department of Molecular and Translational Science, Monash University, Clayton, VIC 3168, Australia
- Correspondence: ; Tel.: +61-85722700
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14
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Samson AL, Fitzgibbon C, Patel KM, Hildebrand JM, Whitehead LW, Rimes JS, Jacobsen AV, Horne CR, Gavin XJ, Young SN, Rogers KL, Hawkins ED, Murphy JM. A toolbox for imaging RIPK1, RIPK3, and MLKL in mouse and human cells. Cell Death Differ 2021; 28:2126-2144. [PMID: 33589776 DOI: 10.1038/s41418-021-00742-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 01/20/2021] [Accepted: 01/25/2021] [Indexed: 12/18/2022] Open
Abstract
Necroptosis is a lytic, inflammatory cell death pathway that is dysregulated in many human pathologies. The pathway is executed by a core machinery comprising the RIPK1 and RIPK3 kinases, which assemble into necrosomes in the cytoplasm, and the terminal effector pseudokinase, MLKL. RIPK3-mediated phosphorylation of MLKL induces oligomerization and translocation to the plasma membrane where MLKL accumulates as hotspots and perturbs the lipid bilayer to cause death. The precise choreography of events in the pathway, where they occur within cells, and pathway differences between species, are of immense interest. However, they have been poorly characterized due to a dearth of validated antibodies for microscopy studies. Here, we describe a toolbox of antibodies for immunofluorescent detection of the core necroptosis effectors, RIPK1, RIPK3, and MLKL, and their phosphorylated forms, in human and mouse cells. By comparing reactivity with endogenous proteins in wild-type cells and knockout controls in basal and necroptosis-inducing conditions, we characterise the specificity of frequently-used commercial and recently-developed antibodies for detection of necroptosis signaling events. Importantly, our findings demonstrate that not all frequently-used antibodies are suitable for monitoring necroptosis by immunofluorescence microscopy, and methanol- is preferable to paraformaldehyde-fixation for robust detection of specific RIPK1, RIPK3, and MLKL signals.
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Affiliation(s)
- André L Samson
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
| | - Cheree Fitzgibbon
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Komal M Patel
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Joanne M Hildebrand
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Lachlan W Whitehead
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Joel S Rimes
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Annette V Jacobsen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Xavier J Gavin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Samuel N Young
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Kelly L Rogers
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Edwin D Hawkins
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - James M Murphy
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.
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15
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Iorga A, Donovan K, Shojaie L, Johnson H, Kwok J, Suda J, Lee BT, Aghajan M, Shao L, Liu ZX, Dara L. Interaction of RIPK1 and A20 modulates MAPK signaling in murine acetaminophen toxicity. J Biol Chem 2021; 296:100300. [PMID: 33460648 PMCID: PMC7948960 DOI: 10.1016/j.jbc.2021.100300] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 01/04/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
Acetaminophen (APAP)-induced liver necrosis is a form of regulated cell death (RCD) in which APAP activates the mitogen-activated protein kinases (MAPKs) and specifically the c-Jun-N-terminal kinase (JNK) pathway, leading to necrotic cell death. Previously, we have shown that receptor interacting protein kinase-1 (RIPK1) knockdown is also protective against APAP RCD upstream of JNK. However, whether the kinase or platform function of RIPK1 is involved in APAP RCD is not known. To answer this question, we used genetic mouse models of targeted hepatocyte RIPK1 knockout (RIPK1HepCKO) or kinase dead knock-in (RIPK1D138N) and adult hepatocyte specific knockout of the cytoprotective protein A20 (A20HepCKO), known to interact with RIPK1, to study its potential involvement in MAPK signaling. We observed no difference in injury between WT and RIPK1D138N mice post APAP. However, RIPK1HepCKO was protective. We found that RIPK1HepCKO mice had attenuated pJNK activation, while A20 was simultaneously upregulated. Conversely, A20HepCKO markedly worsened liver injury from APAP. Mechanistically, we observed a significant upregulation of apoptosis signal-regulating kinase 1 (ASK1) and increased JNK activation in A20HepCKO mice compared with littermate controls. We also demonstrated that A20 coimmunoprecipitated (co-IP) with both RIPK1 and ASK1, and that in the presence of RIPK1, there was less A20-ASK1 association than in its absence. We conclude that the kinase-independent platform function of RIPK1 is involved in APAP toxicity. Adult RIPK1HepCKO mice are protected against APAP by upregulating A20 and attenuating JNK signaling through ASK1, conversely, A20HepCKO worsens injury from APAP.
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Affiliation(s)
- Andrea Iorga
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California, USA; USC Research Center for Liver Disease, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Katherine Donovan
- USC Research Center for Liver Disease, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Layla Shojaie
- USC Research Center for Liver Disease, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Heather Johnson
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California, USA; USC Research Center for Liver Disease, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Janet Kwok
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Jo Suda
- USC Research Center for Liver Disease, Keck School of Medicine of University of Southern California, Los Angeles, California, USA; Cedar Sinai Medical Center, Los Angeles, California, USA
| | - Brian T Lee
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | | | - Ling Shao
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California, USA; USC Research Center for Liver Disease, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Zhang-Xu Liu
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California, USA; USC Research Center for Liver Disease, Keck School of Medicine of University of Southern California, Los Angeles, California, USA
| | - Lily Dara
- Division of Gastrointestinal and Liver Diseases, Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California, USA; USC Research Center for Liver Disease, Keck School of Medicine of University of Southern California, Los Angeles, California, USA.
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