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Galletti G, Halima A, Gjyrezi A, Zhang J, Zimmerman B, Worroll D, Kallergi G, Barreja R, Ocean A, Saxena A, McGraw TE, Nanus DM, Elemento O, Altorki NK, Tagawa ST, Giannakakou P. Transferrin receptor-based circulating tumor cell enrichment provides a snapshot of the molecular landscape of solid tumors and correlates with clinical outcomes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.16.24309003. [PMID: 38947080 PMCID: PMC11213041 DOI: 10.1101/2024.06.16.24309003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Circulating tumor cells (CTCs) captured from the bloodstream of patients with solid tumors have the potential to accelerate precision oncology by providing insight into tumor biology, disease progression and response to treatment. However, their potential is hampered by the lack of standardized CTC enrichment platforms across tumor types. EpCAM-based CTC enrichment, the most commonly used platform, is limited by EpCAM downregulation during metastasis and the low EpCAM expression in certain tumor types, including the highly prevalent and lethal NSCLC. In this study we demonstrate that Transferrin Receptor (TfR) is a selective, efficient biomarker for CTC identification and capture in patients with prostate, pancreatic and NSCLC. TfR identifies significantly higher CTC counts than EpCAM, and TfR + -CTC enumeration correlates with disease progression in metastatic prostate and pancreatic cancers, and overall survival and osimetrinib-resistance in non-small cell lung cancer (NSCLC). Profiling of TfR + -CTCs provides a snapshot of the molecular landscape of each respective tumor type and identifies potential mechanisms underlying treatment response to EGFR TKi and immune checkpoint inhibitors in NSCLC. One sentence summary Transferrin Receptor identifies circulating tumor cells in solid tumors.
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Yalçin Z, Lam SY, Peuscher MH, van der Torre J, Zhu S, Iyengar PV, Salas-Lloret D, de Krijger I, Moatti N, van der Lugt R, Falcone M, Cerutti A, Bleijerveld OB, Hoekman L, González-Prieto R, Jacobs JJL. UBE2D3 facilitates NHEJ by orchestrating ATM signalling through multi-level control of RNF168. Nat Commun 2024; 15:5032. [PMID: 38866770 PMCID: PMC11169547 DOI: 10.1038/s41467-024-49431-6] [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: 04/05/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024] Open
Abstract
Maintenance of genome integrity requires tight control of DNA damage response (DDR) signalling and repair, with phosphorylation and ubiquitination representing key elements. How these events are coordinated to achieve productive DNA repair remains elusive. Here we identify the ubiquitin-conjugating enzyme UBE2D3 as a regulator of ATM kinase-induced DDR that promotes non-homologous end-joining (NHEJ) at telomeres. UBE2D3 contributes to DDR-induced chromatin ubiquitination and recruitment of the NHEJ-promoting factor 53BP1, both mediated by RNF168 upon ATM activation. Additionally, UBE2D3 promotes NHEJ by limiting RNF168 accumulation and facilitating ATM-mediated phosphorylation of KAP1-S824. Mechanistically, defective KAP1-S824 phosphorylation and telomeric NHEJ upon UBE2D3-deficiency are linked to RNF168 hyperaccumulation and aberrant PP2A phosphatase activity. Together, our results identify UBE2D3 as a multi-level regulator of NHEJ that orchestrates ATM and RNF168 activities. Moreover, they reveal a negative regulatory circuit in the DDR that is constrained by UBE2D3 and consists of RNF168- and phosphatase-mediated restriction of KAP1 phosphorylation.
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Affiliation(s)
- Zeliha Yalçin
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Shiu Yeung Lam
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Marieke H Peuscher
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Jaco van der Torre
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Sha Zhu
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Prasanna V Iyengar
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Daniel Salas-Lloret
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
| | - Inge de Krijger
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Nathalie Moatti
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Ruben van der Lugt
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Mattia Falcone
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Aurora Cerutti
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, the Netherlands
- Andalusian Center for Molecular Biology and regenerative Medicine (CABIMER), Universidad de Sevilla-CSIC-Universidad-Pablo de Olavide, Sevilla, Spain
- Departamento de Biología Celular, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands.
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Panagopoulos I, Andersen K, Gorunova L, Lobmaier I. Fusion of Platelet Derived Growth Factor Receptor Alpha ( PDGFRA) With Ubiquitin Specific Peptidase 8 ( USP8) in a Calcified Chondroid Mesenchymal Neoplasm Harboring t(4;15)(q12;q21) as a Sole Aberration. Cancer Genomics Proteomics 2024; 21:252-259. [PMID: 38670591 PMCID: PMC11059595 DOI: 10.21873/cgp.20444] [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: 01/20/2024] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND/AIM The term "calcified chondroid mesenchymal neoplasm" was introduced in 2021 to describe a group of tumors characterized by various morphological features, including the formation of cartilage or chondroid matrix. These tumors frequently carry chimeric genes where the 5'-end partner gene is fibronectin 1 and the 3'-end partner gene codes for receptor tyrosine kinase. Our study explores fusion of the genes platelet-derived growth factor receptor alpha (PDGFRA) and ubiquitin-specific peptidase 8 (USP8) in calcified chondroid mesenchymal neoplasm. CASE REPORT Genetic investigations were conducted on a tumor located in the leg of a 71-year-old woman. G-banding analysis of short-term cultured tumor cells revealed the karyotype 46,XX,t(4;15)(q12;q21)[6]/46,XX[4]. RNA sequencing detected in-frame PDGFRA::USP8 and USP8::PDGFRA chimeric transcripts, which were validated by RT-PCR/Sanger sequencing. The PDGFRA::USP8 chimeric protein is predicted to have cell membrane location and functions as a chimeric ubiquitinyl hydrolase. The USP8::PDGFRA protein was predicted to be nuclear and function as a positive regulator of cellular metabolic process. CONCLUSION We report, for the first time, a calcified chondroid mesenchymal neoplasm carrying a balanced t(4;15)(q12;q21) chromosomal translocation, resulting in the generation of both PDGFRA::USP8 and USP8::PDGFRA chimeras. The PDGFRA::USP8 protein is located on the cell membrane and functions as a chimeric ubiquitinyl hydrolase, activated by PDGFs. Conversely, USP8::PDGFRA is a nuclear protein regulating metabolic processes.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;
| | - Kristin Andersen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
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Kreitmaier P, Park YC, Swift D, Gilly A, Wilkinson JM, Zeggini E. Epigenomic profiling of the infrapatellar fat pad in osteoarthritis. Hum Mol Genet 2024; 33:501-509. [PMID: 37975894 PMCID: PMC10939427 DOI: 10.1093/hmg/ddad198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/13/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Osteoarthritis is a prevalent, complex disease of the joints, and affects multiple intra-articular tissues. Here, we have examined genome-wide DNA methylation profiles of primary infrapatellar fat pad and matched blood samples from 70 osteoarthritis patients undergoing total knee replacement surgery. Comparing the DNA methylation profiles between these tissues reveal widespread epigenetic differences. We produce the first genome-wide methylation quantitative trait locus (mQTL) map of fat pad, and make the resource available to the wider community. Using two-sample Mendelian randomization and colocalization analyses, we resolve osteoarthritis GWAS signals and provide insights into the molecular mechanisms underpinning disease aetiopathology. Our findings provide the first view of the epigenetic landscape of infrapatellar fat pad primary tissue in osteoarthritis.
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Affiliation(s)
- Peter Kreitmaier
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine and Health, Ismaninger Str. 22, Munich 81675, Germany
- Graduate School of Experimental Medicine, TUM School of Medicine and Health, Technical University of Munich, Ismaninger Str. 22, Munich 81675, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - Young-Chan Park
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - Diane Swift
- Department of Oncology and Metabolism, The University of Sheffield, Beech Hill Rd, Sheffield S10 2RX, United Kingdom
| | - Arthur Gilly
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
| | - J Mark Wilkinson
- Department of Oncology and Metabolism, The University of Sheffield, Beech Hill Rd, Sheffield S10 2RX, United Kingdom
| | - Eleftheria Zeggini
- Technical University of Munich (TUM) and Klinikum Rechts der Isar, TUM School of Medicine and Health, Ismaninger Str. 22, Munich 81675, Germany
- Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstr. 1, Neuherberg 85764, Germany
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5
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Joshi K, Mazumdar V, Nandi BR, Radhakrishnan GK. Brucella targets the host ubiquitin-specific protease, Usp8, through the effector protein, TcpB, for facilitating infection of macrophages. Infect Immun 2024; 92:e0028923. [PMID: 38174929 PMCID: PMC10863413 DOI: 10.1128/iai.00289-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/12/2023] [Indexed: 01/05/2024] Open
Abstract
Brucella species are Gram-negative intracellular bacterial pathogens that cause the worldwide zoonotic disease brucellosis. Brucella can infect many mammals, including humans and domestic and wild animals. Brucella manipulates various host cellular processes to invade and multiply in professional and non-professional phagocytic cells. However, the host targets and their modulation by Brucella to facilitate the infection process remain obscure. Here, we report that the host ubiquitin-specific protease, USP8, negatively regulates the invasion of Brucella into macrophages through the plasma membrane receptor, CXCR4. Upon silencing or chemical inhibition of USP8, the membrane localization of the CXCR4 receptor was enriched, which augmented the invasion of Brucella into macrophages. Activation of USP8 through chemical inhibition of 14-3-3 protein affected the invasion of Brucella into macrophages. Brucella suppressed the expression of Usp8 at its early stage of infection in the infected macrophages. Furthermore, we found that only live Brucella could negatively regulate the expression of Usp8, suggesting the role of secreted effector protein of Brucella in modulating the gene expression. Subsequent studies revealed that the Brucella effector protein, TIR-domain containing protein from Brucella, TcpB, plays a significant role in downregulating the expression of Usp8 by targeting the cyclic-AMP response element-binding protein pathway. Treatment of mice with USP8 inhibitor resulted in enhanced survival of B. melitensis, whereas mice treated with CXCR4 or 14-3-3 antagonists showed a diminished bacterial load. Our experimental data demonstrate a novel role of Usp8 in the host defense against microbial intrusion. The present study provides insights into the microbial subversion of host defenses, and this information may ultimately help to develop novel therapeutic interventions for infectious diseases.
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Affiliation(s)
- Kiranmai Joshi
- Laboratory of Immunology and Microbial Pathogenesis, National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Varadendra Mazumdar
- Laboratory of Immunology and Microbial Pathogenesis, National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Binita Roy Nandi
- Laboratory of Immunology and Microbial Pathogenesis, National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
- Regional Centre for Biotechnology (RCB), Faridabad, India
| | - Girish K. Radhakrishnan
- Laboratory of Immunology and Microbial Pathogenesis, National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana, India
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6
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Rebollar-Vega RG, Zuarth-Vázquez JM, Hernández-Ramírez LC. Clinical Spectrum of USP8 Pathogenic Variants in Cushing's Disease. Arch Med Res 2023; 54:102899. [PMID: 37925320 DOI: 10.1016/j.arcmed.2023.102899] [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: 07/18/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023]
Abstract
Cushing's disease (CD) is a life-threatening condition with a challenging diagnostic process and scarce treatment options. CD is caused by usually benign adrenocorticotrophic hormone (ACTH)-secreting pituitary neuroendocrine tumors (PitNETs), known as corticotropinomas. These tumors are predominantly of sporadic origin, and usually derive from the monoclonal expansion of a mutated cell. Somatic activating variants located within a hotspot of the USP8 gene are present in 11-62% of corticotropinomas, making USP8 the most frequent genetic driver of corticotroph neoplasia. In contrast, other somatic defects such as those affecting the glucocorticoid receptor gene (NR3C1), the BRAF oncogene, the deubiquitinase-encoding gene USP48, and TP53 are infrequent. Moreover, patients with familial tumor syndromes, such as multiple endocrine neoplasia, familial isolated pituitary adenoma, and DICER1 rarely develop corticotropinomas. One of the main molecular alterations in USP8-driven tumors is an overactivation of the epidermal growth factor receptor (EGFR) signaling pathway, which induces ACTH production. Hotspot USP8 variants lead to persistent EGFR overexpression, thereby perpetuating the hyper-synthesis of ACTH. More importantly, they condition a characteristic transcriptomic signature that might be useful for the clinical prognosis of patients with CD. Nevertheless, the clinical phenotype associated with USP8 variants is less well defined. Hereby we discuss the current knowledge on the molecular pathogenesis and clinical picture associated with USP8 hotspot variants. We focus on the potential significance of the USP8 mutational status for the design of tailored clinical strategies in CD.
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Affiliation(s)
- Rosa G Rebollar-Vega
- Red de Apoyo a la Investigación, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Julia M Zuarth-Vázquez
- Department of Endocrinology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Laura C Hernández-Ramírez
- Red de Apoyo a la Investigación, Coordinación de la Investigación Científica, Universidad Nacional Autónoma de México e Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico.
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7
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Lin SJ, Lin MC, Liu TJ, Tsai YT, Tsai MT, Lee FJS. Endosomal Arl4A attenuates EGFR degradation by binding to the ESCRT-II component VPS36. Nat Commun 2023; 14:7859. [PMID: 38030597 PMCID: PMC10687025 DOI: 10.1038/s41467-023-42979-9] [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: 10/20/2022] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Ligand-induced epidermal growth factor receptor (EGFR) endocytosis followed by endosomal EGFR signaling and lysosomal degradation plays important roles in controlling multiple biological processes. ADP-ribosylation factor (Arf)-like protein 4 A (Arl4A) functions at the plasma membrane to mediate cytoskeletal remodeling and cell migration, whereas its localization at endosomal compartments remains functionally unknown. Here, we report that Arl4A attenuates EGFR degradation by binding to the endosomal sorting complex required for transport (ESCRT)-II component VPS36. Arl4A plays a role in prolonging the duration of EGFR ubiquitinylation and deterring endocytosed EGFR transport from endosomes to lysosomes under EGF stimulation. Mechanistically, the Arl4A-VPS36 direct interaction stabilizes VPS36 and ESCRT-III association, affecting subsequent recruitment of deubiquitinating-enzyme USP8 by CHMP2A. Impaired Arl4A-VPS36 interaction enhances EGFR degradation and clearance of EGFR ubiquitinylation. Together, we discover that Arl4A negatively regulates EGFR degradation by binding to VPS36 and attenuating ESCRT-mediated late endosomal EGFR sorting.
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Affiliation(s)
- Shin-Jin Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, 10002, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital, 10002, Taipei, Taiwan
| | - Ming-Chieh Lin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, 10002, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital, 10002, Taipei, Taiwan
| | - Tsai-Jung Liu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, 10002, Taipei, Taiwan
- Department of Medical Research, National Taiwan University Hospital, 10002, Taipei, Taiwan
| | - Yueh-Tso Tsai
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, 10002, Taipei, Taiwan
| | - Ming-Ting Tsai
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, 10002, Taipei, Taiwan
| | - Fang-Jen S Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, 10002, Taipei, Taiwan.
- Department of Medical Research, National Taiwan University Hospital, 10002, Taipei, Taiwan.
- Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, 10002, Taiwan.
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8
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Gan J, de Vries J, Akkermans JJLL, Mohammed Y, Tjokrodirijo RTN, de Ru AH, Kim RQ, Vargas DA, Pol V, Fasan R, van Veelen PA, Neefjes J, van Dam H, Ovaa H, Sapmaz A, Geurink PP. Cellular Validation of a Chemically Improved Inhibitor Identifies Monoubiquitination on OTUB2. ACS Chem Biol 2023; 18:2003-2013. [PMID: 37642399 PMCID: PMC10510154 DOI: 10.1021/acschembio.3c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023]
Abstract
Ubiquitin thioesterase OTUB2, a cysteine protease from the ovarian tumor (OTU) deubiquitinase superfamily, is often overexpressed during tumor progression and metastasis. Development of OTUB2 inhibitors is therefore believed to be therapeutically important, yet potent and selective small-molecule inhibitors targeting OTUB2 are scarce. Here, we describe the development of an improved OTUB2 inhibitor, LN5P45, comprising a chloroacethydrazide moiety that covalently reacts to the active-site cysteine residue. LN5P45 shows outstanding target engagement and proteome-wide selectivity in living cells. Importantly, LN5P45 as well as other OTUB2 inhibitors strongly induce monoubiquitination of OTUB2 on lysine 31. We present a route to future OTUB2-related therapeutics and have shown that the OTUB2 inhibitor developed in this study can help to uncover new aspects of the related biology and open new questions regarding the understanding of OTUB2 regulation at the post-translational modification level.
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Affiliation(s)
- Jin Gan
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Jelle de Vries
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Jimmy J. L. L. Akkermans
- Department
of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Yassene Mohammed
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Rayman T. N. Tjokrodirijo
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Robbert Q. Kim
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - David A. Vargas
- Department
of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester, New York 14627, United States
| | - Vito Pol
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Rudi Fasan
- Department
of Chemistry, University of Rochester, Hutchison Hall, 120 Trustee Rd, Rochester, New York 14627, United States
| | - Peter A. van Veelen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Albinusdreef 2, 2333 ZC Leiden, The Netherlands
| | - Jacques Neefjes
- Department
of Cell and Chemical Biology and Oncode Institute, Leiden University Medical Center LUMC, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Hans van Dam
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Huib Ovaa
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Paul P. Geurink
- Department
of Cell and Chemical Biology, Division of Chemical Biology and Drug
Discovery, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
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9
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Tang JQ, Marchand MM, Veggiani G. Ubiquitin Engineering for Interrogating the Ubiquitin-Proteasome System and Novel Therapeutic Strategies. Cells 2023; 12:2117. [PMID: 37626927 PMCID: PMC10453149 DOI: 10.3390/cells12162117] [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: 07/24/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Protein turnover, a highly regulated process governed by the ubiquitin-proteasome system (UPS), is essential for maintaining cellular homeostasis. Dysregulation of the UPS has been implicated in various diseases, including viral infections and cancer, making the proteins in the UPS attractive targets for therapeutic intervention. However, the functional and structural redundancies of UPS enzymes present challenges in identifying precise drug targets and achieving target selectivity. Consequently, only 26S proteasome inhibitors have successfully advanced to clinical use thus far. To overcome these obstacles, engineered peptides and proteins, particularly engineered ubiquitin, have emerged as promising alternatives. In this review, we examine the impact of engineered ubiquitin on UPS and non-UPS proteins, as well as on viral enzymes. Furthermore, we explore their potential to guide the development of small molecules targeting novel surfaces, thereby expanding the range of druggable targets.
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Affiliation(s)
- Jason Q. Tang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, ON M5S3E1, Canada
| | - Mary M. Marchand
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
- Division of Biotechnology and Molecular Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
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10
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Yalçin Z, Koot D, Bezstarosti K, Salas-Lloret D, Bleijerveld OB, Boersma V, Falcone M, González-Prieto R, Altelaar M, Demmers JAA, Jacobs JJL. Ubiquitinome profiling reveals in vivo UBE2D3 targets and implicates UBE2D3 in protein quality control. Mol Cell Proteomics 2023; 22:100548. [PMID: 37059365 DOI: 10.1016/j.mcpro.2023.100548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/16/2023] Open
Abstract
Ubiquitination has crucial roles in many cellular processes and dysregulation of ubiquitin machinery enzymes can result in various forms of pathogenesis. Cells only have a limited set of ubiquitin-conjugating (E2) enzymes to support the ubiquitination of many cellular targets. As individual E2 enzymes have many different substrates and interactions between E2 enzymes and their substrates can be transient, it is challenging to define all in vivo substrates of an individual E2 and the cellular processes it affects. Particularly challenging in this respect is UBE2D3, an E2 enzyme with promiscuous activity in vitro but less defined roles in vivo. Here, we set out to identify in vivo targets of UBE2D3 by using SILAC-based and label-free quantitative ubiquitin diGly proteomics to study global proteome and ubiquitinome changes associated with UBE2D3 depletion. UBE2D3 depletion changed the global proteome, with the levels of proteins from metabolic pathways, in particular retinol metabolism, being the most affected. However, the impact of UBE2D3 depletion on the ubiquitinome was much more prominent. Interestingly, molecular pathways related to mRNA translation were the most affected. Indeed, we find that ubiquitination of the ribosomal proteins RPS10 and RPS20, critical for ribosome-associated protein quality control (RQC), is dependent on UBE2D3. We show by TULIP2 methodology that RPS10 and RPS20 are direct targets of UBE2D3 and demonstrate that UBE2D3's catalytic activity is required to ubiquitinate RPS10 in vivo. In addition, our data suggest that UBE2D3 acts at multiple levels in autophagic protein quality control (PQC). Collectively, our findings show that depletion of an E2 enzyme in combination with quantitative diGly-based ubiquitinome profiling is a powerful tool to identify new in vivo E2 substrates, as we have done here for UBE2D3. Our work provides an important resource for further studies on the in vivo functions of UBE2D3.
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Affiliation(s)
- Zeliha Yalçin
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daniëlle Koot
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karel Bezstarosti
- Proteomics Center, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daniel Salas-Lloret
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vera Boersma
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mattia Falcone
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands; Genome Proteomics Laboratory, Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER), University of Seville, Seville, Spain; Department of Cell Biology, University of Seville, Seville, Spain
| | - Maarten Altelaar
- Proteomics Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, and Netherlands Proteomics Center, Utrecht, The Netherlands
| | | | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
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11
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Sapmaz A, Erson-Bensan AE. EGFR endocytosis: more than meets the eye. Oncotarget 2023; 14:297-301. [PMID: 37036745 PMCID: PMC10085055 DOI: 10.18632/oncotarget.28400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Indexed: 04/11/2023] Open
Abstract
Behind the scenes of signaling cascades initiated by activated receptors, endocytosis determines the fate of internalized proteins through degradation in lysosomes or recycling. Over the years, significant progress has been made in understanding the mechanisms of endocytosis and deregulation in disease states. Here we review the role of the EGF-SNX3-EGFR axis in breast cancers with an extended discussion on deregulated EGFR endocytosis in cancer.
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Affiliation(s)
| | - Ayse Elif Erson-Bensan
- Correspondence to:Ayse Elif Erson-Bensan,Department of Biological Sciences, Middle East Technical University, Dumlupinar Blv No:1, Universiteler Mah., Cankaya, Ankara 06800, Türkiye email
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12
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Fang YZ, Jiang L, He Q, Cao J, Yang B. Commentary: Deubiquitination complex platform: a plausible mechanism for regulating the substrate specificity of deubiquitinating enzymes. Acta Pharm Sin B 2023. [PMID: 37521861 PMCID: PMC10372820 DOI: 10.1016/j.apsb.2023.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) or deubiquitinases facilitate the escape of multiple proteins from ubiquitin‒proteasome degradation and are critical for regulating protein expression levels in vivo. Therefore, dissecting the underlying mechanism of DUB recognition is needed to advance the development of drugs related to DUB signaling pathways. To data, extensive studies on the ubiquitin chain specificity of DUBs have been reported, but substrate protein recognition is still not clearly understood. As a breakthrough, the scaffolding role may be significant to substrate protein selectivity. From this perspective, we systematically characterized the scaffolding proteins and complexes contributing to DUB substrate selectivity. Furthermore, we proposed a deubiquitination complex platform (DCP) as a potentially generic mechanism for DUB substrate recognition based on known examples, which might fill the gaps in the understanding of DUB substrate specificity.
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13
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Berlin I, Sapmaz A, Stévenin V, Neefjes J. Ubiquitin and its relatives as wizards of the endolysosomal system. J Cell Sci 2023; 136:288517. [PMID: 36825571 PMCID: PMC10022685 DOI: 10.1242/jcs.260101] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The endolysosomal system comprises a dynamic constellation of vesicles working together to sense and interpret environmental cues and facilitate homeostasis. Integrating extracellular information with the internal affairs of the cell requires endosomes and lysosomes to be proficient in decision-making: fusion or fission; recycling or degradation; fast transport or contacts with other organelles. To effectively discriminate between these options, the endolysosomal system employs complex regulatory strategies that crucially rely on reversible post-translational modifications (PTMs) with ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. The cycle of conjugation, recognition and removal of different Ub- and Ubl-modified states informs cellular protein stability and behavior at spatial and temporal resolution and is thus well suited to finetune macromolecular complex assembly and function on endolysosomal membranes. Here, we discuss how ubiquitylation (also known as ubiquitination) and its biochemical relatives orchestrate endocytic traffic and designate cargo fate, influence membrane identity transitions and support formation of membrane contact sites (MCSs). Finally, we explore the opportunistic hijacking of Ub and Ubl modification cascades by intracellular bacteria that remodel host trafficking pathways to invade and prosper inside cells.
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Affiliation(s)
- Ilana Berlin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Aysegul Sapmaz
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Virginie Stévenin
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
| | - Jacques Neefjes
- Oncode Institute, Department of Cell and Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 20, 2300RC Leiden, The Netherlands
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14
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Islam MT, Chen FZ, Chen HC, Wahid A. Knockdown of USP8 inhibits prostate cancer cell growth, proliferation, and metastasis and promotes docetaxel’s activity by suppressing the NF-kB signaling pathway. Front Oncol 2022; 12:923270. [PMID: 36338727 PMCID: PMC9632420 DOI: 10.3389/fonc.2022.923270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Ubiquitin-specific protease 8 (USP8) has been recently reported to be involved in tumorigenesis. Prostate cancer (PCa) is the most diagnosed malignancy among men, but USP8’s role in PCa is not yet investigated comprehensively. Therefore, the PCa cell lines DU145 and PC3 were transfected with USP8 siRNA or overexpressing vector together with or without docetaxel. The silencing USP8 and docetaxel treatment reduced cell viability and migration and promoted apoptosis. In contrast, USP8 knockdown was found to enhance docetaxel antitumor activity. In contrast, increased cell viability and migration were noticed upon USP8 overexpression, thereby decreasing apoptosis and suppressing docetaxel antitumor activity. Notably, although EGFR, PI3K, and NF-kB were found to be increased in both USP8 overexpression and docetaxel treatment, it significantly attenuated the effects in USP8 silencing followed by with or without docetaxel. Although EGFR silencing decreased PI3K and NF-kB activation, overexpression of USP8 was shown to counteract SiEGFR’s effects on NF-kB signaling by increasing PI3K expression. Our findings revealed that USP8 plays an oncogenic role in PCa and can suppress docetaxel activity. Additionally, as EGFR/PI3K/NF-kB was previously reported to develop docetaxel resistance, the combination treatment of USP8 knockdown with docetaxel might be a potential PCa therapeutic.
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Affiliation(s)
- Md. Tariqul Islam
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, China
| | - Fang-Zhi Chen
- Department of Urology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Han-Chun Chen
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Central South University, Changsha, China
- *Correspondence: Han-Chun Chen,
| | - Abdul Wahid
- Department of Cardiology of the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
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15
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Simon J, Theodoropoulou M. Genetics of Cushing's disease. J Neuroendocrinol 2022; 34:e13148. [PMID: 35596671 DOI: 10.1111/jne.13148] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/12/2022] [Accepted: 04/18/2022] [Indexed: 11/28/2022]
Abstract
Corticotroph tumours are primarily sporadic monoclonal neoplasms and only rarely found in genetic syndromes. Recurrent mutations in the ubiquitin specific protease 8 (USP8) gene are found in around half of cases. Mutations in other genes such as USP48 and NR3C1 are less frequent, found in less than ~20% of cases. TP53 and ATXR mutations are reported in up to one out of four cases, when focusing in USP8 wild type or aggressive corticotroph tumours and carcinomas. At present, USP8 mutations are the primary driver alterations in sporadic corticotroph tumours, TP53 and ATXR mutations may indicate transition to more aggressive tumour phenotype. Next generation sequencing efforts have identified additional genomic alterations, whose role and importance in corticotroph tumorigenesis remains to be elucidated.
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Affiliation(s)
- Julia Simon
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marily Theodoropoulou
- Medizinische Klinik und Poliklinik IV, LMU Klinikum, Ludwig-Maximilians-Universität München, Munich, Germany
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16
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Tian Y, Liu K, Liu R, Qiu Z, Xu Y, Wei W, Xu X, Wang J, Ding H, Li Z, Bian J. Discovery of Potent Small-Molecule USP8 Inhibitors for the Treatment of Breast Cancer through Regulating ERα Expression. J Med Chem 2022; 65:8914-8932. [PMID: 35786929 DOI: 10.1021/acs.jmedchem.2c00013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ubiquitin-specific protease 8 (USP8), belonging to the deubiquitinase family, has been implicated to be closely related to the occurrence of many malignant tumors, but only a few USP8-targeting inhibitors have been reported to date. In this study, we present virtual screening to discover novel hit candidates that inhibit the catalytic activity of USP8. Exploration of the structure-activity relationship led to the identification of compound DC-U4106, which binds to USP8 with a KD value of 4.7 μM and is selective over USP2 and USP7. Western blotting and immunoprecipitation showed that DC-U4106 could target the ubiquitin pathway and facilitate the degradation of ERα. In a xenograft tumor model, DC-U4106 also significantly inhibited tumor growth with minimal toxicity. Overall, our findings suggest that DC-U4106 is a promising drug candidate and targeting the USP8-ERα complex could be a new approach to treat ER-positive or drug-resistant breast cancer.
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Affiliation(s)
- Yucheng Tian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Kang Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Ruoyi Liu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Zhixia Qiu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Yifan Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Wei Wei
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Xi Xu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Jubo Wang
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Hong Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Material Medical, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai201203, China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing210009, China
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17
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Senatore E, Iannucci R, Chiuso F, Delle Donne R, Rinaldi L, Feliciello A. Pathophysiology of Primary Cilia: Signaling and Proteostasis Regulation. Front Cell Dev Biol 2022; 10:833086. [PMID: 35646931 PMCID: PMC9130585 DOI: 10.3389/fcell.2022.833086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/21/2022] [Indexed: 01/29/2023] Open
Abstract
Primary cilia are microtubule-based, non-motile sensory organelles present in most types of growth-arrested eukaryotic cells. They are transduction hubs that receive and transmit external signals to the cells in order to control growth, differentiation and development. Mutations of genes involved in the formation, maintenance or disassembly of ciliary structures cause a wide array of developmental genetic disorders, also known as ciliopathies. The primary cilium is formed during G1 in the cell cycle and disassembles at the G2/M transition. Following the completion of the cell division, the cilium reassembles in G1. This cycle is finely regulated at multiple levels. The ubiquitin-proteasome system (UPS) and the autophagy machinery, two main protein degradative systems in cells, play a fundamental role in cilium dynamics. Evidence indicate that UPS, autophagy and signaling pathways may act in synergy to control the ciliary homeostasis. However, the mechanisms involved and the links between these regulatory systems and cilium biogenesis, dynamics and signaling are not well defined yet. Here, we discuss the reciprocal regulation of signaling pathways and proteolytic machineries in the control of the assembly and disassembly of the primary cilium, and the impact of the derangement of these regulatory networks in human ciliopathies.
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18
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USP8 inhibition reshapes an inflamed tumor microenvironment that potentiates the immunotherapy. Nat Commun 2022; 13:1700. [PMID: 35361799 PMCID: PMC8971425 DOI: 10.1038/s41467-022-29401-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/15/2022] [Indexed: 01/20/2023] Open
Abstract
Anti-PD-1/PD-L1 immunotherapy has achieved impressive therapeutic outcomes in patients with multiple cancer types. However, the underlined molecular mechanism(s) for moderate response rate (15–25%) or resistance to PD-1/PD-L1 blockade remains not completely understood. Here, we report that inhibiting the deubiquitinase, USP8, significantly enhances the efficacy of anti-PD-1/PD-L1 immunotherapy through reshaping an inflamed tumor microenvironment (TME). Mechanistically, USP8 inhibition increases PD-L1 protein abundance through elevating the TRAF6-mediated K63-linked ubiquitination of PD-L1 to antagonize K48-linked ubiquitination and degradation of PD-L1. In addition, USP8 inhibition also triggers innate immune response and MHC-I expression largely through activating the NF-κB signaling. Based on these mechanisms, USP8 inhibitor combination with PD-1/PD-L1 blockade significantly activates the infiltrated CD8+ T cells to suppress tumor growth and improves the survival benefit in several murine tumor models. Thus, our study reveals a potential combined therapeutic strategy to utilize a USP8 inhibitor and PD-1/PD-L1 blockade for enhancing anti-tumor efficacy. The regulatory mechanisms of PD-L1 posttranslational modifications are not completely understood. Here the authors show that USP8 negatively regulates PD-L1 protein abundance by removing the K63-linked ubiquitination of PD-L1; while USP8 inhibition increases MHC-I expression and triggers anti-tumour immune responses through activating NF-κB signalling.
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19
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Sarri N, Wang K, Tsioumpekou M, Castillejo-López C, Lennartsson J, Heldin CH, Papadopoulos N. Deubiquitinating enzymes USP4 and USP17 finetune the trafficking of PDGFRβ and affect PDGF-BB-induced STAT3 signalling. Cell Mol Life Sci 2022; 79:85. [PMID: 35064336 PMCID: PMC8782881 DOI: 10.1007/s00018-022-04128-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/10/2021] [Accepted: 12/29/2021] [Indexed: 12/24/2022]
Abstract
Interaction of platelet-derived growth factor (PDGF) isoforms with their receptors results in activation and internalization of receptors, with a concomitant activation of downstream signalling pathways. Ubiquitination of PDGFRs serves as a mark to direct the internalization and sorting of the receptors. By overexpressing a panel of deubiquitinating enzymes (DUBs), we found that USP17 and USP4 efficiently deubiquitinate PDGF receptor β (PDGFRβ) and are able to remove both Lys63 and Lys48-linked polyubiquitin chains from the receptor. Deubiquitination of PDGFRβ did not affect its stability, but regulated the timing of its trafficking, whereby USP17 prolonged the presence of the receptor at the cell surface, while USP4 affected the speed of trafficking towards early endosomes. Induction of each of the DUBs in BJhTERT fibroblasts and U2OS osteosarcoma cells led to prolonged and/or shifted activation of STAT3 in response to PDGF-BB stimulation, which in turn led to increased transcriptional activity of STAT3. Induction of USP17 promoted acute upregulation of the mRNA expression of STAT3-inducible genes STAT3, CSF1, junB and c-myc, while causing long-term changes in the expression of myc and CDKN1A. Deletion of USP17 was lethal to fibroblasts, while deletion of USP4 led to a decreased proliferative response to stimulation by PDGF-BB. Thus, USP17- and USP4-mediated changes in ubiquitination of PDFGRβ lead to dysregulated signalling and transcription downstream of STAT3, resulting in defects in the control of cell proliferation.
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Affiliation(s)
- Niki Sarri
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Kehuan Wang
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
| | - Maria Tsioumpekou
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | | | - Johan Lennartsson
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Carl-Henrik Heldin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
| | - Natalia Papadopoulos
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, 75123 Uppsala, Sweden
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20
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Snyder NA, Silva GM. Deubiquitinating enzymes (DUBs): Regulation, homeostasis, and oxidative stress response. J Biol Chem 2021; 297:101077. [PMID: 34391779 PMCID: PMC8424594 DOI: 10.1016/j.jbc.2021.101077] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/17/2022] Open
Abstract
Ubiquitin signaling is a conserved, widespread, and dynamic process in which protein substrates are rapidly modified by ubiquitin to impact protein activity, localization, or stability. To regulate this process, deubiquitinating enzymes (DUBs) counter the signal induced by ubiquitin conjugases and ligases by removing ubiquitin from these substrates. Many DUBs selectively regulate physiological pathways employing conserved mechanisms of ubiquitin bond cleavage. DUB activity is highly regulated in dynamic environments through protein-protein interaction, posttranslational modification, and relocalization. The largest family of DUBs, cysteine proteases, are also sensitive to regulation by oxidative stress, as reactive oxygen species (ROS) directly modify the catalytic cysteine required for their enzymatic activity. Current research has implicated DUB activity in human diseases, including various cancers and neurodegenerative disorders. Due to their selectivity and functional roles, DUBs have become important targets for therapeutic development to treat these conditions. This review will discuss the main classes of DUBs and their regulatory mechanisms with a particular focus on DUB redox regulation and its physiological impact during oxidative stress.
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Affiliation(s)
- Nathan A Snyder
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Gustavo M Silva
- Department of Biology, Duke University, Durham, North Carolina, USA.
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21
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Rossio V, Paulo JA, Chick J, Brasher B, Gygi SP, King RW. Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity. Cell Chem Biol 2021; 28:487-502.e5. [PMID: 33417828 PMCID: PMC8052291 DOI: 10.1016/j.chembiol.2020.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/30/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Deubiquitylating enzymes (DUBs) counteract ubiquitylation to control stability or activity of substrates. Identification of DUB substrates is challenging because multiple DUBs can act on the same substrate, thwarting genetic approaches. Here, we circumvent redundancy by chemically inhibiting multiple DUBs simultaneously in Xenopus egg extract. We used quantitative mass spectrometry to identify proteins whose ubiquitylation or stability is altered by broad DUB inhibition, and confirmed their DUB-dependent regulation with human orthologs, demonstrating evolutionary conservation. We next extended this method to profile DUB specificity. By adding recombinant DUBs to extract where DUB activity was broadly inhibited, but ubiquitylation and degradation were active at physiological rates, we profiled the ability of DUBs to rescue degradation of these substrates. We found that USP7 has a unique ability to broadly antagonize degradation. Together, we present an approach to identify DUB substrates and characterize DUB specificity that overcomes challenges posed by DUB redundancy.
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Affiliation(s)
- Valentina Rossio
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Joel Chick
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Bradley Brasher
- Boston Biochem, a Bio-Techne Brand, Cambridge, MA 02139, USA
| | - Steven P Gygi
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Randall W King
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA.
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22
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The oncogenic role of ubiquitin specific peptidase (USP8) and its signaling pathways targeting for cancer therapeutics. Arch Biochem Biophys 2021; 701:108811. [PMID: 33600786 DOI: 10.1016/j.abb.2021.108811] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 01/08/2021] [Accepted: 02/11/2021] [Indexed: 01/06/2023]
Abstract
USP8 is a deubiquitinating enzyme in the family of ubiquitin-specific proteases (USPs) which can remove ubiquitin from the substrate and protect the substrate from degradation. The upregulated or mutated USP8 becomes hyperactivated and stabilizes numerous oncogenes or proto-oncogenes leading to cancer progression and survival by activating multiple signaling pathways. Moreover, USP8 inhibition is also important to overcome anticancer drug-resistant. This review is the first study to find, combine, analyze, and represent the multiple oncogenic signaling pathways with their downstream and upstream regulation activated or enhanced by USP8, which will help the researchers to find any therapeutic strategy for drug discovery by inhibiting or suppressing the multi-targeted USP8.
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23
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Martín-Rodríguez C, Song M, Anta B, González-Calvo FJ, Deogracias R, Jing D, Lee FS, Arevalo JC. TrkB deubiquitylation by USP8 regulates receptor levels and BDNF-dependent neuronal differentiation. J Cell Sci 2020; 133:jcs247841. [PMID: 33288548 PMCID: PMC7774901 DOI: 10.1242/jcs.247841] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 11/13/2020] [Indexed: 01/04/2023] Open
Abstract
Ubiquitylation of receptor tyrosine kinases (RTKs) regulates both the levels and functions of these receptors. The neurotrophin receptor TrkB (also known as NTRK2), a RTK, is ubiquitylated upon activation by brain-derived neurotrophic factor (BDNF) binding. Although TrkB ubiquitylation has been demonstrated, there is a lack of knowledge regarding the precise repertoire of proteins that regulates TrkB ubiquitylation. Here, we provide mechanistic evidence indicating that ubiquitin carboxyl-terminal hydrolase 8 (USP8) modulates BDNF- and TrkB-dependent neuronal differentiation. USP8 binds to the C-terminus of TrkB using its microtubule-interacting domain (MIT). Immunopurified USP8 deubiquitylates TrkB in vitro, whereas knockdown of USP8 results in enhanced ubiquitylation of TrkB upon BDNF treatment in neurons. As a consequence of USP8 depletion, TrkB levels and its activation are reduced. Moreover, USP8 protein regulates the differentiation and correct BDNF-dependent dendritic formation of hippocampal neurons in vitro and in vivo We conclude that USP8 positively regulates the levels and activation of TrkB, modulating BDNF-dependent neuronal differentiation.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Carlos Martín-Rodríguez
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
- Institute of Biomedical Research of Salamanca, 37007 Salamanca, Spain
| | - Minseok Song
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea
| | - Begoña Anta
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
- Institute of Biomedical Research of Salamanca, 37007 Salamanca, Spain
| | - Francisco J González-Calvo
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
| | - Rubén Deogracias
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
| | - Deqiang Jing
- Department of Psychiatry, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Francis S Lee
- Department of Psychiatry, Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Juan Carlos Arevalo
- Departmento de Biología Celular y Patología, Instituto de Neurociencias de Castilla y León, University of Salamanca, Salamanca 37007, Spain
- Institute of Biomedical Research of Salamanca, 37007 Salamanca, Spain
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24
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Cooperation and Interplay between EGFR Signalling and Extracellular Vesicle Biogenesis in Cancer. Cells 2020; 9:cells9122639. [PMID: 33302515 PMCID: PMC7764760 DOI: 10.3390/cells9122639] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/13/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) takes centre stage in carcinogenesis throughout its entire cellular trafficking odyssey. When loaded in extracellular vesicles (EVs), EGFR is one of the key proteins involved in the transfer of information between parental cancer and bystander cells in the tumour microenvironment. To hijack EVs, EGFR needs to play multiple signalling roles in the life cycle of EVs. The receptor is involved in the biogenesis of specific EV subpopulations, it signals as an active cargo, and it can influence the uptake of EVs by recipient cells. EGFR regulates its own inclusion in EVs through feedback loops during disease progression and in response to challenges such as hypoxia, epithelial-to-mesenchymal transition and drugs. Here, we highlight how the spatiotemporal rules that regulate EGFR intracellular function intersect with and influence different EV biogenesis pathways and discuss key regulatory features and interactions of this interplay. We also elaborate on outstanding questions relating to EGFR-driven EV biogenesis and available methods to explore them. This mechanistic understanding will be key to unravelling the functional consequences of direct anti-EGFR targeted and indirect EGFR-impacting cancer therapies on the secretion of pro-tumoural EVs and on their effects on drug resistance and microenvironment subversion.
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Ubiquitin-specific peptidase 8 regulates the trafficking and stability of the human organic anion transporter 1. Biochim Biophys Acta Gen Subj 2020; 1864:129701. [PMID: 32818533 DOI: 10.1016/j.bbagen.2020.129701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 11/23/2022]
Abstract
Background Organic anion transporter 1 (OAT1) plays a vital role in avoiding the potential toxicity of various anionic drugs through the involvement of kidney elimination. We previously demonstrated that ubiquitin conjugation to OAT1 led to OAT1 internalization from cell surface, followed by degradation. Ubiquitination is a dynamic process, where deubiquitination is catalyzed by a class of ubiquitin-specific peptidases. Methods The role of ubiquitin-specific peptidase 8 (USP8) in hOAT1 function, expression and ubiquitination was assessed by conducting transporter uptake assay, biotinylation assay and ubiquitination assay. Results We demonstrated that USP8 overexpression in hOAT1-expressing cells led to an increased hOAT1 transporter activity and expression, which correlated well with a reduced hOAT1 ubiquitination. Such phenomenon was not observed in inactive USP8 mutant-transfected cells. In addition, the knockdown of endogenous USP8 by USP8-specific siRNA resulted in an increased hOAT1 ubiquitination, which correlated well with a decrease in hOAT1 expression and transport activity. Biotinylation experiments demonstrated that USP8-induced increase in hOAT1 expression and transport activity occurred through a deceleration of the rates of hOAT1 internalization and degradation. Conclusions These results indicated the regulatory role of USP8 in OAT1 function, expression, trafficking, and stability. General significance USP8 could be a new target for modulating OAT1-mediated drug transport.
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Zhao J, Bi W, Zhang J, Xiao S, Zhou R, Tsang CK, Lu D, Zhu L. USP8 protects against lipopolysaccharide-induced cognitive and motor deficits by modulating microglia phenotypes through TLR4/MyD88/NF-κB signaling pathway in mice. Brain Behav Immun 2020; 88:582-596. [PMID: 32335193 DOI: 10.1016/j.bbi.2020.04.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 11/16/2022] Open
Abstract
Ubiquitin-specific protease 8 (USP8) regulates inflammation in vitro; however, the mechanisms by which USP8 inhibits neuroinflammation and its pathophysiological functions are not completely understood. In this study, we aimed to determine whether USP8 exerts neuroprotective effects in a mouse model of lipopolysaccharide (LPS)-induced cognitive and motor impairment. We commenced intracerebroventricular USP8 administration 7 days prior to i.p. injection of LPS (750 μg/kg). All treatments and behavioral experiments were performed once per day for 7 consecutive days. Behavioral tests and pathological/biochemical assays were performed to evaluate LPS-induced hippocampal damage. USP8 attenuated LPS-induced cognitive and motor impairments in mice. Moreover, USP8 downregulated several pro-inflammatory cytokines [nitric oxide (NO), tumor necrosis factor α (TNF-α), prostaglandin E2 (PGE2), and interleukin-1β (IL-1β)] in the serum and brain, and the relevant protein factors [inducible nitric oxide synthase (iNOS) and cyclooxygenase 2 (COX-2)] in the brain. Furthermore, USP8 upregulated the anti-inflammatory mediators interleukin (IL)-4 and IL-10 in the serum and brain, and promoted a shift from pro-inflammatory to anti-inflammatory microglial phenotypes. The LPS-induced microglial pro-inflammatory phenotype was abolished by TLR4 inhibitor and in TLR4-/- mice; these effects were similar to those of USP8 treatment. Mechanistically, we found that USP8 increased the expression of neuregulin receptor degradation protein-1 (Nrdp1), potently downregulated the expression of TLR4 and myeloid differentiation primary response protein 88 (MyD88) protein, and inhibited the phosphorylation of IκB kinase (IKK) β and kappa B-alpha (IκBα), thereby reducing nuclear translocation of p65 by inhibiting the activation of the nuclear factor-kappaB (NF-κB) signaling pathway in LPS-induced mice. Our results demonstrated that USP8 exerts protective effects against LPS-induced cognitive and motor deficits in mice by modulating microglial phenotypes via TLR4/MyD88/NF-κB signaling.
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Affiliation(s)
- JiaYi Zhao
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong Province 510632, China
| | - Wei Bi
- Department of Neurology, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong Province 510630, China
| | - JiaWei Zhang
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong Province 510632, China
| | - Shu Xiao
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong Province 510632, China
| | - RuiYi Zhou
- Department of Neurology, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong Province 510630, China
| | - Chi Kwan Tsang
- Clinical Neuoscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong Province 510630, China
| | - DaXiang Lu
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong Province 510632, China
| | - Lihong Zhu
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong Province 510632, China.
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Ubiquitin-specific protease 8 (USP8/UBPy): a prototypic multidomain deubiquitinating enzyme with pleiotropic functions. Biochem Soc Trans 2020; 47:1867-1879. [PMID: 31845722 PMCID: PMC6925526 DOI: 10.1042/bst20190527] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/29/2019] [Accepted: 12/02/2019] [Indexed: 01/07/2023]
Abstract
Protein modification by ubiquitin is one of the most versatile posttranslational regulations and counteracted by almost 100 deubiquitinating enzymes (DUBs). USP8 was originally identified as a growth regulated ubiquitin-specific protease and is like many other DUBs characterized by its multidomain architecture. Besides the catalytic domain, specific protein-protein interaction modules were characterized which contribute to USP8 substrate recruitment, regulation and targeting to distinct protein complexes. Studies in mice and humans impressively showed the physiological relevance and non-redundant function of USP8 within the context of the whole organism. USP8 knockout (KO) mice exhibit early embryonic lethality while induced deletion in adult animals rapidly causes lethal liver failure. Furthermore, T-cell specific ablation disturbs T-cell development and function resulting in fatal autoimmune inflammatory bowel disease. In human patients, somatic mutations in USP8 were identified as the underlying cause of adrenocorticotropic hormone (ACTH) releasing pituitary adenomas causing Cushing's disease (CD). Here we provide an overview of the versatile molecular, cellular and pathology associated function and regulation of USP8 which appears to depend on specific protein binding partners, substrates and the cellular context.
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Bi W, Lan X, Zhang J, Xiao S, Cheng X, Wang H, Lu D, Zhu L. USP8 ameliorates cognitive and motor impairments via microglial inhibition in a mouse model of sepsis-associated encephalopathy. Brain Res 2019; 1719:40-48. [PMID: 31075263 DOI: 10.1016/j.brainres.2019.05.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 02/08/2023]
Abstract
Sepsis-associated encephalopathy (SAE) is a common and serious complication of sepsis, which is thought to be caused by neuroinflammation. In our previous study, ubiquitin-specific protease 8 (USP8), was reported to regulate inflammation in vitro. In the current study, we investigated whether increased USP8 expression would ameliorate the cognitive and motor impairments induced by cecal ligation and puncture (CLP) in mice, a model of SAE. Male adult mice were randomly divided into four groups: control, sham, CLP, and CLP + USP8 groups. The CLP + USP8 mice showed reduced weight loss on day 4 post-CLP, with a slight increase noted on day 7. The mortality rate in the CLP group was 70% 48 h after CLP; however, USP8 significantly improved survival after CLP. USP8 modulated the neurobehavioral scores in CLP mice. Our results also indicate that USP8 attenuated the CLP-induced cognitive and motor impairments, based on the performance of mice in the Morris water maze (MWM), pole-climbing, and wire suspension tests. USP8 suppressed the release of pro-inflammatory mediators, including prostaglandin E2(PGE2) in the serum and nitric oxide (NO) in brain tissue, as well as levels of inducible NO synthase (iNOS) and cyclooxygenase-2 (COX-2) in brain tissue. Immunofluorescence experiments revealed that USP8 inhibited CLP-induced increases in microglial size and density in the hippocampus, and protected hippocampal neurons. Our findings indicate that neuroinflammation occurs in the brains of CLP mice, and that USP8 exerts protective effects against CLP-induced neuroinflammation and cognitive and motor impairments, which may aid in the development of novel therapeutic strategies for SAE.
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Affiliation(s)
- Wei Bi
- Department of Neurology, The First Affiliated Hospital of Jinan University, Guangzhou 510630, PR China
| | - Xin Lan
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou 510632, PR China
| | - JiaWei Zhang
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou 510632, PR China
| | - Shu Xiao
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou 510632, PR China
| | - XiaoFeng Cheng
- Department of Neurology, The First Affiliated Hospital of Jinan University, Guangzhou 510630, PR China
| | - HuaDong Wang
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou 510632, PR China
| | - DaXiang Lu
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou 510632, PR China
| | - Lihong Zhu
- Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou 510632, PR China.
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USP32 regulates late endosomal transport and recycling through deubiquitylation of Rab7. Nat Commun 2019; 10:1454. [PMID: 30926795 PMCID: PMC6440979 DOI: 10.1038/s41467-019-09437-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/06/2019] [Indexed: 12/26/2022] Open
Abstract
The endosomal system is a highly dynamic multifunctional organelle, whose complexity is regulated in part by reversible ubiquitylation. Despite the wide-ranging influence of ubiquitin in endosomal processes, relatively few enzymes utilizing ubiquitin have been described to control endosome integrity and function. Here we reveal the deubiquitylating enzyme (DUB) ubiquitin-specific protease 32 (USP32) as a powerful player in this context. Loss of USP32 inhibits late endosome (LE) transport and recycling of LE cargos, resulting in dispersion and swelling of the late compartment. Using SILAC-based ubiquitome profiling we identify the small GTPase Rab7—the logistical centerpiece of LE biology—as a substrate of USP32. Mechanistic studies reveal that LE transport effector RILP prefers ubiquitylation-deficient Rab7, while retromer-mediated LE recycling benefits from an intact cycle of Rab7 ubiquitylation. Collectively, our observations suggest that reversible ubiquitylation helps switch Rab7 between its various functions, thereby maintaining global spatiotemporal order in the endosomal system. Though ubiquitin is known to broadly influence endosomal trafficking, few ubiquitin-utilizing enzymes targeting endosomal regulators are known. Here, the authors find that the deubiquitylating enzyme (DUB) USP32 influences endosomal membrane dynamics by deubiquitinating Rab7.
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Deubiquitinating Enzymes Related to Autophagy: New Therapeutic Opportunities? Cells 2018; 7:cells7080112. [PMID: 30126257 PMCID: PMC6116007 DOI: 10.3390/cells7080112] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 12/21/2022] Open
Abstract
Autophagy is an evolutionary conserved catabolic process that allows for the degradation of intracellular components by lysosomes. This process can be triggered by nutrient deprivation, microbial infections or other challenges to promote cell survival under these stressed conditions. However, basal levels of autophagy are also crucial for the maintenance of proper cellular homeostasis by ensuring the selective removal of protein aggregates and dysfunctional organelles. A tight regulation of this process is essential for cellular survival and organismal health. Indeed, deregulation of autophagy is associated with a broad range of pathologies such as neuronal degeneration, inflammatory diseases, and cancer progression. Ubiquitination and deubiquitination of autophagy substrates, as well as components of the autophagic machinery, are critical regulatory mechanisms of autophagy. Here, we review the main evidence implicating deubiquitinating enzymes (DUBs) in the regulation of autophagy. We also discuss how they may constitute new therapeutic opportunities in the treatment of pathologies such as cancers, neurodegenerative diseases or infections.
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Liu C, Shen W, Yang C, Zeng L, Gao C. Knowns and unknowns of plasma membrane protein degradation in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:55-61. [PMID: 29807606 DOI: 10.1016/j.plantsci.2018.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/02/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
Plasma membrane (PM) not only creates a physical barrier to enclose the intracellular compartments but also mediates the direct communication between plants and the ever-changing environment. A tight control of PM protein homeostasis by selective degradation is thus crucial for proper plant development and plant-environment interactions. Accumulated evidences have shown that a number of plant PM proteins undergo clathrin-dependent or membrane microdomain-associated endocytic routes to vacuole for degradation in a cargo-ubiquitination dependent or independent manner. Besides, several trans-acting determinants involved in the regulation of endocytosis, recycling and multivesicular body-mediated vacuolar sorting have been identified in plants. More interestingly, recent findings have uncovered the participation of selective autophagy in PM protein turnover in plants. Although great progresses have been made to identify the PM proteins that undergo dynamic changes in subcellular localizations and to explore the factors that control the membrane protein trafficking, several questions remain to be answered regarding the molecular mechanisms of PM protein degradation in plants. In this short review article, we briefly summarize recent progress in our understanding of the internalization, sorting and degradation of plant PM proteins. More specifically, we focus on discussing the elusive aspects underlying the pathways of PM protein degradation in plants.
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Affiliation(s)
- Chuanliang Liu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Wenjin Shen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Chao Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lizhang Zeng
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Caiji Gao
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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32
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Crespo-Yàñez X, Aguilar-Gurrieri C, Jacomin AC, Journet A, Mortier M, Taillebourg E, Soleilhac E, Weissenhorn W, Fauvarque MO. CHMP1B is a target of USP8/UBPY regulated by ubiquitin during endocytosis. PLoS Genet 2018; 14:e1007456. [PMID: 29933386 PMCID: PMC6033466 DOI: 10.1371/journal.pgen.1007456] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 07/05/2018] [Accepted: 05/30/2018] [Indexed: 11/29/2022] Open
Abstract
Integration and down-regulation of cell growth and differentiation signals rely on plasma membrane receptor endocytosis and sorting towards either recycling vesicles or degradative lysosomes via multivesicular bodies (MVB). In this process, the endosomal sorting complex-III required for transport (ESCRT-III) controls membrane deformation and scission triggering intraluminal vesicle (ILV) formation at early endosomes. Here, we show that the ESCRT-III member CHMP1B can be ubiquitinated within a flexible loop known to undergo conformational changes during polymerization. We demonstrate further that CHMP1B is deubiquitinated by the ubiquitin specific protease USP8 (syn. UBPY) and found fully devoid of ubiquitin in a ~500 kDa large complex that also contains its ESCRT-III partner IST1. Moreover, EGF stimulation induces the rapid and transient accumulation of ubiquitinated forms of CHMP1B on cell membranes. Accordingly, CHMP1B ubiquitination is necessary for CHMP1B function in both EGF receptor trafficking in human cells and wing development in Drosophila. Based on these observations, we propose that CHMP1B is dynamically regulated by ubiquitination in response to EGF and that USP8 triggers CHMP1B deubiquitination possibly favoring its subsequent assembly into a membrane-associated ESCRT-III polymer. In multicellular organisms, the interpretation and transmission of cell growth and differentiation signals strongly rely on plasma membrane receptors. Once activated by their ligands, these receptors activate downstream signaling cascades and are rapidly internalized into intracellular vesicles that fuse inside the cell to form the endosomal compartment. From there, the receptors are sorted towards either recycling vesicles or degradative lysosomes via multivesicular bodies. Receptors sorting therefore plays a crucial role in the integration and regulation of intracellular signals during development and numerous physio-pathological processes. It requires extensive membrane remodeling and scission events at the level of the endosomal compartment by so-called ESCRT proteins, including CHMP1B. In this study, we provide evidence for dynamic regulation of CHMP1B function and subcellular localization by ubiquitin linkage. We also show the contribution of the ubiquitin specific protease USP8 in this regulation, which is a known actor of intracellular trafficking and Cushing’s disease.
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Affiliation(s)
- Xènia Crespo-Yàñez
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Carmen Aguilar-Gurrieri
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Anne-Claire Jacomin
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Agnès Journet
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Magda Mortier
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Emmanuel Taillebourg
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Emmanuelle Soleilhac
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
| | - Winfried Weissenhorn
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Marie-Odile Fauvarque
- Institut de Biosciences et Biotechnologies de Grenoble (BIG), Univ. Grenoble Alpes, INSERM U1038, CEA, Grenoble, France
- * E-mail:
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Wijesuriya TM, De Ceuninck L, Masschaele D, Sanderson MR, Carias KV, Tavernier J, Wevrick R. The Prader-Willi syndrome proteins MAGEL2 and necdin regulate leptin receptor cell surface abundance through ubiquitination pathways. Hum Mol Genet 2018; 26:4215-4230. [PMID: 28973533 DOI: 10.1093/hmg/ddx311] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022] Open
Abstract
In Prader-Willi syndrome (PWS), obesity is caused by the disruption of appetite-controlling pathways in the brain. Two PWS candidate genes encode MAGEL2 and necdin, related melanoma antigen proteins that assemble into ubiquitination complexes. Mice lacking Magel2 are obese and lack leptin sensitivity in hypothalamic pro-opiomelanocortin neurons, suggesting dysregulation of leptin receptor (LepR) activity. Hypothalamus from Magel2-null mice had less LepR and altered levels of ubiquitin pathway proteins that regulate LepR processing (Rnf41, Usp8, and Stam1). MAGEL2 increased the cell surface abundance of LepR and decreased their degradation. LepR interacts with necdin, which interacts with MAGEL2, which complexes with RNF41 and USP8. Mutations in the MAGE homology domain of MAGEL2 suppress RNF41 stabilization and prevent the MAGEL2-mediated increase of cell surface LepR. Thus, MAGEL2 and necdin together control LepR sorting and degradation through a dynamic ubiquitin-dependent pathway. Loss of MAGEL2 and necdin may uncouple LepR from ubiquitination pathways, providing a cellular mechanism for obesity in PWS.
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Affiliation(s)
| | - Leentje De Ceuninck
- Department of Biochemistry, VIB Center for Medical Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Delphine Masschaele
- Department of Biochemistry, VIB Center for Medical Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Matthea R Sanderson
- Department of Medical Genetics, University of Alberta, Edmonton T6G 2H7, Canada
| | | | - Jan Tavernier
- Department of Biochemistry, VIB Center for Medical Biotechnology and Faculty of Medicine and Health Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton T6G 2H7, Canada
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Critchley WR, Pellet-Many C, Ringham-Terry B, Harrison MA, Zachary IC, Ponnambalam S. Receptor Tyrosine Kinase Ubiquitination and De-Ubiquitination in Signal Transduction and Receptor Trafficking. Cells 2018; 7:E22. [PMID: 29543760 PMCID: PMC5870354 DOI: 10.3390/cells7030022] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 12/13/2022] Open
Abstract
Receptor tyrosine kinases (RTKs) are membrane-based sensors that enable rapid communication between cells and their environment. Evidence is now emerging that interdependent regulatory mechanisms, such as membrane trafficking, ubiquitination, proteolysis and gene expression, have substantial effects on RTK signal transduction and cellular responses. Different RTKs exhibit both basal and ligand-stimulated ubiquitination, linked to trafficking through different intracellular compartments including the secretory pathway, plasma membrane, endosomes and lysosomes. The ubiquitin ligase superfamily comprising the E1, E2 and E3 enzymes are increasingly implicated in this post-translational modification by adding mono- and polyubiquitin tags to RTKs. Conversely, removal of these ubiquitin tags by proteases called de-ubiquitinases (DUBs) enables RTK recycling for another round of ligand sensing and signal transduction. The endocytosis of basal and activated RTKs from the plasma membrane is closely linked to controlled proteolysis after trafficking and delivery to late endosomes and lysosomes. Proteolytic RTK fragments can also have the capacity to move to compartments such as the nucleus and regulate gene expression. Such mechanistic diversity now provides new opportunities for modulating RTK-regulated cellular responses in health and disease states.
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Affiliation(s)
- William R Critchley
- Endothelial Cell Biology Unit, School of Molecular & Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Caroline Pellet-Many
- Centre for Cardiovascular Biology & Medicine, Rayne Building, University College London, London WC1E 6PT, UK.
| | - Benjamin Ringham-Terry
- Centre for Cardiovascular Biology & Medicine, Rayne Building, University College London, London WC1E 6PT, UK.
| | | | - Ian C Zachary
- Centre for Cardiovascular Biology & Medicine, Rayne Building, University College London, London WC1E 6PT, UK.
| | - Sreenivasan Ponnambalam
- Endothelial Cell Biology Unit, School of Molecular & Cellular Biology, University of Leeds, Leeds LS2 9JT, UK.
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Bakker J, Spits M, Neefjes J, Berlin I. The EGFR odyssey - from activation to destruction in space and time. J Cell Sci 2017; 130:4087-4096. [PMID: 29180516 DOI: 10.1242/jcs.209197] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
When cell surface receptors engage their cognate ligands in the extracellular space, they become competent to transmit potent signals to the inside of the cell, thereby instigating growth, differentiation, motility and many other processes. In order to control these signals, activated receptors are endocytosed and thoroughly curated by the endosomal network of intracellular vesicles and proteolytic organelles. In this Review, we follow the epidermal growth factor (EGF) receptor (EGFR) from ligand engagement, through its voyage on endosomes and, ultimately, to its destruction in the lysosome. We focus on the spatial and temporal considerations underlying the molecular decisions that govern this complex journey and discuss how additional cellular organelles - particularly the ER - play active roles in the regulation of receptor lifespan. In summarizing the functions of relevant molecules on the endosomes and the ER, we cover the order of molecular events in receptor activation, trafficking and downregulation, and provide an overview of how signaling is controlled at the interface between these organelles.
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Affiliation(s)
- Jeroen Bakker
- Department of Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 22, 2333 ZC, Leiden, The Netherlands
| | - Menno Spits
- Department of Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 22, 2333 ZC, Leiden, The Netherlands
| | - Jacques Neefjes
- Department of Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 22, 2333 ZC, Leiden, The Netherlands
| | - Ilana Berlin
- Department of Chemical Biology, Leiden University Medical Center LUMC, Einthovenweg 22, 2333 ZC, Leiden, The Netherlands
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Goodwin JM, Dowdle WE, DeJesus R, Wang Z, Bergman P, Kobylarz M, Lindeman A, Xavier RJ, McAllister G, Nyfeler B, Hoffman G, Murphy LO. Autophagy-Independent Lysosomal Targeting Regulated by ULK1/2-FIP200 and ATG9. Cell Rep 2017; 20:2341-2356. [PMID: 28877469 PMCID: PMC5699710 DOI: 10.1016/j.celrep.2017.08.034] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/26/2017] [Accepted: 08/07/2017] [Indexed: 12/20/2022] Open
Abstract
Iron is vital for many homeostatic processes, and its liberation from ferritin nanocages occurs in the lysosome. Studies indicate that ferritin and its binding partner nuclear receptor coactivator-4 (NCOA4) are targeted to lysosomes by a form of selective autophagy. By using genome-scale functional screening, we identify an alternative lysosomal transport pathway for ferritin that requires FIP200, ATG9A, VPS34, and TAX1BP1 but lacks involvement of the ATG8 lipidation machinery that constitutes classical macroautophagy. TAX1BP1 binds directly to NCOA4 and is required for lysosomal trafficking of ferritin under basal and iron-depleted conditions. Under basal conditions ULK1/2-FIP200 controls ferritin turnover, but its deletion leads to TAX1BP1-dependent activation of TBK1 that regulates redistribution of ATG9A to the Golgi enabling continued trafficking of ferritin. Cells expressing an amyotrophic lateral sclerosis (ALS)-associated TBK1 allele are incapable of degrading ferritin suggesting a molecular mechanism that explains the presence of iron deposits in patient brain biopsies.
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Affiliation(s)
- Jonathan M Goodwin
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - William E Dowdle
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rowena DeJesus
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Zuncai Wang
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Philip Bergman
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Marek Kobylarz
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Alicia Lindeman
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ramnik J Xavier
- Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, USA
| | - Gregory McAllister
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Beat Nyfeler
- Novartis Institutes for Biomedical Research, Novartis Campus, 4056 Basel, Switzerland.
| | - Gregory Hoffman
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Leon O Murphy
- Novartis Institutes for Biomedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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37
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Deubiquitylating enzymes in receptor endocytosis and trafficking. Biochem J 2017; 473:4507-4525. [PMID: 27941029 DOI: 10.1042/bcj20160826] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 12/25/2022]
Abstract
In recent times, our knowledge of the roles ubiquitin plays in multiple cellular processes has expanded exponentially, with one example being the role of ubiquitin in receptor endocytosis and trafficking. This has prompted a multitude of studies examining how the different machinery involved in the addition and removal of ubiquitin can influence this process. Multiple deubiquitylating enzymes (DUBs) have been implicated either in facilitating receptor endocytosis and lysosomal degradation or in rescuing receptor levels by preventing endocytosis and/or promoting recycling to the plasma membrane. In this review, we will discuss in detail what is currently known about the role of DUBs in regulating the endocytosis of various transmembrane receptors and ion channels. We will also expand upon the role DUBs play in receptor sorting at the multivesicular body to determine whether a receptor is recycled or trafficked to the lysosome for degradation. Finally, we will briefly discuss how the DUBs implicated in these processes may contribute to the pathogenesis of a range of diseases, and thus the potential these have as therapeutic targets.
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Bednash JS, Weathington N, Londino J, Rojas M, Gulick DL, Fort R, Han S, McKelvey AC, Chen BB, Mallampalli RK. Targeting the deubiquitinase STAMBP inhibits NALP7 inflammasome activity. Nat Commun 2017; 8:15203. [PMID: 28492230 PMCID: PMC5437278 DOI: 10.1038/ncomms15203] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 03/08/2017] [Indexed: 01/06/2023] Open
Abstract
Inflammasomes regulate innate immune responses by facilitating maturation of inflammatory cytokines, interleukin (IL)-1β and IL-18. NACHT, LRR and PYD domains-containing protein 7 (NALP7) is one inflammasome constituent, but little is known about its cellular handling. Here we show a mechanism for NALP7 protein stabilization and activation of the inflammasome by Toll-like receptor (TLR) agonism with bacterial lipopolysaccharide (LPS) and the synthetic acylated lipopeptide Pam3CSK4. NALP7 is constitutively ubiquitinated and recruited to the endolysosome for degradation. With TLR ligation, the deubiquitinase enzyme, STAM-binding protein (STAMBP) impedes NALP7 trafficking to lysosomes to increase NALP7 abundance. STAMBP deubiquitinates NALP7 and STAMBP knockdown abrogates LPS or Pam3CSK4-induced increases in NALP7 protein. A small-molecule inhibitor of STAMBP deubiquitinase activity, BC-1471, decreases NALP7 protein levels and suppresses IL-1β release after TLR agonism. These findings describe a unique pathway of inflammasome regulation with the identification of STAMBP as a potential therapeutic target to reduce pro-inflammatory stress.
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Affiliation(s)
- Joseph S. Bednash
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Nathaniel Weathington
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - James Londino
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Mauricio Rojas
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Dexter L. Gulick
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Robert Fort
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - SeungHye Han
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Alison C. McKelvey
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Bill B. Chen
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
| | - Rama K. Mallampalli
- Department of Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, UPMC Montefiore, NW 628, Pittsburgh, Pennsylvania 15213, USA
- Departments of Cell Biology and Physiology and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
- Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania 15240, USA
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Qiu GZ, Sun W, Jin MZ, Lin J, Lu PG, Jin WL. The bad seed gardener: Deubiquitinases in the cancer stem-cell signaling network and therapeutic resistance. Pharmacol Ther 2017; 172:127-138. [DOI: 10.1016/j.pharmthera.2016.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Clague MJ, Urbé S. Integration of cellular ubiquitin and membrane traffic systems: focus on deubiquitylases. FEBS J 2017; 284:1753-1766. [PMID: 28064438 PMCID: PMC5484354 DOI: 10.1111/febs.14007] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 12/29/2016] [Accepted: 01/06/2017] [Indexed: 12/17/2022]
Abstract
The cell is comprised of integrated multilevel protein networks or systems. The ubiquitin, protein homeostasis and membrane trafficking systems are highly integrated. Here, we look at the influence of reversible ubiquitylation on membrane trafficking and organelle dynamics. We review the regulation of endocytic sorting, selective autophagy and the secretory pathway by ubiquitin signals, with a particular focus on detailing the contribution of deubiquitylating enzymes.
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Affiliation(s)
- Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, UK
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, UK
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Hologne M, Cantrelle FX, Riviere G, Guillière F, Trivelli X, Walker O. NMR Reveals the Interplay among the AMSH SH3 Binding Motif, STAM2, and Lys63-Linked Diubiquitin. J Mol Biol 2016; 428:4544-4558. [PMID: 27725184 DOI: 10.1016/j.jmb.2016.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/30/2016] [Accepted: 10/01/2016] [Indexed: 01/31/2023]
Abstract
AMSH [associated molecule with a Src homology 3 domain of signal transducing adaptor molecule (STAM)] is one of the deubiquitinating enzymes associated in the regulation of endocytic cargo trafficking. It shows an exquisite selectivity for Lys63-linked polyubiquitin chains that are the main chains involved in cargo sorting. The first step requires the ESCRT-0 complex that comprises the STAM and hepatocyte growth factor-regulated substrate (Hrs) proteins. Previous studies have shown that the presence of the STAM protein increases the efficiency of Lys63-linked polyubiquitin chain cleavage by AMSH, one of the deubiquitinating enzyme involved in lysosomal degradation. In the present study, we are seeking to understand if a particular structural organization among these three key players is responsible for the stimulation of the catalytic activity of AMSH. To address this question, we first monitored the interaction between the ubiquitin interacting motif (UIM)-SH3 construct of STAM2 and the Lys63-linked diubiquitin (Lys63-Ub2) chains by means of NMR. We show that Lys63-Ub2 is able to bind either the UIM or the SH3 domain without any selectivity. We further demonstrate that the SH3 binding motif (SBM) of AMSH (AMSH-SBM) outcompetes Lys63-Ub2 for binding SH3. Additionally, we show how different AMSH-SBM variants, modified by their sequence and length, exhibit similar equilibrium dissociation constants when binding SH3 but significantly differ in their dissociation rate constants. Finally, we report the solution NMR structure of the AMSH-SBM/SH3 complex and propose a structural organization where the AMSH-SBM interacts with the STAM2-SH3 domain and contributes to the correct positioning of AMSH prior to polyubiquitin chains' cleavage.
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Affiliation(s)
- Maggy Hologne
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - François-Xavier Cantrelle
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Gwladys Riviere
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Florence Guillière
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France
| | - Xavier Trivelli
- Université de Lille, CNRS, UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
| | - Olivier Walker
- Université de Lyon, CNRS, Université Claude Bernard Lyon1, Ens de Lyon, Institut des Sciences Analytiques, UMR 5280, 5 rue de la Doua, F-69100 Villeurbanne, France.
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Yeates EFA, Tesco G. The Endosome-associated Deubiquitinating Enzyme USP8 Regulates BACE1 Enzyme Ubiquitination and Degradation. J Biol Chem 2016; 291:15753-66. [PMID: 27302062 DOI: 10.1074/jbc.m116.718023] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 01/04/2023] Open
Abstract
The β-site amyloid precursor protein-cleaving enzyme (BACE1) is the rate-limiting enzyme in the production of amyloid-β, the toxic peptide that accumulates in the brain of subjects affected by Alzheimer disease. Our previous studies have shown that BACE1 is degraded via the lysosomal pathway and that that depletion of the trafficking molecule Golgi-localized γ-ear-containing ARF-binding protein 3 (GGA3) results in increased BACE1 levels and activity because of impaired lysosomal degradation. We also determined that GGA3 regulation of BACE1 levels requires its ability to bind ubiquitin. Accordingly, we reported that BACE1 is ubiquitinated at lysine 501 and that lack of ubiquitination at lysine 501 produces BACE1 stabilization. Ubiquitin conjugation is a reversible process mediated by deubiquitinating enzymes. The ubiquitin-specific peptidase 8 (USP8), an endosome-associated deubiquitinating enzyme, regulates the ubiquitination, trafficking, and lysosomal degradation of several plasma membrane proteins. Here, we report that RNAi-mediated depletion of USP8 reduced levels of both ectopically expressed and endogenous BACE1 in H4 human neuroglioma cells. Moreover, USP8 depletion increased BACE1 ubiquitination, promoted BACE1 accumulation in the early endosomes and late endosomes/lysosomes, and decreased levels of BACE1 in the recycling endosomes. We also found that decreased BACE1 protein levels were accompanied by a decrease in BACE1-mediated amyloid precursor protein cleavage and amyloid-β levels. Our findings demonstrate that USP8 plays a key role in the trafficking and degradation of BACE1 by deubiquitinating lysine 501. These studies suggest that therapies able to accelerate BACE1 degradation (e.g. by increasing BACE1 ubiquitination) may represent a potential treatment for Alzheimer disease.
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Affiliation(s)
| | - Giuseppina Tesco
- From the Department of Neuroscience, Tufts University School of Medicine, Boston, Massachusetts 02111
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Abstract
A majority of proteins in the cell can be modified by ubiquitination, thereby altering their function or stability. This ubiquitination is controlled by both ubiquitinating and deubiquitinating enzymes (DUBs). The number of ubiquitin ligases exceeds that of DUBs by about eightfold, indicating that DUBs may have much broader substrate specificity. Despite this, DUBs have been shown to have quite specific physiological functions. This functional specificity is likely due to very precise regulation of activity arising from the sophisticated use of all mechanisms of enzyme regulation. In this commentary, we briefly review key features of DUBs with more emphasis on regulation. In particular, we focus on localization of the enzymes as a critical regulatory mechanism which when integrated with control of expression, substrate activation, allosteric regulation, and post-translational modifications results in precise spatial and temporal deubiquitination of proteins and therefore specific physiological functions. Identification of compounds that target the structural elements in DUBs that dictate localization may be a more promising approach to development of drugs with specificity of action than targeting the enzymatic activity, which for most DUBs is dependent on a thiol group that can react non-specifically with many compounds in large-scale screening.
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Affiliation(s)
- Erin S Coyne
- Polypeptide Laboratory, Departments of Medicine and Biochemistry, McGill University, McGill University Health Centre Research Institute, Montreal, QC, Canada
| | - Simon S Wing
- Polypeptide Laboratory, Departments of Medicine and Biochemistry, McGill University, McGill University Health Centre Research Institute, Montreal, QC, Canada
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44
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Jacomin AC, Bescond A, Soleilhac E, Gallet B, Schoehn G, Fauvarque MO, Taillebourg E. The Deubiquitinating Enzyme UBPY Is Required for Lysosomal Biogenesis and Productive Autophagy in Drosophila. PLoS One 2015; 10:e0143078. [PMID: 26571504 PMCID: PMC4646453 DOI: 10.1371/journal.pone.0143078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/30/2015] [Indexed: 12/31/2022] Open
Abstract
Autophagy is a catabolic process that delivers cytoplasmic components to the lysosomes. Protein modification by ubiquitination is involved in this pathway: it regulates the stability of autophagy regulators such as BECLIN-1 and it also functions as a tag targeting specific substrates to autophagosomes. In order to identify deubiquitinating enzymes (DUBs) involved in autophagy, we have performed a genetic screen in the Drosophila larval fat body. This screen identified Uch-L3, Usp45, Usp12 and Ubpy. In this paper, we show that Ubpy loss of function results in the accumulation of autophagosomes due to a blockade of the autophagy flux. Furthermore, analysis by electron and confocal microscopy of Ubpy-depleted fat body cells revealed altered lysosomal morphology, indicating that Ubpy inactivation affects lysosomal maintenance and/or biogenesis. Lastly, we have shown that shRNA mediated inactivation of UBPY in HeLa cells affects autophagy in a different way: in UBPY-depleted HeLa cells autophagy is deregulated.
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Affiliation(s)
- Anne-Claire Jacomin
- Université Grenoble-Alpes, F-38041, Grenoble, France; CEA-DSV-iRTSV-BGE-Gen&Chem, F-38054, Grenoble, France; INSERM, U1038, F-38054, Grenoble, France
| | - Amandine Bescond
- Université Grenoble-Alpes, F-38041, Grenoble, France; CEA-DSV-iRTSV-BGE-Gen&Chem, F-38054, Grenoble, France; INSERM, U1038, F-38054, Grenoble, France
| | - Emmanuelle Soleilhac
- Université Grenoble-Alpes, F-38041, Grenoble, France; CEA-DSV-iRTSV-BGE-Gen&Chem, F-38054, Grenoble, France; INSERM, U1038, F-38054, Grenoble, France
| | - Benoît Gallet
- Université Grenoble Alpes, IBS, F-38044, Grenoble, France; CNRS, IBS, F-38044, Grenoble, France; CEA, IBS, F-38044, Grenoble, France
| | - Guy Schoehn
- Université Grenoble Alpes, IBS, F-38044, Grenoble, France; CNRS, IBS, F-38044, Grenoble, France; CEA, IBS, F-38044, Grenoble, France
| | - Marie-Odile Fauvarque
- Université Grenoble-Alpes, F-38041, Grenoble, France; CEA-DSV-iRTSV-BGE-Gen&Chem, F-38054, Grenoble, France; INSERM, U1038, F-38054, Grenoble, France
- * E-mail: (ET); (MOF)
| | - Emmanuel Taillebourg
- Université Grenoble-Alpes, F-38041, Grenoble, France; CEA-DSV-iRTSV-BGE-Gen&Chem, F-38054, Grenoble, France; INSERM, U1038, F-38054, Grenoble, France
- * E-mail: (ET); (MOF)
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45
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Recurrent gain-of-function USP8 mutations in Cushing's disease. Cell Res 2015; 25:306-17. [PMID: 25675982 PMCID: PMC4349249 DOI: 10.1038/cr.2015.20] [Citation(s) in RCA: 222] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 01/30/2015] [Accepted: 02/02/2015] [Indexed: 12/12/2022] Open
Abstract
Cushing's disease, also known as adrenocorticotropic hormone (ACTH)-secreting pituitary adenomas (PAs) that cause excess cortisol production, accounts for up to 85% of corticotrophin-dependent Cushing's syndrome cases. However, the genetic alterations in this disease are unclear. Here, we performed whole-exome sequencing of DNA derived from 12 ACTH-secreting PAs and matched blood samples, which revealed three types of somatic mutations in a candidate gene, USP8 (encoding ubiquitin-specific protease 8), exclusively in exon 14 in 8 of 12 ACTH-secreting PAs. We further evaluated somatic USP8 mutations in additional 258 PAs by Sanger sequencing. Targeted sequencing further identified a total of 17 types of USP8 variants in 67 of 108 ACTH-secreting PAs (62.04%). However, none of these mutations was detected in other types of PAs (n = 150). These mutations aggregate within the 14-3-3 binding motif of USP8 and disrupt the interaction between USP8 and 14-3-3 protein, resulting in an elevated capacity to protect EGFR from lysosomal degradation. Accordingly, PAs with mutated USP8 display a higher incidence of EGFR expression, elevated EGFR protein abundance and mRNA expression levels of POMC, which encodes the precursor of ACTH. PAs with mutated USP8 are significantly smaller in size and have higher ACTH production than wild-type PAs. In surgically resected primary USP8-mutated tumor cells, USP8 knockdown or blocking EGFR effectively attenuates ACTH secretion. Taken together, somatic gain-of-function USP8 mutations are common and contribute to ACTH overproduction in Cushing's disease. Inhibition of USP8 or EGFR is promising for treating USP8-mutated corticotrophin adenoma. Our study highlights the potentially functional mutated gene in Cushing's disease and provides insights into the therapeutics of this disease.
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Zhu L, Bi W, Lu D, Zhang C, Shu X, Wang H, Qi R, Shi Q, Lu D. Regulation of ubiquitin-specific processing protease 8 suppresses neuroinflammation. Mol Cell Neurosci 2015; 64:74-83. [PMID: 24861766 DOI: 10.1016/j.mcn.2014.05.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 03/14/2014] [Accepted: 05/21/2014] [Indexed: 02/05/2023] Open
Abstract
In our previous study, we reported that luteolin might exert neuroprotective functions by inhibiting the production of proinflammatory mediators, thereby suppressing microglial activation. In this study, we used two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) to study the effect of ubiquitin-specific processing protease 8 (USP8) in luteolin-treated microglia. Western blot analysis verified that USP8 expression is upregulated by luteolin. Researchers have found that USP8 markedly enhanced the stability of neuregulin receptor degradation protein-1 (Nrdp1), which in turn inhibited the production of proinflammatory cytokines in toll-like receptor-triggered macrophages. We next hypothesized that luteolin inhibits microglial inflammation by regulating USP8 gene expression. After transfecting BV2-immortalized murine microglial cells with USP8, a significant reduction in the degradation of Nrdp1 was observed. USP8 overexpression also reduced the production of lipopolysaccharide (LPS)-induced proinflammatory mediators such as inducible nitric oxide synthase (iNOS), nitric oxide (NO), cyclooxygenase-2 (COX-2), and prostaglandin E2 (PGE2). We also found that USP8 siRNA blocked luteolin inhibition of pro-inflammatory gene expression such as iNOS, NO, COX-2, and PGE2. Taken together, our findings suggested that luteolin inhibits microglial inflammation by enhancing USP8 protein production. We concluded that in addition to anti-inflammatory luteolin, USP8 might represent a novel mechanism for the treatment of neuroinflammation and neurodegeneration.
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Affiliation(s)
- Lihong Zhu
- Department of Pathophysiology, Institute of Brain Research, School of Medicine, JiNan University, Guangzhou 510632, PR China
| | - Wei Bi
- Department of Neurology, First Affiliated Hospital of JiNan University, Guangzhou 510630, PR China
| | - Dan Lu
- Department of Pathophysiology, Institute of Brain Research, School of Medicine, JiNan University, Guangzhou 510632, PR China
| | - Chanjuan Zhang
- Department of Pathophysiology, Institute of Brain Research, School of Medicine, JiNan University, Guangzhou 510632, PR China
| | - Xiaoming Shu
- Department of Pathophysiology, Institute of Brain Research, School of Medicine, JiNan University, Guangzhou 510632, PR China
| | - Huadong Wang
- Department of Pathophysiology, Institute of Brain Research, School of Medicine, JiNan University, Guangzhou 510632, PR China
| | - Renbing Qi
- Department of Pathophysiology, Institute of Brain Research, School of Medicine, JiNan University, Guangzhou 510632, PR China
| | - Qiaoyun Shi
- Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94304, USA
| | - Daxiang Lu
- Department of Pathophysiology, Institute of Brain Research, School of Medicine, JiNan University, Guangzhou 510632, PR China.
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47
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Erpapazoglou Z, Walker O, Haguenauer-Tsapis R. Versatile roles of k63-linked ubiquitin chains in trafficking. Cells 2014; 3:1027-88. [PMID: 25396681 PMCID: PMC4276913 DOI: 10.3390/cells3041027] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/14/2014] [Accepted: 10/21/2014] [Indexed: 12/11/2022] Open
Abstract
Modification by Lys63-linked ubiquitin (UbK63) chains is the second most abundant form of ubiquitylation. In addition to their role in DNA repair or kinase activation, UbK63 chains interfere with multiple steps of intracellular trafficking. UbK63 chains decorate many plasma membrane proteins, providing a signal that is often, but not always, required for their internalization. In yeast, plants, worms and mammals, this same modification appears to be critical for efficient sorting to multivesicular bodies and subsequent lysosomal degradation. UbK63 chains are also one of the modifications involved in various forms of autophagy (mitophagy, xenophagy, or aggrephagy). Here, in the context of trafficking, we report recent structural studies investigating UbK63 chains assembly by various E2/E3 pairs, disassembly by deubiquitylases, and specifically recognition as sorting signals by receptors carrying Ub-binding domains, often acting in tandem. In addition, we address emerging and unanticipated roles of UbK63 chains in various recycling pathways that function by activating nucleators required for actin polymerization, as well as in the transient recruitment of signaling molecules at the plasma or ER membrane. In this review, we describe recent advances that converge to elucidate the mechanisms underlying the wealth of trafficking functions of UbK63 chains.
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Affiliation(s)
- Zoi Erpapazoglou
- Institut Jacques Monod-CNRS, UMR 7592, Université-Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
| | - Olivier Walker
- Institut des Sciences Analytiques, UMR5280, Université de Lyon/Université Lyon 1, 69100 Villeurbanne, France.
| | - Rosine Haguenauer-Tsapis
- Institut Jacques Monod-CNRS, UMR 7592, Université-Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
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Tu C, Ahmad G, Mohapatra B, Bhattacharyya S, Ortega-Cava CF, Chung BM, Wagner KU, Raja SM, Naramura M, Band V, Band H. ESCRT proteins: Double-edged regulators of cellular signaling. BIOARCHITECTURE 2014; 1:45-48. [PMID: 21866262 DOI: 10.4161/bioa.1.1.15173] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Accepted: 02/15/2011] [Indexed: 12/29/2022]
Abstract
ESCRT pathway proteins play a key role in sorting ubiquitinated membrane receptors towards lysosomes providing an important mechanism for attenuating cell surface receptor signaling. However, recent studies point to a positive role of ESCRT proteins in signal transduction in multiple species studied under physiological and pathological conditions. ESCRT components such as Tsg101 and Hrs are overexpressed in human cancers and Tsg101 depletion is detrimental for cell proliferation, survival and transformed phenotype of tumor cells. However, the mechanisms underlying the positive contributions of ESCRT pathway to surface receptor signaling have remained unclear. In a recent study, we showed that Tsg101 and Vps4 are essential for translocation of active Src from endosomes to focal adhesion and invadopodia, thereby revealing a role of ESCRT pathway in promoting Src-mediated migration and invasion. We discuss the implications of these and other recent studies which together suggest a role for the ESCRT pathway in recycling of endocytic cargo proteins, aside from its role in lysosomal targeting, potentially explaining the positive roles of ESCRT proteins in signal transduction.
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Affiliation(s)
- Chun Tu
- Eppley Institute for Research in Cancer and Allied Diseases and UNMC-Eppley Cancer Center; Omaha, NE USA
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49
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Durcan TM, Tang MY, Pérusse JR, Dashti EA, Aguileta MA, McLelland GL, Gros P, Shaler TA, Faubert D, Coulombe B, Fon EA. USP8 regulates mitophagy by removing K6-linked ubiquitin conjugates from parkin. EMBO J 2014; 33:2473-91. [PMID: 25216678 DOI: 10.15252/embj.201489729] [Citation(s) in RCA: 283] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mutations in the Park2 gene, encoding the E3 ubiquitin-ligase parkin, are responsible for a familial form of Parkinson's disease (PD). Parkin-mediated ubiquitination is critical for the efficient elimination of depolarized dysfunctional mitochondria by autophagy (mitophagy). As damaged mitochondria are a major source of toxic reactive oxygen species within the cell, this pathway is believed to be highly relevant to the pathogenesis of PD. Little is known about how parkin-mediated ubiquitination is regulated during mitophagy or about the nature of the ubiquitin conjugates involved. We report here that USP8/UBPY, a deubiquitinating enzyme not previously implicated in mitochondrial quality control, is critical for parkin-mediated mitophagy. USP8 preferentially removes non-canonical K6-linked ubiquitin chains from parkin, a process required for the efficient recruitment of parkin to depolarized mitochondria and for their subsequent elimination by mitophagy. This work uncovers a novel role for USP8-mediated deubiquitination of K6-linked ubiquitin conjugates from parkin in mitochondrial quality control.
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Affiliation(s)
- Thomas M Durcan
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Matthew Y Tang
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Joëlle R Pérusse
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Eman A Dashti
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Miguel A Aguileta
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Gian-Luca McLelland
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | - Priti Gros
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
| | | | - Denis Faubert
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC, Canada Department of Biochemistry, Université de Montréal, Montréal, QC, Canada
| | - Edward A Fon
- McGill Parkinson Program, Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montréal, QC, Canada
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50
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Funakoshi Y, Chou MM, Kanaho Y, Donaldson JG. TRE17/USP6 regulates ubiquitylation and trafficking of cargo proteins that enter cells by clathrin-independent endocytosis. J Cell Sci 2014; 127:4750-61. [PMID: 25179595 DOI: 10.1242/jcs.156786] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plasma membrane proteins that enter cells by clathrin-independent endocytosis (CIE) are sorted either to lysosomes for degradation or recycled back to the plasma membrane. Expression of some MARCH E3 ubiquitin ligases promotes trafficking of CIE cargo proteins to lysosomes by ubiquitylating the proteins. Here, we show that co-expression of the ubiquitin-specific protease TRE17/USP6 counteracts the MARCH-dependent targeting of CIE cargo proteins, but not that of transferrin receptor, to lysosomes, leading to recovery of the stability and cell surface level of the proteins. The ubiquitylation of CIE cargo proteins by MARCH8 was reversed by TRE17, suggesting that TRE17 leads to deubiquitylation of CIE cargo proteins. The effects of TRE17 were dependent on its deubiquitylating activity and expression of TRE17 alone led to a stabilization of surface major histocompatibility complex class I (MHCI) molecules, a CIE cargo, suggesting that deubiquitylation of endogenous CIE cargo proteins promotes their stability. This study demonstrates that cycles of ubiquitylation and deubiquitylation can determine whether CIE cargo proteins are degraded or recycled.
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Affiliation(s)
- Yuji Funakoshi
- Cell Biology & Physiology Center, NHLBI, NIH, Bethesda, MD 20891, USA Department of Physiological Chemistry, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Margaret M Chou
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, 3615 Civic Center Boulevard, Philadelphia, PA19104, USA
| | - Yasunori Kanaho
- Department of Physiological Chemistry, Faculty of Medicine and Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Julie G Donaldson
- Cell Biology & Physiology Center, NHLBI, NIH, Bethesda, MD 20891, USA
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