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Roy AS, Feroz T, Islam MK, Munim MA, Supti DA, Antora NJ, Al Reza H, Gosh S, Bahadur NM, Alam MR, Hossain MS. A computational approach for structural and functional analyses of disease-associated mutations in the human CYLD gene. Genomics Inform 2024; 22:4. [PMID: 38907316 PMCID: PMC11184958 DOI: 10.1186/s44342-024-00007-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/26/2023] [Indexed: 06/23/2024] Open
Abstract
Tumor suppressor cylindromatosis protein (CYLD) regulates NF-κB and JNK signaling pathways by cleaving K63-linked poly-ubiquitin chain from its substrate molecules and thus preventing the progression of tumorigenesis and metastasis of the cancer cells. Mutations in CYLD can cause aberrant structure and abnormal functionality leading to tumor formation. In this study, we utilized several computational tools such as PANTHER, PROVEAN, PredictSNP, PolyPhen-2, PhD-SNP, PON-P2, and SIFT to find out deleterious nsSNPs. We also highlighted the damaging impact of those deleterious nsSNPs on the structure and function of the CYLD utilizing ConSurf, I-Mutant, SDM, Phyre2, HOPE, Swiss-PdbViewer, and Mutation 3D. We shortlisted 18 high-risk nsSNPs from a total of 446 nsSNPs recorded in the NCBI database. Based on the conservation profile, stability status, and structural impact analysis, we finalized 13 nsSNPs. Molecular docking analysis and molecular dynamic simulation concluded the study with the findings of two significant nsSNPs (R830K, H827R) which have a remarkable impact on binding affinity, RMSD, RMSF, radius of gyration, and hydrogen bond formation during CYLD-ubiquitin interaction. The principal component analysis compared native and two mutants R830K and H827R of CYLD that signify structural and energy profile fluctuations during molecular dynamic (MD) simulation. Finally, the protein-protein interaction network showed CYLD interacts with 20 proteins involved in several biological pathways that mutations can impair. Considering all these in silico analyses, our study recommended conducting large-scale association studies of nsSNPs of CYLD with cancer as well as designing precise medications against diseases associated with these polymorphisms.
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Affiliation(s)
- Arpita Singha Roy
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Tasmiah Feroz
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Kobirul Islam
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Md Adnan Munim
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Dilara Akhter Supti
- Department of Food Technology & Nutrition Sciences, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Nusrat Jahan Antora
- Department of Genetic Engineering and Biotechnology, East West University, Dhaka, 1212, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Supriya Gosh
- Department of Food Technology & Nutrition Sciences, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - Mohammad Rahanur Alam
- Department of Food Technology & Nutrition Sciences, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
| | - Md Shahadat Hossain
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh.
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Lee MJ, Hammouda MB, Miao W, Okafor AE, Jin YJ, Sun H, Jain V, Markovtsov V, Diao Y, Gregory SG, Zhang JY. UBE2N Is Essential for Maintenance of Skin Homeostasis and Suppression of Inflammation. J Invest Dermatol 2024:S0022-202X(24)00376-2. [PMID: 38796140 DOI: 10.1016/j.jid.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 05/28/2024]
Abstract
UBE2N, a Lys63 ubiquitin-conjugating enzyme, plays critical roles in embryogenesis and immune system development and function. However, its roles in adult epithelial tissue homeostasis and pathogenesis are unclear. We generated conditional mouse models that deleted Ube2n in skin cells in a temporally and spatially controlled manner. We found that Ube2n knockout in the adult skin keratinocytes induced a range of inflammatory skin defects characteristic of psoriatic and actinic keratosis. These included inflammation, epidermal and dermal thickening, parakeratosis, and increased immune cell infiltration as well as signs of edema and blistering. Single-cell transcriptomic analyses and RT-qPCR showed that Ube2n-knockout keratinocytes expressed elevated myeloid cell chemoattractants such as Cxcl1 and Cxcl2 and decreased the homeostatic T lymphocyte chemoattractant Ccl27a. Consistently, the infiltrating immune cells were predominantly myeloid-derived cells, including neutrophils and M1-like macrophages, which expressed high levels of inflammatory cytokines such as Il1β and Il24. Pharmacological blockade of the IL-1 receptor associated kinases (IRAK1/4) alleviated inflammation, epidermal and dermal thickening, and immune infiltration of the Ube2n-mutant skin. Together, these findings highlight a key role of keratinocyte UBE2N in maintenance of epidermal homeostasis and skin immunity and identify IRAK1/4 as potential therapeutic target for inflammatory skin disorders.
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Affiliation(s)
- Min Jin Lee
- Department of Dermatology, School of Medicine, Duke University, Durham, North Carolina, USA; Department of Molecular Genetics & Microbiology, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Manel Ben Hammouda
- Department of Dermatology, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Wanying Miao
- Department of Dermatology, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Arinze E Okafor
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Yingai J Jin
- Department of Dermatology, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Huiying Sun
- Department of Dermatology, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Durham, North Carolina, USA
| | | | - Yarui Diao
- Department of Cell Biology, School of Medicine, Duke University, Durham, North Carolina, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Durham, North Carolina, USA
| | - Jennifer Y Zhang
- Department of Dermatology, School of Medicine, Duke University, Durham, North Carolina, USA; Department of Pathology, School of Medicine, Duke University, Durham, North Carolina, USA.
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3
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Bolhuis DL, Emanuele MJ, Brown NG. Friend or foe? Reciprocal regulation between E3 ubiquitin ligases and deubiquitinases. Biochem Soc Trans 2024; 52:BST20230454. [PMID: 38414432 DOI: 10.1042/bst20230454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 02/29/2024]
Abstract
Protein ubiquitination is a post-translational modification that entails the covalent attachment of the small protein ubiquitin (Ub), which acts as a signal to direct protein stability, localization, or interactions. The Ub code is written by a family of enzymes called E3 Ub ligases (∼600 members in humans), which can catalyze the transfer of either a single ubiquitin or the formation of a diverse array of polyubiquitin chains. This code can be edited or erased by a different set of enzymes termed deubiquitinases (DUBs; ∼100 members in humans). While enzymes from these distinct families have seemingly opposing activities, certain E3-DUB pairings can also synergize to regulate vital cellular processes like gene expression, autophagy, innate immunity, and cell proliferation. In this review, we highlight recent studies describing Ub ligase-DUB interactions and focus on their relationships.
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Affiliation(s)
- Derek L Bolhuis
- Department of Biochemistry and Biophysics, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
| | - Michael J Emanuele
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
| | - Nicholas G Brown
- Department of Pharmacology and Lineberger Comprehensive Care Center, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, U.S.A
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Hermanns T, Uthoff M, Baumann U, Hofmann K. The structural basis for deubiquitination by the fingerless USP-type effector TssM. Life Sci Alliance 2024; 7:e202302422. [PMID: 38170641 PMCID: PMC10719079 DOI: 10.26508/lsa.202302422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Intracellular bacteria are threatened by ubiquitin-mediated autophagy, whenever the bacterial surface or enclosing membrane structures become targets of host ubiquitin ligases. As a countermeasure, many intracellular pathogens encode deubiquitinase (DUB) effectors to keep their surfaces free of ubiquitin. Most bacterial DUBs belong to the OTU or CE-clan families. The betaproteobacteria Burkholderia pseudomallei and Burkholderia mallei, causative agents of melioidosis and glanders, respectively, encode the TssM effector, the only known bacterial DUB belonging to the USP class. TssM is much shorter than typical eukaryotic USP enzymes and lacks the canonical ubiquitin-recognition region. By solving the crystal structures of isolated TssM and its complex with ubiquitin, we found that TssM lacks the entire "Fingers" subdomain of the USP fold. Instead, the TssM family has evolved the functionally analog "Littlefinger" loop, which is located towards the end of the USP domain and recognizes different ubiquitin interfaces than those used by USPs. The structures revealed the presence of an N-terminal immunoglobulin-fold domain, which is able to form a strand-exchange dimer and might mediate TssM localization to the bacterial surface.
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Affiliation(s)
- Thomas Hermanns
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
| | - Matthias Uthoff
- https://ror.org/00rcxh774 Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Ulrich Baumann
- https://ror.org/00rcxh774 Institute of Biochemistry, University of Cologne, Cologne, Germany
| | - Kay Hofmann
- https://ror.org/00rcxh774 Institute for Genetics, University of Cologne, Cologne, Germany
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Li Y, Yang C, Xie L, Shi F, Tang M, Luo X, Liu N, Hu X, Zhu Y, Bode AM, Gao Q, Zhou J, Fan J, Li X, Cao Y. CYLD induces high oxidative stress and DNA damage through class I HDACs to promote radiosensitivity in nasopharyngeal carcinoma. Cell Death Dis 2024; 15:95. [PMID: 38287022 PMCID: PMC10824711 DOI: 10.1038/s41419-024-06419-w] [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: 07/13/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/31/2024]
Abstract
Abnormal expression of Cylindromatosis (CYLD), a tumor suppressor molecule, plays an important role in tumor development and treatment. In this work, we found that CYLD binds to class I histone deacetylases (HDAC1 and HDAC2) through its N-terminal domain and inhibits HDAC1 activity. RNA sequencing showed that CYLD-HDAC axis regulates cellular antioxidant response via Nrf2 and its target genes. Then we revealed a mechanism that class I HDACs mediate redox abnormalities in CYLD low-expressing tumors. HDACs are central players in the DNA damage signaling. We further confirmed that CYLD regulates radiation-induced DNA damage and repair response through inhibiting class I HDACs. Furthermore, CYLD mediates nasopharyngeal carcinoma cell radiosensitivity through class I HDACs. Thus, we identified the function of the CYLD-HDAC axis in radiotherapy and blocking HDACs by Chidamide can increase the sensitivity of cancer cells and tumors to radiation therapy both in vitro and in vivo. In addition, ChIP and luciferase reporter assays revealed that CYLD could be transcriptionally regulated by zinc finger protein 202 (ZNF202). Our findings offer novel insight into the function of CYLD in tumor and uncover important roles for CYLD-HDAC axis in radiosensitivity, which provide new molecular target and therapeutic strategy for tumor radiotherapy.
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Affiliation(s)
- Yueshuo Li
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410078, China
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders/ Xiangya Hospital, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, 410078, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Chenxing Yang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Longlong Xie
- Children's Hospital, Xiangya School of Medicine, Central South University, Changsha, Hunan, 410008, China
| | - Feng Shi
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Min Tang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, 410078, China
- Molecular Imaging Research Center of Central South University, Changsha, 410008, Hunan, China
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, 410078, China
- Molecular Imaging Research Center of Central South University, Changsha, 410008, Hunan, China
| | - Na Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Xudong Hu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410078, China
- Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Yongwei Zhu
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders/ Xiangya Hospital, Central South University, Changsha, 410078, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Qiang Gao
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Zhongshan Hospital, Shanghai Medical School, Fudan University, Shanghai, 200000, China
| | - Jian Zhou
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Zhongshan Hospital, Shanghai Medical School, Fudan University, Shanghai, 200000, China
| | - Jia Fan
- Key Laboratory for Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Zhongshan Hospital, Shanghai Medical School, Fudan University, Shanghai, 200000, China
| | - Xuejun Li
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410078, China.
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders/ Xiangya Hospital, Central South University, Changsha, 410078, China.
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Ya Cao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Chinese Ministry of Education, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, 410078, China.
- Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha, 410078, China.
- Molecular Imaging Research Center of Central South University, Changsha, 410008, Hunan, China.
- Department of Radiology, National Clinical Research Center for Geriatric Disorders/ Xiangya Hospital, Central South University, Changsha, 410078, China.
- Research Center for Technologies of Nucleic Acid-Based Diagnostics and Therapeutics Hunan Province, Changsha, 410078, China.
- National Joint Engineering Research Center for Genetic Diagnostics of Infectious Diseases and Cancer, Changsha, 410078, China.
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Zhou G, Wang S. YTHDC2 Retards Cell Proliferation and Triggers Apoptosis in Papillary Thyroid Cancer by Regulating CYLD-Mediated Inactivation of Akt Signaling. Appl Biochem Biotechnol 2024; 196:588-603. [PMID: 37162682 DOI: 10.1007/s12010-023-04540-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/11/2023]
Abstract
N6-Methyladenosine (m6A) mRNA methylation modification is regarded as an important mechanism involved in diverse physiological processes. YT521-B homology (YTH) domain family members are associated with the tumorigenesis of several cancers. However, the role of YTHDC2 in papillary thyroid cancer (PTC) progression remains unknown. Results showed that YTHDC1, YTHDF1, YTHDF2, and YTHDF3 showed no observable difference in thyroid cancer samples. YTHDC2 was significantly downregulated in thyroid cancer samples and cells. YTHDC2 inhibited cell proliferation in PTC cells. YTHDC2 elicited apoptosis in PTC cells, as demonstrated by the elevated expression of pro-apoptotic factors cl-caspase-3/caspase-3 and Bcl-2-associated (Bax), and the reduced anti-apoptotic B cell lymphoma-2 (Bcl-2) expression. There was a positive correlation between YTHDC2 and cylindromatosis (CYLD) expression based on GEPIA database. YTHDC2 increased CYLD expression in PTC cells. CYLD knockdown abolished the effects of YTHDC2 on PTC cell proliferation and apoptosis. Additionally, YTHDC2 inactivated the protein kinase B (Akt) pathway by increasing CYLD in PTC cells. Overall, YTHDC2 inhibited cell proliferation and induced apoptosis in PTC cells by regulating CYLD-mediated inactivation of Akt pathway.
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Affiliation(s)
- Guangying Zhou
- Department of Thyroid and Breast Surgery, Shandong Provincial Third Hospital, Shandong University, Jinan, 250031, China
| | - Shasha Wang
- Department of Radiotherapy, the 960Th Hospital of Chinese PLA, No. 25 Shifan Road, Jinan, 250031, China.
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Lee MJ, Hammouda MB, Miao W, Okafor A, Jin Y, Sun H, Jain V, Markovtsov V, Diao Y, Gregory SG, Zhang JY. UBE2N is essential for maintenance of skin homeostasis and suppression of inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569631. [PMID: 38105982 PMCID: PMC10723344 DOI: 10.1101/2023.12.01.569631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
UBE2N, a Lys63-ubiquitin conjugating enzyme, plays critical roles in embryogenesis and immune system development and function. However, its roles in adult epithelial tissue homeostasis and pathogenesis are unclear. We generated conditional mouse models that deleted Ube2n in skin cells in a temporally and spatially controlled manner. We found that Ube2n-knockout (KO) in the adult skin keratinocytes induced a range of inflammatory skin defects characteristic of psoriatic and actinic keratosis. These included eczematous inflammation, epidermal and dermal thickening, parakeratosis, and increased immune cell infiltration, as well as signs of edema and blistering. Single cell transcriptomic analyses and RT-qPCR showed that Ube2n KO keratinocytes expressed elevated myeloid cell chemo-attractants such as Cxcl1 and Cxcl2 and decreased the homeostatic T lymphocyte chemo-attractant, Ccl27a. Consistently, the infiltrating immune cells of Ube2n-KO skin were predominantly myeloid-derived cells including neutrophils and M1-like macrophages that were highly inflammatory, as indicated by expression of Il1β and Il24. Pharmacological blockade of the IL-1 receptor associated kinases (IRAK1/4) alleviated eczema, epidermal and dermal thickening, and immune infiltration of the Ube2n mutant skin. Together, these findings highlight a key role of keratinocyte-UBE2N in maintenance of epidermal homeostasis and skin immunity and identify IRAK1/4 as potential therapeutic target for inflammatory skin disorders.
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Affiliation(s)
- Min Jin Lee
- Department of Dermatology, Duke University, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | | | - Wanying Miao
- Department of Dermatology, Duke University, Durham, NC, USA
| | - Arinze Okafor
- Department of Cell Biology, Duke University, Durham, NC, USA
| | - Yingai Jin
- Department of Dermatology, Duke University, Durham, NC, USA
| | - Huiying Sun
- Department of Dermatology, Duke University, Durham, NC, USA
| | - Vaibhav Jain
- Duke Molecular Physiology Institute, Durham, NC, USA
| | | | - Yarui Diao
- Department of Cell Biology, Duke University, Durham, NC, USA
| | | | - Jennifer Y Zhang
- Department of Dermatology, Duke University, Durham, NC, USA
- Department of Pathology, Duke University, Durham, NC, USA
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8
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Cheng N, Trejo J. An siRNA library screen identifies CYLD and USP34 as deubiquitinases that regulate GPCR-p38 MAPK signaling and distinct inflammatory responses. J Biol Chem 2023; 299:105370. [PMID: 37865315 PMCID: PMC10694601 DOI: 10.1016/j.jbc.2023.105370] [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: 05/04/2023] [Revised: 10/08/2023] [Accepted: 10/09/2023] [Indexed: 10/23/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are highly druggable and implicated in numerous diseases, including vascular inflammation. GPCR signals are transduced from the plasma membrane as well as from endosomes and controlled by posttranslational modifications. The thrombin-activated GPCR protease-activated receptor-1 is modified by ubiquitin. Ubiquitination of protease-activated receptor-1 drives recruitment of transforming growth factor-β-activated kinase-1-binding protein 2 (TAB2) and coassociation of TAB1 on endosomes, which triggers p38 mitogen-activated protein kinase-dependent inflammatory responses in endothelial cells. Other endothelial GPCRs also induce p38 activation via a noncanonical TAB1-TAB2-dependent pathway. However, the regulatory processes that control GPCR ubiquitin-driven p38 inflammatory signaling remains poorly understood. We discovered mechanisms that turn on GPCR ubiquitin-dependent p38 signaling, however, the mechanisms that turn off the pathway are not known. We hypothesize that deubiquitination is an important step in regulating ubiquitin-driven p38 signaling. To identify specific deubiquitinating enzymes (DUBs) that control GPCR-p38 mitogen-activated protein kinase signaling, we conducted a siRNA library screen targeting 96 DUBs in endothelial cells and HeLa cells. We identified nine DUBs and validated the function two DUBs including cylindromatosis and ubiquitin-specific protease-34 that specifically regulate thrombin-induced p38 phosphorylation. Depletion of cylindromatosis expression by siRNA enhanced thrombin-stimulated p38 signaling, endothelial barrier permeability, and increased interleukin-6 cytokine expression. Conversely, siRNA knockdown of ubiquitin-specific protease-34 expression decreased thrombin-promoted interleukin-6 expression and had no effect on thrombin-induced endothelial barrier permeability. These studies suggest that specific DUBs distinctly regulate GPCR-induced p38-mediated inflammatory responses.
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Affiliation(s)
- Norton Cheng
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California, USA; Biomedical Sciences Graduate Program, School of Medicine, University of California, San Diego, La Jolla, California, USA
| | - JoAnn Trejo
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California, USA.
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Kim J, Chang N, Kim Y, Lee J, Oh D, Choi J, Kim O, Kim S, Choi M, Lee J, Lee J, Kim J, Cho M, Kim M, Lee K, Hwang D, Sa JK, Park S, Baek S, Im D. The Novel Tetra-Specific Drug C-192, Conjugated Using UniStac, Alleviates Non-Alcoholic Steatohepatitis in an MCD Diet-Induced Mouse Model. Pharmaceuticals (Basel) 2023; 16:1601. [PMID: 38004466 PMCID: PMC10674394 DOI: 10.3390/ph16111601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a complex disease resulting from chronic liver injury associated with obesity, type 2 diabetes, and inflammation. Recently, the importance of developing multi-target drugs as a strategy to address complex diseases such as NASH has been growing; however, their manufacturing processes remain time- and cost-intensive and inefficient. To overcome these limitations, we developed UniStac, a novel enzyme-mediated conjugation platform for multi-specific drug development. UniStac demonstrated high conjugation yields, optimal thermal stabilities, and robust biological activities. We designed a tetra-specific compound, C-192, targeting glucagon-like peptide 1 (GLP-1), glucagon (GCG), fibroblast growth factor 21 (FGF21), and interleukin-1 receptor antagonist (IL-1RA) simultaneously for the treatment of NASH using UniStac. The biological activity and treatment efficacy of C-192 were confirmed both in vitro and in vivo using a methionine-choline-deficient (MCD) diet-induced mouse model. C-192 exhibited profound therapeutic efficacies compared to conventional drugs, including liraglutide and dulaglutide. C-192 significantly improved alanine transaminase levels, triglyceride accumulation, and the non-alcoholic fatty liver disease activity score. In this study, we demonstrated the feasibility of UniStac in creating multi-specific drugs and confirmed the therapeutic potential of C-192, a drug that integrates multiple mechanisms into a single molecule for the treatment of NASH.
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Affiliation(s)
- Jihye Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Nakho Chang
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Yunki Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Jaehyun Lee
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Daeseok Oh
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Jaeyoung Choi
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Onyou Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Sujin Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Myongho Choi
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Junyeob Lee
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Junghwa Lee
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Jungyul Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Minji Cho
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Minsu Kim
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Kwanghwan Lee
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Dukhyun Hwang
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Jason K. Sa
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul 02841, Republic of Korea
| | - Sungjin Park
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
| | - Seungjae Baek
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Daeseong Im
- Onegene Biotechnology, Inc., 205 Ace Gwanggyo Tower 2, 91 Changnyong-daero 256 beon-gil, Yeongtong-gu, Suwon-si 16229, Republic of Korea; (J.K.); (J.C.); (J.K.); (K.L.)
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10
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Maurer SK, Mayer MP, Ward SJ, Boudjema S, Halawa M, Zhang J, Caulton SG, Emsley J, Dreveny I. Ubiquitin-specific protease 11 structure in complex with an engineered substrate mimetic reveals a molecular feature for deubiquitination selectivity. J Biol Chem 2023; 299:105300. [PMID: 37777157 PMCID: PMC10637973 DOI: 10.1016/j.jbc.2023.105300] [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: 05/22/2023] [Revised: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023] Open
Abstract
Ubiquitin-specific proteases (USPs) are crucial for controlling cellular proteostasis and signaling pathways but how deubiquitination is selective remains poorly understood, in particular between paralogues. Here, we developed a fusion tag method by mining the Protein Data Bank and trapped USP11, a key regulator of DNA double-strand break repair, in complex with a novel engineered substrate mimetic. Together, this enabled structure determination of USP11 as a Michaelis-like complex that revealed key S1 and S1' binding site interactions with a substrate. Combined mutational, enzymatic, and binding experiments identified Met77 in linear diubiquitin as a significant residue that leads to substrate discrimination. We identified an aspartate "gatekeeper" residue in the S1' site of USP11 as a contributing feature for discriminating against linear diubiquitin. When mutated to a glycine, the corresponding residue in paralog USP15, USP11 acquired elevated activity toward linear diubiquitin in-gel shift assays, but not controls. The reverse mutation in USP15 confirmed that this position confers paralog-specific differences impacting diubiquitin cleavage rates. The results advance our understanding of the molecular basis for the higher selectivity of USP11 compared to USP15 and may aid targeted inhibitor development. Moreover, the reported carrier-based crystallization strategy may be applicable to other challenging targets.
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Affiliation(s)
- Sigrun K Maurer
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Matthias P Mayer
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Stephanie J Ward
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Sana Boudjema
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Mohamed Halawa
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Jiatong Zhang
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Simon G Caulton
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Jonas Emsley
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom
| | - Ingrid Dreveny
- Biodiscovery Institute, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom.
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11
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Clancy A, Rusilowicz-Jones EV, Wallace I, Swatek KN, Urbé S, Clague MJ. ISGylation-independent protection of cell growth by USP18 following interferon stimulation. Biochem J 2023; 480:1571-1581. [PMID: 37756534 PMCID: PMC10586769 DOI: 10.1042/bcj20230301] [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: 07/21/2023] [Revised: 09/20/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023]
Abstract
Type 1 interferon stimulation highly up-regulates all elements of a ubiquitin-like conjugation system that leads to ISGylation of target proteins. An ISG15-specific member of the deubiquitylase family, USP18, is up-regulated in a co-ordinated manner. USP18 can also provide a negative feedback by inhibiting JAK-STAT signalling through protein interactions independently of DUB activity. Here, we provide an acute example of this phenomenon, whereby the early expression of USP18, post-interferon treatment of HCT116 colon cancer cells is sufficient to fully suppress the expression of the ISG15 E1 enzyme, UBA7. Stimulation of lung adenocarcinoma A549 cells with interferon reduces their growth rate but they remain viable. In contrast, A549 USP18 knock-out cells show similar growth characteristics under basal conditions, but upon interferon stimulation, a profound inhibition of cell growth is observed. We show that this contingency on USP18 is independent of ISGylation, suggesting non-catalytic functions are required for viability. We also demonstrate that global deISGylation kinetics are very slow compared with deubiquitylation. This is not influenced by USP18 expression, suggesting that enhanced ISGylation in USP18 KO cells reflects increased conjugating activity.
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Affiliation(s)
- Anne Clancy
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, U.K
| | - Emma V. Rusilowicz-Jones
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, U.K
| | - Iona Wallace
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Kirby N. Swatek
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Sylvie Urbé
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, U.K
| | - Michael J. Clague
- Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 3BX, U.K
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12
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Zhao Z, O’Dea R, Wendrich K, Kazi N, Gersch M. Native Semisynthesis of Isopeptide-Linked Substrates for Specificity Analysis of Deubiquitinases and Ubl Proteases. J Am Chem Soc 2023; 145:20801-20812. [PMID: 37712884 PMCID: PMC10540217 DOI: 10.1021/jacs.3c04062] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 09/16/2023]
Abstract
Post-translational modifications with ubiquitin (Ub) and ubiquitin-like proteins (Ubls) are regulated by isopeptidases termed deubiquitinases (DUBs) and Ubl proteases. Here, we describe a mild chemical method for the preparation of fluorescence polarization substrates for these enzymes that is based on the activation of C-terminal Ub/Ubl hydrazides to acyl azides and their subsequent functionalization to isopeptides. The procedure is complemented by native purification routes and thus circumvents the previous need for desulfurization and refolding. Its broad applicability was demonstrated by the generation of fully cleavable substrates for Ub, SUMO1, SUMO2, NEDD8, ISG15, and Fubi. We employed these reagents for the investigation of substrate specificities of human UCHL3, USPL1, USP2, USP7, USP16, USP18, and USP36. Pronounced selectivity of USPL1 for SUMO2/3 over SUMO1 was observed, which we rationalize with crystal structures and biochemical assays, revealing a SUMO paralogue specificity mechanism distinct from SENP family deSUMOylases. Moreover, we investigated the recently identified Fubi proteases USP16 and USP36 and found both to act as bona fide deFubiylases, harboring catalytic activity against isopeptide-linked Fubi. Surprisingly, we also noticed the activity of both enzymes toward ISG15, previously not identified in chemoproteomics, which makes USP16 and USP36 the first human DUBs with specific isopeptidase activity toward three distinct modifiers. The methods described here for the preparation of isopeptide-linked, fully folded substrates will aid in the characterization of further DUBs/Ubl proteases. More broadly, our findings highlight possible limitations associated with fluorogenic substrates and Ubl activity-based probes and stress the importance of isopeptide-containing reagents for validating isopeptidase activities and quantifying substrate specificities.
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Affiliation(s)
- Zhou Zhao
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Rachel O’Dea
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Kim Wendrich
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Nafizul Kazi
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
| | - Malte Gersch
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn-Str. 15, 44227 Dortmund, Germany
- Department
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn-Str.
15, 44227 Dortmund, Germany
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13
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Huang Z, Tan Y. The Potential of Cylindromatosis (CYLD) as a Therapeutic Target in Oxidative Stress-Associated Pathologies: A Comprehensive Evaluation. Int J Mol Sci 2023; 24:ijms24098368. [PMID: 37176077 PMCID: PMC10179184 DOI: 10.3390/ijms24098368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/25/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Oxidative stress (OS) arises as a consequence of an imbalance between the formation of reactive oxygen species (ROS) and the capacity of antioxidant defense mechanisms to neutralize them. Excessive ROS production can lead to the damage of critical biomolecules, such as lipids, proteins, and DNA, ultimately contributing to the onset and progression of a multitude of diseases, including atherosclerosis, chronic obstructive pulmonary disease, Alzheimer's disease, and cancer. Cylindromatosis (CYLD), initially identified as a gene linked to familial cylindromatosis, has a well-established and increasingly well-characterized function in tumor inhibition and anti-inflammatory processes. Nevertheless, burgeoning evidence suggests that CYLD, as a conserved deubiquitination enzyme, also plays a pivotal role in various key signaling pathways and is implicated in the pathogenesis of numerous diseases driven by oxidative stress. In this review, we systematically examine the current research on the function and pathogenesis of CYLD in diseases instigated by oxidative stress. Therapeutic interventions targeting CYLD may hold significant promise for the treatment and management of oxidative stress-induced human diseases.
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Affiliation(s)
- Zhenzhou Huang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250358, China
| | - Yanjie Tan
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan 250358, China
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14
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SPATA2 restricts OTULIN-dependent LUBAC activity independently of CYLD. Cell Rep 2023; 42:111961. [PMID: 36640323 DOI: 10.1016/j.celrep.2022.111961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/10/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023] Open
Abstract
SPATA2 mediates the recruitment of CYLD to immune receptor complexes by bridging the interaction of CYLD with the linear ubiquitylation assembly complex (LUBAC) component HOIP. Whether SPATA2 exhibits functions independently of CYLD is unclear. Here, we show that, while Cyld-/- and Spata2-/- mice are viable, double mutants exhibit highly penetrant perinatal lethality, indicating independent functions of SPATA2 and CYLD. Cyld-/-Spata2-/- fibroblasts show increased M1-linked TNFR1-SC ubiquitylation and, similar to Cyld-/-Spata2-/- macrophages and intestinal epithelial cells, elevated pro-inflammatory gene expression compared with Cyld-/- or Spata2-/- cells. We show that SPATA2 competes with OTULIN for binding to HOIP via its PUB-interacting motif (PIM) and its zinc finger domain, thereby promoting autoubiquitylation of LUBAC. Consistently, increased pro-inflammatory signaling in Cyld-/-Spata2-/- cells depends on the presence of OTULIN. Our data therefore indicate that SPATA2 counteracts, independently of CYLD, the deubiquitylation of LUBAC by OTULIN and thereby attenuates LUBAC activity and pro-inflammatory signaling.
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15
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Zhang X, Zhao Y, Zhang X, Shen G, Li W, Wang Q. Deubiquitinase cylindromatosis (CYLD) regulates antibacterial immunity and apoptosis in Chinese mitten crab (Eriocheir sinensis). FISH & SHELLFISH IMMUNOLOGY 2023; 132:108454. [PMID: 36442704 DOI: 10.1016/j.fsi.2022.108454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 06/16/2023]
Abstract
Ubiquitination and deubiquitination of target proteins is an important mechanism for cells to rapidly respond to changes in the external environment. The deubiquitinase, cylindromatosis (CYLD), is a tumor suppressor protein. CYLD from Drosophila melanogaster participates in the antimicrobial immune response. In vertebrates, CYLD also regulates bacterial-induced apoptosis. However, whether CYLD can regulate the bacterial-induced innate immune response in crustaceans is unknown. In the present study, we reported the identification and cloning of CYLD in Chinese mitten crab, Eriocheir sinensis. Quantitative real-time reverse transcription polymerase chain reaction analysis showed that EsCYLD was widely expressed in all the examined tissues and was upregulated in the hemolymph after Vibrio parahaemolyticus challenge. Knockdown of EsCYLD in hemocytes promoted the cytoplasm-to-nucleus translocation of transcription factor Relish under V. parahaemolyticus stimulation and increased the expression of corresponding antimicrobial peptides. In vivo, silencing of EsCYLD promoted the removal of bacteria from the crabs and enhanced their survival. In addition, interfering with EsCYLD expression inhibited apoptosis of crab hemocytes caused by V. parahaemolyticus stimulation. In summary, our findings revealed that EsCYLD negatively regulates the nuclear translocation of Relish to affect the expression of corresponding antimicrobial peptides and regulates the apoptosis of crab hemocytes, thus indirectly participating in the innate immunity of E. sinensis.
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Affiliation(s)
- Xiaona Zhang
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yuehong Zhao
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiaoli Zhang
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Guoqing Shen
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Weiwei Li
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Qun Wang
- Laboratory of Invertebrate Immunological Defense & Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China.
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16
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Structural Insights into the Phosphorylation-Enhanced Deubiquitinating Activity of UCHL3 and Ubiquitin Chain Cleavage Preference Analysis. Int J Mol Sci 2022; 23:ijms231810789. [PMID: 36142702 PMCID: PMC9501053 DOI: 10.3390/ijms231810789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 11/22/2022] Open
Abstract
Ubiquitin C-terminal hydrolase-L3 (UCHL3), an important member of the ubiquitin C-terminal hydrolase family, is involved in DNA repair and cancer development. UCHL3 can cleave only complexes of monoubiquitin and its conjugates, such as Ub-AMC, His, or small ubiquitin-like modifier, but not polyubiquitin chains. Phosphorylation of Ser75 promotes the cleavage activity of UCHL3 toward poly-ubiquitin chains in vivo, but biochemical evidence in vitro is still lacking. Here, we first analyzed the structure of simulated phosphorylated UCHL3S75E and the complex of UCHL3S75E with Ub-PA and preliminarily explained the structural mechanism of phosphorylation-enhanced UCHL3 deubiquitinating activity. Additionally, the cleavage activity of UCHL3 toward different types of synthesized poly-ubiquitin chains in vitro was tested. The results showed that purified UCHL3S75E enhanced the cleavage activity toward Ub-AMC compared to UCHL3WT. Meanwhile, UCHL3S75E and UCHL3WT did not show any cleavage activity for different types of di-ubiquitin and tri-ubiquitin chains. However, UCHL3 could hydrolyze the K48 tetra-ubiquitin chain, providing compelling in vitro evidence confirming previous in vivo results. Thus, this study shows that UCHL3 can hydrolyze and has a cleavage preference for polyubiquitin chains, which expands our understanding of the phosphorylation regulation of UCHL3 and lays a foundation for further elucidation of its physiological role.
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17
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Zhan Y, Xu D, Tian Y, Qu X, Sheng M, Lin Y, Ke M, Jiang L, Xia Q, Kaldas FM, Farmer DG, Ke B. Novel role of macrophage TXNIP-mediated CYLD-NRF2-OASL1 axis in stress-induced liver inflammation and cell death. JHEP Rep 2022; 4:100532. [PMID: 36035360 PMCID: PMC9404660 DOI: 10.1016/j.jhepr.2022.100532] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 06/04/2022] [Accepted: 06/25/2022] [Indexed: 11/16/2022] Open
Abstract
Background & Aims The stimulator of interferon genes (STING)/TANK-binding kinase 1 (TBK1) pathway is vital in mediating innate immune and inflammatory responses during oxidative/endoplasmic reticulum (ER) stress. However, it remains unknown whether macrophage thioredoxin-interacting protein (TXNIP) may regulate TBK1 function and cell death pathways during oxidative/ER stress. Methods A mouse model of hepatic ischaemia/reperfusion injury (IRI), the primary hepatocytes, and bone marrow-derived macrophages were used in the myeloid-specific TXNIP knockout (TXNIPM-KO) and TXNIP-proficient (TXNIPFL/FL) mice. Results The TXNIPM-KO mice were resistant to ischaemia/reperfusion (IR) stress-induced liver damage with reduced serum alanine aminotransferase (ALT)/aspartate aminotransferase (AST) levels, macrophage/neutrophil infiltration, and pro-inflammatory mediators compared with the TXNIPFL/FL controls. IR stress increased TXNIP, p-STING, and p-TBK1 expression in ischaemic livers. However, TXNIPM-KO inhibited STING, TBK1, interferon regulatory factor 3 (IRF3), and NF-κB activation with interferon-β (IFN-β) expression. Interestingly, TXNIPM-KO augmented nuclear factor (erythroid-derived 2)-like 2 (NRF2) activity, increased antioxidant gene expression, and reduced macrophage reactive oxygen species (ROS) production and hepatic apoptosis/necroptosis in IR-stressed livers. Mechanistically, macrophage TXNIP deficiency promoted cylindromatosis (CYLD), which colocalised and interacted with NADPH oxidase 4 (NOX4) to enhance NRF2 activity by deubiquitinating NOX4. Disruption of macrophage NRF2 or its target gene 2',5' oligoadenylate synthetase-like 1 (OASL1) enhanced Ras GTPase-activating protein-binding protein 1 (G3BP1) and TBK1-mediated inflammatory response. Notably, macrophage OASL1 deficiency induced hepatocyte apoptotic peptidase activating factor 1 (APAF1), cytochrome c, and caspase-9 activation, leading to increased caspase-3-initiated apoptosis and receptor-interacting serine/threonine-protein kinase 3 (RIPK3)-mediated necroptosis. Conclusions Macrophage TXNIP deficiency enhances CYLD activity and activates the NRF2-OASL1 signalling, controlling IR stress-induced liver injury. The target gene OASL1 regulated by NRF2 is crucial for modulating STING-mediated TBK1 activation and Apaf1/cytochrome c/caspase-9-triggered apoptotic/necroptotic cell death pathway. Our findings underscore a novel role of macrophage TXNIP-mediated CYLD-NRF2-OASL1 axis in stress-induced liver inflammation and cell death, implying the potential therapeutic targets in liver inflammatory diseases. Lay summary Liver inflammation and injury induced by ischaemia and reperfusion (the absence of blood flow to the liver tissue followed by the resupply of blood) is a significant cause of hepatic dysfunction and failure following liver transplantation, resection, and haemorrhagic shock. Herein, we uncover an underlying mechanism that contributes to liver inflammation and cell death in this setting and could be a therapeutic target in stress-induced liver inflammatory injury.
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Key Words
- ALT, alanine aminotransferase
- APAF1, apoptotic peptidase activating factor 1
- ASK1, apoptosis signal-regulating kinase 1
- AST, aspartate aminotransferase
- Apoptosis
- BMM, bone marrow-derived macrophage
- CXCL-10, C-X-C motif chemokine ligand 10
- CYLD, cyclindromatosis
- ChIP, chromatin immunoprecipitation
- DAMP, damage-associated molecular pattern
- DUB, deubiquitinating enzyme
- ER, endoplasmic reticulum
- ES, embryonic stem
- G3BP1
- G3BP1, Ras GTPase-activating protein-binding protein 1
- GCLC, glutamate-cysteine ligase catalytic subunit
- GCLM, glutamate-cysteine ligase regulatory subunit
- IHC, immunohistochemistry
- INF-β, interferon-β
- IR, ischaemia/reperfusion
- IRF3
- IRF3, interferon regulatory factor 3
- IRF7, IFN-regulating transcription factor 7
- IRI, ischaemia/reperfusion injury
- Innate immunity
- KO, knockout
- LPS, lipopolysaccharide
- Liver inflammation
- Lyz2, Lysozyme 2
- MCP-1, monocyte chemoattractant protein 1
- NOX2, NADPH oxidase 2
- NOX4, NADPH oxidase 4
- NQO1, NAD(P)H quinone dehydrogenase 1
- NRF2, nuclear factor (erythroid-derived 2)-like 2
- NS, non-specific
- Necroptosis
- OASL1, 2′,5′oligoadenylate synthetase-like 1
- PAMP, pathogen-derived molecular pattern
- RIPK3, receptor-interacting serine/threonine-protein kinase 3
- ROS, reactive oxygen species
- STING
- STING, stimulator of interferon genes
- TBK1, TANK-binding kinase 1
- TLR4, Toll-like receptor 4
- TNF-α, tumour necrosis factor-alpha
- TRX, thioredoxin
- TSS, transcription start sites
- TXNIP, thioredoxin-interacting protein
- TXNIPFL/FL, floxed TXNIP
- TXNIPM-KO, myeloid-specific TXNIP KO
- UTR, untranslated region
- sALT, serum ALT
- sAST, serum AST
- siRNA, small interfering RNA
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Affiliation(s)
- Yongqiang Zhan
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital of Shenzhen University, Shenzhen Second People’s Hospital, Shenzhen, China
| | - Dongwei Xu
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yizhu Tian
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Xiaoye Qu
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Mingwei Sheng
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Yuanbang Lin
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Michael Ke
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Longfeng Jiang
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fady M. Kaldas
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Douglas G. Farmer
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Bibo Ke
- The Dumont-UCLA Transplant Center, Division of Liver and Pancreas Transplantation, Department of Surgery, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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18
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Xiao X, Xu T, Liu H, Liu X, Liao X, Zhou Y, Zhou L, Wang X, Zhu Y, Yang Q, Hao X, Liu Y, Jiang H, Guo J, Wang J, Tang B, Li J, Shen L, Jiao B. CYLD variants identified in Alzheimer's disease and frontotemporal dementia patients. Ann Clin Transl Neurol 2022; 9:1596-1601. [PMID: 36000313 PMCID: PMC9539372 DOI: 10.1002/acn3.51655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Objectives CYLD was a novel causative gene for frontotemporal dementia (FTD) and amyotrophic lateral sclerosis. Given the clinical and pathological overlap of FTD and Alzheimer's disease (AD), it is necessary to screen CYLD in AD patients and FTD patients in the Chinese population. Methods In our study, using a targeted sequencing panel, we sequenced the CYLD gene in a large cohort of 2485 participants in the Chinese population, including 1008 AD patients, 105 FTD patients, and 1372 controls. Results In the present study, the average onset age of AD and FTD patients was 66.84 ± 30.42 years old and 60 ± 10.00 years old, respectively. Our study reported three novel CYLD variants: p.Phe288Leu (patient No. 1, AD), p.Tyr485Phe (patients No. 6–9, all AD) and p.Thr951Ala (patient No. 10, AD), plus a previously reported variant: p.Arg397Ser (patient No. 2–5, AD and No. 11, FTD). These variants were absent in our in‐house controls and predicted to be deleterious according to the MutationTaster. The variant carriers were composed of 10 AD patients and one FTD patient, and the average onset age was 61.2 ± 10.9 years. The frequency of CYLD variants in AD was similar to that in FTD, which was 0.99% (10/1008) and 0.95% (1/105), respectively. Interpretation Our finding extended the genotype and phenotype of the CYLD gene and demonstrated that CYLD rare damaging variants may be implicated in AD and FTD pathogenesis.
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Affiliation(s)
- Xuewen Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Tianyan Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hui Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xixi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xinxin Liao
- Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Yafang Zhou
- Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Lu Zhou
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xin Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Zhu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Qijie Yang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoli Hao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yingzi Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Jifeng Guo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Junling Wang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Jinchen Li
- Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
| | - Lu Shen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China.,Key Laboratory of Organ Injury, Aging and Regenerative Medicine of Hunan Province, Changsha, China
| | - Bin Jiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China.,Bioinformatics Center and National Clinical Research Center for Geriatric Disorders, Central South University, Changsha, China.,Engineering Research Center of Hunan Province in Cognitive Impairment Disorders, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.,Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, China
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19
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Chen Y, Zhou D, Yao Y, Sun Y, Yao F, Ma L. Monoubiquitination in Homeostasis and Cancer. Int J Mol Sci 2022; 23:ijms23115925. [PMID: 35682605 PMCID: PMC9180643 DOI: 10.3390/ijms23115925] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/17/2022] [Accepted: 05/20/2022] [Indexed: 02/06/2023] Open
Abstract
Monoubiquitination is a post-translational modification (PTM), through which a single ubiquitin molecule is covalently conjugated to a lysine residue of the target protein. Monoubiquitination regulates the activity, subcellular localization, protein-protein interactions, or endocytosis of the substrate. In doing so, monoubiquitination is implicated in diverse cellular processes, including gene transcription, endocytosis, signal transduction, cell death, and DNA damage repair, which in turn regulate cell-cycle progression, survival, proliferation, and stress response. In this review, we summarize the functions of monoubiquitination and discuss how this PTM modulates homeostasis and cancer.
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Affiliation(s)
- Yujie Chen
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (Y.C.); (D.Z.); (Y.Y.)
| | - Dandan Zhou
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (Y.C.); (D.Z.); (Y.Y.)
| | - Yinan Yao
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (Y.C.); (D.Z.); (Y.Y.)
| | - Yutong Sun
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Fan Yao
- Hubei Hongshan Laboratory, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, China; (Y.C.); (D.Z.); (Y.Y.)
- Hubei Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan 442000, China
- Correspondence: (F.Y.); (L.M.)
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
- Correspondence: (F.Y.); (L.M.)
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20
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Xu G, Su H, Lu L, Liu X, Zhao L, Tang B, Ming Z. Structural insights into the catalytic mechanism and ubiquitin recognition of USP34. J Mol Biol 2022; 434:167634. [PMID: 35588869 DOI: 10.1016/j.jmb.2022.167634] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/01/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022]
Abstract
Ubiquitination, an important posttranslational modification, participates in virtually all aspects of cellular functions and is reversed by deubiquitinating enzymes (DUBs). Ubiquitin-specific protease 34 (USP34) plays an essential role in cancer, neurodegenerative diseases, and osteogenesis. Despite its functional importance, how USP34 recognizes ubiquitin and catalyzes deubiquitination remains structurally uncharacterized. Here, we report the crystal structures of the USP34 catalytic domain in free state and after binding with ubiquitin. In the free state, USP34 adopts an inactive conformation, which contains a misaligned catalytic histidine in the triad. Comparison of USP34 structures before and after ubiquitin binding reveals a structural basis for ubiquitin recognition and elucidates a mechanism by which the catalytic triad is realigned. Transition from an open inactive state to a relatively closed active state is coupled to a process by which the "fingertips" of USP34 intimately grip ubiquitin, and this has not been reported before. Our structural and biochemical analyses provide important insights into the catalytic mechanism and ubiquitin recognition of USP34.
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Affiliation(s)
- Guolyu Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Huizhao Su
- Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, P. R. China
| | - Lining Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China
| | - Xiaomeng Liu
- Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, P. R. China
| | - Liang Zhao
- Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, P. R. China
| | - Bo Tang
- Department of Hepatobiliary Surgery and Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, P. R. China.
| | - Zhenhua Ming
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi Key Laboratory for Sugarcane Biology, Guangxi University, Nanning 530004, P.R. China.
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21
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Rossi FA, Rossi M. Emerging Role of Ubiquitin-Specific Protease 19 in Oncogenesis and Cancer Development. Front Cell Dev Biol 2022; 10:889166. [PMID: 35646888 PMCID: PMC9133600 DOI: 10.3389/fcell.2022.889166] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/26/2022] [Indexed: 12/21/2022] Open
Abstract
Ubiquitination and ubiquitin-like post-translational modifications control the activity and stability of different tumor suppressors and oncoproteins. Hence, regulation of this enzymatic cascade offers an appealing scenario for novel antineoplastic targets discovery. Among the different families of enzymes that participate in the conjugation of Ubiquitin, deubiquitinating enzymes (DUBs), responsible for removing ubiquitin or ubiquitin-like peptides from substrate proteins, have attracted increasing attention. In this regard, increasing evidence is accumulating suggesting that the modulation of the catalytic activity of DUBs represents an attractive point of therapeutic intervention in cancer treatment. In particular, different lines of research indicate that USP19, a member of the DUBs, plays a role in the control of tumorigenesis and cancer dissemination. This review aims at summarizing the current knowledge of USP19 wide association with the control of several cellular processes in different neoplasms, which highlights the emerging role of USP19 as a previously unrecognized prognosis factor that possesses both positive and negative regulation activities in tumor biology. These observations indicate that USP19 might represent a novel putative pharmacologic target in oncology and underscores the potential of identifying specific modulators to test in clinical settings.
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22
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Zajicek AS, Ruan H, Dai H, Skolfield MC, Phillips HL, Burnette WJ, Javidfar B, Sun SC, Akbarian S, Yao WD. Cylindromatosis drives synapse pruning and weakening by promoting macroautophagy through Akt-mTOR signaling. Mol Psychiatry 2022; 27:2414-2424. [PMID: 35449295 PMCID: PMC9278694 DOI: 10.1038/s41380-022-01571-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/09/2022]
Abstract
The lysine-63 deubiquitinase cylindromatosis (CYLD) is long recognized as a tumor suppressor in immunity and inflammation, and its loss-of-function mutations lead to familial cylindromatosis. However, recent studies reveal that CYLD is enriched in mammalian brain postsynaptic densities, and a gain-of-function mutation causes frontotemporal dementia (FTD), suggesting critical roles at excitatory synapses. Here we report that CYLD drives synapse elimination and weakening by acting on the Akt-mTOR-autophagy axis. Mice lacking CYLD display abnormal sociability, anxiety- and depression-like behaviors, and cognitive inflexibility. These behavioral impairments are accompanied by excessive synapse numbers, increased postsynaptic efficacy, augmented synaptic summation, and impaired NMDA receptor-dependent hippocampal long-term depression (LTD). Exogenous expression of CYLD results in removal of established dendritic spines from mature neurons in a deubiquitinase activity-dependent manner. In search of underlying molecular mechanisms, we find that CYLD knockout mice display marked overactivation of Akt and mTOR and reduced autophagic flux, and conversely, CYLD overexpression potently suppresses Akt and mTOR activity and promotes autophagy. Consequently, abrogating the Akt-mTOR-autophagy signaling pathway abolishes CYLD-induced spine loss, whereas enhancing autophagy in vivo by the mTOR inhibitor rapamycin rescues the synaptic pruning and LTD deficits in mutant mice. Our findings establish CYLD, via Akt-mTOR signaling, as a synaptic autophagy activator that exerts critical modulations on synapse maintenance, function, and plasticity.
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Affiliation(s)
- Alexis S Zajicek
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Hongyu Ruan
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Huihui Dai
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mary C Skolfield
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Hannah L Phillips
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Wendi J Burnette
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Behnam Javidfar
- Friedman Brain Institute, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shao-Cong Sun
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wei-Dong Yao
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA.
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA.
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA.
- Harvard Medical School, New England Primate Research Center, Southborough, MA, USA.
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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23
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Kelsall IR, McCrory EH, Xu Y, Scudamore CL, Nanda SK, Mancebo-Gamella P, Wood NT, Knebel A, Matthews SJ, Cohen P. HOIL-1 ubiquitin ligase activity targets unbranched glucosaccharides and is required to prevent polyglucosan accumulation. EMBO J 2022; 41:e109700. [PMID: 35274759 PMCID: PMC9016349 DOI: 10.15252/embj.2021109700] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 01/05/2022] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
HOIL-1, a component of the linear ubiquitin chain assembly complex (LUBAC), ubiquitylates serine and threonine residues in proteins by esterification. Here, we report that mice expressing an E3 ligase-inactive HOIL-1[C458S] mutant accumulate polyglucosan in brain, heart and other organs, indicating that HOIL-1's E3 ligase activity is essential to prevent these toxic polysaccharide deposits from accumulating. We found that HOIL-1 monoubiquitylates glycogen and α1:4-linked maltoheptaose in vitro and identify the C6 hydroxyl moiety of glucose as the site of ester-linked ubiquitylation. The monoubiquitylation of maltoheptaose was accelerated > 100-fold by the interaction of Met1-linked or Lys63-linked ubiquitin oligomers with the RBR domain of HOIL-1. HOIL-1 also transferred pre-formed ubiquitin oligomers to maltoheptaose en bloc, producing polyubiquitylated maltoheptaose in one catalytic step. The Sharpin and HOIP components of LUBAC, but not HOIL-1, bound to unbranched and infrequently branched glucose polymers in vitro, but not to highly branched mammalian glycogen, suggesting a potential function in targeting HOIL-1 to unbranched glucosaccharides in cells. We suggest that monoubiquitylation of unbranched glucosaccharides may initiate their removal from cells, preventing precipitation as polyglucosan.
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Affiliation(s)
- Ian R Kelsall
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Elisha H McCrory
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Yingqi Xu
- Cross-Faculty NMR Centre, Department of Life Sciences, Imperial College London, London, UK
| | | | - Sambit K Nanda
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Paula Mancebo-Gamella
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicola T Wood
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Stephen J Matthews
- Cross-Faculty NMR Centre, Department of Life Sciences, Imperial College London, London, UK
| | - Philip Cohen
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
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24
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Crystal structure of a tandem B-box domain from Arabidopsis CONSTANS. Biochem Biophys Res Commun 2022; 599:38-42. [DOI: 10.1016/j.bbrc.2022.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 11/18/2022]
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25
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Chen R, Pang X, Li L, Zeng Z, Chen M, Zhang S. Ubiquitin-specific proteases in inflammatory bowel disease-related signalling pathway regulation. Cell Death Dis 2022; 13:139. [PMID: 35145062 PMCID: PMC8831562 DOI: 10.1038/s41419-022-04566-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
The exact pathogenesis of inflammatory bowel disease (IBD), a chronic gastrointestinal inflammatory disease comprising Crohn’s disease and ulcerative colitis, remains unclear. Studies on ubiquitination, which regulates the degradation of inflammation signalling pathway molecules, and deubiquitination have provided novel insights. Targeting the ubiquitin-specific protease (USP) family of deubiquitinases elucidates IBD signalling pathway mechanisms and possibly, IBD therapeutic solutions. Here, we characterised USPs as chief regulators of pro-inflammatory signalling pathways, including nuclear factor-κB and transforming growth factor-β; analysed the relationship between USPs and IBD pathogenesis in terms of genetic susceptibility, intestinal epithelial barrier, immunity, and gut microbiota; and discussed future research prospects.
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Affiliation(s)
- Rirong Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaobai Pang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Li Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shenghong Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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26
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Choi HS, Baek KH. Pro-apoptotic and anti-apoptotic regulation mediated by deubiquitinating enzymes. Cell Mol Life Sci 2022; 79:117. [PMID: 35118522 PMCID: PMC11071826 DOI: 10.1007/s00018-022-04132-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/20/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022]
Abstract
Although damaged cells can be repaired, cells that are considered unlikely to be repaired are eliminated through apoptosis, a type of predicted cell death found in multicellular organisms. Apoptosis is a structured cell death involving alterations to the cell morphology and internal biochemical changes. This process involves the expansion and cracking of cells, changes in cell membranes, nuclear fragmentation, chromatin condensation, and chromosome cleavage, culminating in the damaged cells being eaten and processed by other cells. The ubiquitin-proteasome system (UPS) is a major cellular pathway that regulates the protein levels through proteasomal degradation. This review proposes that apoptotic proteins are regulated through the UPS and describes a unique direction for cancer treatment by controlling proteasomal degradation of apoptotic proteins, and small molecules targeted to enzymes associated with UPS.
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Affiliation(s)
- Hae-Seul Choi
- Department of Biomedical Science, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 13488, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 13488, Republic of Korea.
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27
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Long S, Yang L, Dang W, Xin S, Jiang M, Zhang W, Li J, Wang Y, Zhang S, Lu J. Cellular Deubiquitylating Enzyme: A Regulatory Factor of Antiviral Innate Immunity. Front Microbiol 2021; 12:805223. [PMID: 34966378 PMCID: PMC8710732 DOI: 10.3389/fmicb.2021.805223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Deubiquitylating enzymes (DUBs) are proteases that crack the ubiquitin code from ubiquitylated substrates to reverse the fate of substrate proteins. Recently, DUBs have been found to mediate various cellular biological functions, including antiviral innate immune response mediated by pattern-recognition receptors (PRRs) and NLR Family pyrin domain containing 3 (NLRP3) inflammasomes. So far, many DUBs have been identified to exert a distinct function in fine-tuning antiviral innate immunity and are utilized by viruses for immune evasion. Here, the recent advances in the regulation of antiviral responses by DUBs are reviewed. We also discussed the DUBs-mediated interaction between the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and antiviral innate immunity. The understanding of the mechanisms on antiviral innate immunity regulated by DUBs may provide therapeutic opportunities for viral infection.
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Affiliation(s)
- Sijing Long
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Li Yang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Wei Dang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Shuyu Xin
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Mingjuan Jiang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Wentao Zhang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Jing Li
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Yiwei Wang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Senmiao Zhang
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
| | - Jianhong Lu
- Department of Hematology, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China.,NHC Key Laboratory of Carcinogenesis, The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.,China-Africa Research Center of Infectious Diseases, Central South University, Changsha, China
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28
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Gu X, Chen Y, Wei Q, Hou Y, Cao B, Zhang L, Ou R, Lin J, Liu K, Zhao B, Shang H. Rare CYLD Variants in Chinese Patients With Amyotrophic Lateral Sclerosis. Front Genet 2021; 12:740052. [PMID: 34868212 PMCID: PMC8633398 DOI: 10.3389/fgene.2021.740052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/14/2021] [Indexed: 02/05/2023] Open
Abstract
Background: CYLD Lysine 63 Deubiquitinase gene (CYLD) was recently identified to be a novel causative gene for frontal temporal dementia (FTD)-amyotrophic lateral sclerosis (ALS). In the current study, we aimed to (1) systematically screen the mutations of CYLD in a large cohort of Chinese ALS patients, (2) study the genotype–phenotype correlation, and (3) explore the role of CYLD in ALS via rare variants burden analysis. Methods: A total of 978 Chinese sporadic ALS (sALS) patients and 46 familial ALS (fALS) patients were sequenced with whole-exome sequencing and analyzed rare variants in CYLD with minor allele frequency <0.1%. Results: In total, seven rare missense variants in CYLD have been identified in 7 (0.72%) patients among 978 sALS patients. Two (4.3%) rare missense variants were identified among the 46 fALS cases, in which one patient was diagnosed as having comorbidity of ALS and progressive supranuclear palsy (PSP). Moreover, the burden analysis indicated no enrichment of rare variants in CYLD among patients with ALS. Conclusion: In conclusion, our study extended the genotype and phenotype of CYLD in ALS, but the pathogenicity of these variants needs to be further verified. Moreover, burden analysis argued against the role of CYLD in the pathogenesis of ALS. More studies from different ethnicities would be needed.
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Affiliation(s)
- Xiaojing Gu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yongping Chen
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qianqian Wei
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yanbing Hou
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bei Cao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lingyu Zhang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ruwei Ou
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Junyu Lin
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Kuncheng Liu
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bi Zhao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
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29
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TRIM proteins in fibrosis. Biomed Pharmacother 2021; 144:112340. [PMID: 34678729 DOI: 10.1016/j.biopha.2021.112340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023] Open
Abstract
Fibrosis is an outcome of tissue repair after different types of injuries. The homeostasis of extracellular matrix is broken, and excessive deposition occurs, affecting the normal function of tissues and organs, which could become prostrated in serious cases.Finding a suitable target to regulate the repair process and reduce the damage caused by fibrosis is a hot research topic at present. The TRIM family is number of one of the E3 ubiquitin ligase subfamilies and participates in various biological processes including intracellular signal transduction, apoptosis, autophagy, and immunity by regulating the ubiquitination of target proteins. For the past few years, the important role of TRIM in the occurrence and development of fibrosis has been gradually revealed. In this review, we focus on the recent emerging topics on TRIM proteins in the regulation of fibrosis, fibrosis-related cytokines and pathways.
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30
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Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Gräwert TW, Knebel A, Svergun DI, Kulathu Y. Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2. Mol Cell 2021; 81:4176-4190.e6. [PMID: 34529927 PMCID: PMC8550791 DOI: 10.1016/j.molcel.2021.08.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 03/29/2021] [Accepted: 08/19/2021] [Indexed: 01/10/2023]
Abstract
Of the eight distinct polyubiquitin (polyUb) linkages that can be assembled, the roles of K48-linked polyUb (K48-polyUb) are the most established, with K48-polyUb modified proteins being targeted for degradation. MINDY1 and MINDY2 are members of the MINDY family of deubiquitinases (DUBs) that have exquisite specificity for cleaving K48-polyUb, yet we have a poor understanding of their catalytic mechanism. Here, we analyze the crystal structures of MINDY1 and MINDY2 alone and in complex with monoUb, di-, and penta-K48-polyUb, identifying 5 distinct Ub binding sites in the catalytic domain that explain how these DUBs sense both Ub chain length and linkage type to cleave K48-polyUb chains. The activity of MINDY1/2 is inhibited by the Cys-loop, and we find that substrate interaction relieves autoinhibition to activate these DUBs. We also find that MINDY1/2 use a non-canonical catalytic triad composed of Cys-His-Thr. Our findings highlight multiple layers of regulation modulating DUB activity in MINDY1 and MINDY2. The catalytic domain of MINDY1/2 has five distinct Ub binding sites Dynamics of the Cys loop regulate DUB activity Non-canonical catalytic triad composed of Cys-His-Thr MINDY1/2 uses an exo- or endo-cleavage mode that is determined by Ub chain length
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Affiliation(s)
- Syed Arif Abdul Rehman
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - Lee A Armstrong
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Sven M Lange
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Yosua Adi Kristariyanto
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Tobias W Gräwert
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Axel Knebel
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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31
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Elliott PR, Leske D, Wagstaff J, Schlicher L, Berridge G, Maslen S, Timmermann F, Ma B, Fischer R, Freund SMV, Komander D, Gyrd-Hansen M. Regulation of CYLD activity and specificity by phosphorylation and ubiquitin-binding CAP-Gly domains. Cell Rep 2021; 37:109777. [PMID: 34610306 PMCID: PMC8511506 DOI: 10.1016/j.celrep.2021.109777] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 12/24/2022] Open
Abstract
Non-degradative ubiquitin chains and phosphorylation events govern signaling responses by innate immune receptors. The deubiquitinase CYLD in complex with SPATA2 is recruited to receptor signaling complexes by the ubiquitin ligase LUBAC and regulates Met1- and Lys63-linked polyubiquitin and receptor signaling outcomes. Here, we investigate the molecular determinants of CYLD activity. We reveal that two CAP-Gly domains in CYLD are ubiquitin-binding domains and demonstrate a requirement of CAP-Gly3 for CYLD activity and regulation of immune receptor signaling. Moreover, we identify a phosphorylation switch outside of the catalytic USP domain, which activates CYLD toward Lys63-linked polyubiquitin. The phosphorylated residue Ser568 is a novel tumor necrosis factor (TNF)-regulated phosphorylation site in CYLD and works in concert with Ser418 to enable CYLD-mediated deubiquitination and immune receptor signaling. We propose that phosphorylated CYLD, together with SPATA2 and LUBAC, functions as a ubiquitin-editing complex that balances Lys63- and Met1-linked polyubiquitin at receptor signaling complexes to promote LUBAC signaling.
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Affiliation(s)
- Paul R Elliott
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
| | - Derek Leske
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jane Wagstaff
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Lisa Schlicher
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Georgina Berridge
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Sarah Maslen
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Frederik Timmermann
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Biao Ma
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Roman Fischer
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Stefan M V Freund
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville VIC 3052, Australia; Department for Medical Biology, University of Melbourne, Melbourne VIC 3000, Australia.
| | - Mads Gyrd-Hansen
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus Research Building, Off-Roosevelt Drive, Oxford OX3 7DQ, UK; LEO Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, University of Copenhagen, Maersk Tower, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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32
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The COP9 Signalosome Variant CSNCSN7A Stabilizes the Deubiquitylating Enzyme CYLD Impeding Hepatic Steatosis. LIVERS 2021. [DOI: 10.3390/livers1030011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Hepatic steatosis is a consequence of distorted lipid storage and plays a vital role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). This study aimed to explore the role of the COP9 signalosome (CSN) in the development of hepatic steatosis and its interplay with the deubiquitylating enzyme (DUB) cylindromatosis (CYLD). CSN occurs as CSNCSN7A and CSNCSN7B variants regulating the ubiquitin proteasome system. It is a deneddylating complex and associates with other DUBs. CYLD cleaves Lys63-ubiquitin chains, regulating a signal cascade that mitigates hepatic steatosis. CSN subunits CSN1 and CSN7B, as well as CYLD, were downregulated with specific siRNA in HepG2 cells and human primary hepatocytes. The same cells were transfected with Flag-CSN7A or Flag-CSN7B for pulldowns. Hepatic steatosis in cell culture was induced by palmitic acid (PA). Downregulation of CSN subunits led to reduced PPAR-γ expression. Flag-pulldowns in both LiSa-2 and HepG2 cells and human primary hepatocytes revealed binding of CYLD preferentially to CSNCSN7A. This was influenced by PA treatment. Silencing of CSNCSN7B blocked lipid droplet formation caused a compensatory increase of CSNCSN7A stabilizing CYLD. Our results demonstrate that CSNCSN7A-mediated CYLD stabilization impedes hepatic steatosis. Therefore, stabilizing CSNCSN7A-CYLD interaction might be a strategy to retard hepatic steatosis.
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33
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Danis J, Kelemen E, Rajan N, Nagy N, Széll M, Ádám É. TRAF3 and NBR1 both influence the effect of the disease-causing CYLD(Arg936X) mutation on NF-κB activity. Exp Dermatol 2021; 30:1705-1710. [PMID: 33999445 DOI: 10.1111/exd.14365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/17/2021] [Accepted: 04/26/2021] [Indexed: 12/01/2022]
Abstract
Recently described Hungarian and Anglo-Saxon pedigrees that are affected by CYLD cutaneous syndrome (syn: Brooke-Spiegler syndrome (BSS)) carry the same disease-causing mutation (c.2806C>T, p.Arg936X) of the cylindromatosis (CYLD) gene but exhibit striking phenotypic differences. Using whole exome sequencing, missense genetic variants of the TRAF3 and NBR1 genes were identified in the affected family members of the Hungarian pedigree that are not present in the Anglo-Saxon pedigree. This suggested that the affected proteins (TRAF3 and NBR1) are putative phenotype-modifying factors. An in vitro experimental system was set up to clarify how wild type and mutant TRAF3 and NBR1 modify the effect of CYLD on the NF-κB signal transduction pathway. Our study revealed that the combined expression of mutant CYLD(Arg936X) with TRAF3 and NBR1 caused increased NF-κB activity, regardless of the presence or absence of mutations in TRAF3 and NBR1. We concluded that increased expression levels of these proteins further strengthen the effect of the CYLD(Arg936X) mutation on NF-κB activity in HEK293 cells and may explain the phenotype-modifying effect of these genes in CYLD cutaneous syndrome. These results raise the potential that detecting the levels of TRAF3 and NBR1 might help explaining phenotypic differences and prognosis of CCS.
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Affiliation(s)
- Judit Danis
- MTA-SZTE Dermatological Research Group, Eötvös Loránd Research Network, Szeged, Hungary.,HCEMM-USZ Skin Research Group, Szeged, Hungary.,Department of Medical Genetics, University of Szeged, Szeged, Hungary
| | - Evelyn Kelemen
- Department of Medical Genetics, University of Szeged, Szeged, Hungary.,Department of Dermatology and Allergology, University of Szeged, Szeged, Hungary
| | - Neil Rajan
- Translational and Clinical Research Institute, Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - Nikoletta Nagy
- MTA-SZTE Dermatological Research Group, Eötvös Loránd Research Network, Szeged, Hungary.,Department of Medical Genetics, University of Szeged, Szeged, Hungary
| | - Márta Széll
- MTA-SZTE Dermatological Research Group, Eötvös Loránd Research Network, Szeged, Hungary.,Department of Medical Genetics, University of Szeged, Szeged, Hungary
| | - Éva Ádám
- Department of Medical Genetics, University of Szeged, Szeged, Hungary
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34
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Liang X, Cao Y, Li C, Yu H, Yang C, Liu H. MALT1 as a promising target to treat lymphoma and other diseases related to MALT1 anomalies. Med Res Rev 2021; 41:2388-2422. [PMID: 33763890 DOI: 10.1002/med.21799] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/23/2020] [Accepted: 03/03/2021] [Indexed: 12/25/2022]
Abstract
Mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is a key adaptor protein that regulates the NF-κB pathway, in which MALT1 functions as a scaffold protein and protease to trigger downstream signals. The abnormal expression of MALT1 is closely associated with lymphomagenesis and other diseases, including solid tumors and autoimmune diseases. MALT1 is the only protease in the underlying pathogenesis of these diseases, and its proteolytic activity can be pharmacologically regulated. Therefore, MALT1 is a potential and promising target for anti-lymphoma and other MALT1-related disease treatments. Currently, the development of MALT1 inhibitors is still in its early stages. This review presents an overview of MALT1, particularly its X-ray structures and biological functions, and elaborates on the pathogenesis of diseases associated with its dysregulation. We then summarize previously reported MALT1 inhibitors, focusing on their molecular structure, biological activity, structure-activity relationship, and limitations. Finally, we propose future research directions to accelerate the discovery of novel MALT1 inhibitors with clinical applications. Overall, this review provides a comprehensive and systematic overview of MALT1-related research advances and serves as a theoretical basis for drug discovery and research.
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Affiliation(s)
- Xuewu Liang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - YiChun Cao
- School of Pharmacy, Fudan University, Shanghai, China
| | - Chunpu Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Haolan Yu
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Chenghua Yang
- Department of Urology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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35
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Hu B, Zhang D, Zhao K, Wang Y, Pei L, Fu Q, Ma X. Spotlight on USP4: Structure, Function, and Regulation. Front Cell Dev Biol 2021; 9:595159. [PMID: 33681193 PMCID: PMC7935551 DOI: 10.3389/fcell.2021.595159] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/15/2021] [Indexed: 02/05/2023] Open
Abstract
The deubiquitinating enzyme (DUB)–mediated cleavage of ubiquitin plays a critical role in balancing protein synthesis and degradation. Ubiquitin-specific protease 4 (USP4), a member of the largest subfamily of cysteine protease DUBs, removes monoubiquitinated and polyubiquitinated chains from its target proteins. USP4 contains a DUSP (domain in USP)–UBL (ubiquitin-like) domain and a UBL-insert catalytic domain, sharing a common domain organization with its paralogs USP11 and USP15. USP4 plays a critical role in multiple cellular and biological processes and is tightly regulated under normal physiological conditions. When its expression or activity is aberrant, USP4 is implicated in the progression of a wide range of pathologies, especially cancers. In this review, we comprehensively summarize the current knowledge of USP4 structure, biological functions, pathological roles, and cellular regulation, highlighting the importance of exploring effective therapeutic interventions to target USP4.
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Affiliation(s)
- Binbin Hu
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Dingyue Zhang
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Kejia Zhao
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yang Wang
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lijiao Pei
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Qianmei Fu
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xuelei Ma
- Department of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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36
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Cockram PE, Kist M, Prakash S, Chen SH, Wertz IE, Vucic D. Ubiquitination in the regulation of inflammatory cell death and cancer. Cell Death Differ 2021; 28:591-605. [PMID: 33432113 PMCID: PMC7798376 DOI: 10.1038/s41418-020-00708-5] [Citation(s) in RCA: 163] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022] Open
Abstract
The ubiquitin system is complex, multifaceted, and is crucial for the modulation of a vast number of cellular processes. Ubiquitination is tightly regulated at different levels by a range of enzymes including E1s, E2s, and E3s, and an array of DUBs. The UPS directs protein degradation through the proteasome, and regulates a wide array of cellular processes including transcription and epigenetic factors as well as key oncoproteins. Ubiquitination is key to the dynamic regulation of programmed cell death. Notably, the TNF signaling pathway is controlled by competing ubiquitin conjugation and deubiquitination, which governs both proteasomal degradation and signaling complex formation. In the inflammatory response, ubiquitination is capable of both activating and dampening inflammasome activation through the control of either protein stability, complex formation, or, in some cases, directly affecting receptor activity. In this review, we discuss the enzymes and targets in the ubiquitin system that regulate fundamental cellular processes regulating cell death, and inflammation, as well as disease consequences resulting from their dysregulation. Finally, we highlight several pre-clinical and clinical compounds that regulate ubiquitin system enzymes, with the aim of restoring homeostasis and ameliorating diseases.
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Affiliation(s)
- Peter E Cockram
- Departments of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.,Departments of Discovery Chemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Matthias Kist
- Departments of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Sumit Prakash
- Departments of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Si-Han Chen
- Departments of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ingrid E Wertz
- Departments of Discovery Oncology, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA. .,Departments of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Domagoj Vucic
- Departments of Early Discovery Biochemistry, Genentech, 1 DNA Way, South San Francisco, CA, 94080, USA.
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37
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Remodeling without destruction: non-proteolytic ubiquitin chains in neural function and brain disorders. Mol Psychiatry 2021; 26:247-264. [PMID: 32709994 PMCID: PMC9229342 DOI: 10.1038/s41380-020-0849-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/31/2022]
Abstract
Ubiquitination is a fundamental posttranslational protein modification that regulates diverse biological processes, including those in the CNS. Several topologically and functionally distinct polyubiquitin chains can be assembled on protein substrates, modifying their fates. The classical and most prevalent polyubiquitin chains are those that tag a substrate to the proteasome for degradation, which has been established as a major mechanism driving neural circuit deconstruction and remodeling. In contrast, proteasome-independent non-proteolytic polyubiquitin chains regulate protein scaffolding, signaling complex formation, and kinase activation, and play essential roles in an array of signal transduction processes. Despite being a cornerstone in immune signaling and abundant in the mammalian brain, these non-proteolytic chains are underappreciated in neurons and synapses in the brain. Emerging studies have begun to generate exciting insights about some fundamental roles played by these non-degradative chains in neuronal function and plasticity. In addition, their roles in a number of brain diseases are being recognized. In this article, we discuss recent advances on these nonconventional ubiquitin chains in neural development, function, plasticity, and related pathologies.
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38
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Bonacci T, Emanuele MJ. Dissenting degradation: Deubiquitinases in cell cycle and cancer. Semin Cancer Biol 2020; 67:145-158. [PMID: 32201366 PMCID: PMC7502435 DOI: 10.1016/j.semcancer.2020.03.008] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/27/2020] [Accepted: 03/09/2020] [Indexed: 01/01/2023]
Abstract
Since its discovery forty years ago, protein ubiquitination has been an ever-expanding field. Virtually all biological processes are controlled by the post-translational conjugation of ubiquitin onto target proteins. In addition, since ubiquitin controls substrate degradation through the action of hundreds of enzymes, many of which represent attractive therapeutic candidates, harnessing the ubiquitin system to reshape proteomes holds great promise for improving disease outcomes. Among the numerous physiological functions controlled by ubiquitin, the cell cycle is among the most critical. Indeed, the discovery that the key drivers of cell cycle progression are regulated by the ubiquitin-proteasome system (UPS) epitomizes the connection between ubiquitin signaling and proliferation. Since cancer is a disease of uncontrolled cell cycle progression and proliferation, targeting the UPS to stop cancer cells from cycling and proliferating holds enormous therapeutic potential. Ubiquitination is reversible, and ubiquitin is removed from substrates by catalytic proteases termed deubiquitinases or DUBs. While ubiquitination is tightly linked to proliferation and cancer, the role of DUBs represents a layer of complexity in this landscape that remains poorly captured. Due to their ability to remodel the proteome by altering protein degradation dynamics, DUBs play an important and underappreciated role in the cell cycle and proliferation of both normal and cancer cells. Moreover, due to their enzymatic protease activity and an open ubiquitin binding pocket, DUBs are likely to be important in the future of cancer treatment, since they are among the most druggable enzymes in the UPS. In this review we summarize new and important findings linking DUBs to cell cycle and proliferation, as well as to the etiology and treatment of cancer. We also highlight new advances in developing pharmacological approaches to attack DUBs for therapeutic benefit.
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Affiliation(s)
- Thomas Bonacci
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Michael J Emanuele
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.
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Lin Y, Wang L, Luo W, Zhou X, Chen Y, Yang K, Liao J, Wu D, Cai L. CYLD Promotes Apoptosis of Nasopharyngeal Carcinoma Cells by Regulating NDRG1. Cancer Manag Res 2020; 12:10639-10649. [PMID: 33149672 PMCID: PMC7604974 DOI: 10.2147/cmar.s268216] [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: 06/17/2020] [Accepted: 10/02/2020] [Indexed: 12/15/2022] Open
Abstract
Purpose Nasopharyngeal carcinoma (NPC) is among the most common malignancies derived from the epithelium of the nasopharynx. To date, the regulatory networks involved in NPC have not been fully identified. Previous studies revealed multiple loss-of-function mutations in NPC and specifically in cylindromatosis lysine 63 deubiquitinase (CYLD); however, the exact role of CYLD in NPC progression and its potential mechanism remains unclear. Methods We performed immunohistochemical (IHC) staining and real-time quantitative polymerase chain reaction (qPCR) to measure CYLD expression in NPC tissues, and Western blot was conducted to determine CYLD levels in NPC cell lines. Cell proliferation was detected by CCK8 assay and colony formation analysis, and apoptosis was determined by Annexin V/propidium iodide staining. Potential targets of CYLD were verified by co-immunoprecipitation and mass spectrometry. Xenograft assay was conducted to confirm the role of CYLD in vivo. Results We found that CYLD levels were significantly decreased in both NPC tissues and cell lines, and that CYLD overexpression inhibited NPC cell proliferation and promoted apoptosis. Additionally, we revealed that CYLD bound and upregulated N-Myc downstream regulated 1 (NDRG1), and that silencing NDRG1 abolished the tumor-suppressor effect of CYLD on NPC cells. Furthermore, CYLD suppressed tumor growth in xenograft mice models. Conclusion These results suggest CYLD as a tumor suppressor, potential biomarker for diagnosing NPC, and therapeutic target.
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Affiliation(s)
- Yanling Lin
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Lingzhi Wang
- First Clinical Medical College, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Wenxiao Luo
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xiaohan Zhou
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yuting Chen
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Kaifan Yang
- Department of Orthopaedics and Traumatology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jinrong Liao
- Second Clinical Medical College, Zhujiang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Dehua Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Longmei Cai
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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40
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Huang X, Zhang X, Xu J, Wang X, Zhang G, Tang T, Shen X, Liang T, Bai X. Deubiquitinating Enzyme: A Potential Secondary Checkpoint of Cancer Immunity. Front Oncol 2020; 10:1289. [PMID: 32850399 PMCID: PMC7426525 DOI: 10.3389/fonc.2020.01289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
The efficacy of cancer immunotherapy depends on the fine interplay between tumoral immune checkpoints and host immune system. However, the up-to-date clinical performance of checkpoint blockers in cancer therapy revealed that higher-level regulation should be further investigated for better therapeutic outcomes. It is becoming increasingly evident that the expression of immune checkpoints is largely associated to the immunotherapeutic response and consequent prognosis. Deubiquitinating enzymes (DUBs) with their role of cleaving ubiquitin from proteins and other molecules, thus reversing ubiquitination-mediated protein degradation, modulate multiple cellular processes, including, but not limited to, transcriptional regulation, cell cycle progression, tissue development, and antiviral response. Accumulating evidence indicates that DUBs also have the critical influence on anticancer immunity, simply by stabilizing pivotal checkpoints or key regulators of T-cell functions. Therefore, this review summarizes the current knowledge about DUBs, highlights the secondary checkpoint-like role of DUBs in cancer immunity, in particular their direct effects on the stability control of pivotal checkpoints and key regulators of T-cell functions, and suggests the therapeutic potential of DUBs-based strategy in targeted immunotherapy for cancer.
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Affiliation(s)
- Xing Huang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
| | - Xiaozhen Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
| | - Jian Xu
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
| | - Xun Wang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
| | - Gang Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
| | - Tianyu Tang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
| | - Xiaochao Shen
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
| | - Tingbo Liang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
| | - Xueli Bai
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,Innovation Center for the Study of Pancreatic Diseases, Hangzhou, China
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41
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Wang H, Meng Q, Ding Y, Xiong M, Zhu M, Yang Y, Su H, Gu L, Xu Y, Shi L, Zhou H, Zhang N. USP28 and USP25 are downregulated by Vismodegib in vitro and in colorectal cancer cell lines. FEBS J 2020; 288:1325-1342. [PMID: 32578360 DOI: 10.1111/febs.15461] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/23/2020] [Accepted: 06/16/2020] [Indexed: 12/19/2022]
Abstract
Deubiquitinase USP28 plays a crucial role in tumorigenesis by enhancing the stabilities of multiple cancer-related proteins including c-Myc, Notch1, and LSD1, and has become an attractive target for anticancer drug development. However, to date, only a few of USP28-targeted active compounds have been developed, and the active compound-binding pocket in USP28 has not been experimentally revealed yet. In this study, bioassay-based high-throughput screening was applied to discover USP28-targeted inhibitors from the commercially available drug library. Vismodegib, an inhibitor of Hedgehog signaling pathway and FDA-approved drug for the treatment of basal cell carcinoma, was found to exhibit inhibition activity against USP28 (IC50 : 4.41 ± 1.08 μm). Multiple biophysical and biochemical techniques including NMR, ITC, thermal shift assay, HDX-MS, and site-directed mutagenesis analysis were then used to characterize the interaction between Vismodegib and USP28. The binding pocket in USP28 for Vismodegib, which is mainly composed of two helical structures spanning D255-N278 and N286-Y293, was revealed. According to the possible binding pose generated by HDX-MS data-defined molecular docking, the binding cavity occupied by Vismodegib in USP28 aligns well with one of the reported-binding pockets in USP7 for its inhibitors. Furthermore, cellular assays were conducted to confirm that Vismodegib could interact with the evolutionarily related deubiquitinases USP28 and USP25 and downregulate the levels of the two enzymes' substrate proteins c-Myc, Notch1, and Tankyrase-1/2.
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Affiliation(s)
- Hui Wang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Qian Meng
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yiluan Ding
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Muya Xiong
- University of the Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Mengying Zhu
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Yuanyuan Yang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Haixia Su
- University of the Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Lei Gu
- University of the Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yechun Xu
- University of the Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Li Shi
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hu Zhou
- University of the Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Naixia Zhang
- Department of Analytical Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of the Chinese Academy of Sciences, Beijing, China
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A Human DUB Protein Array for Clarification of Linkage Specificity of Polyubiquitin Chain and Application to Evaluation of Its Inhibitors. Biomedicines 2020; 8:biomedicines8060152. [PMID: 32512835 PMCID: PMC7344921 DOI: 10.3390/biomedicines8060152] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Protein ubiquitinations play pivotal roles in many cellular processes, including homeostasis, responses to various stimulations, and progression of diseases. Deubiquitinating enzymes (DUBs) remove ubiquitin molecules from ubiquitinated proteins and cleave the polyubiquitin chain, thus negatively regulating numerous ubiquitin-dependent processes. Dysfunctions of many DUBs reportedly cause various diseases; therefore, DUBs are considered as important drug targets, although the biochemical characteristics and cellular functions of many DUBs are still unclear. Here, we established a human DUB protein array to detect the activity and linkage specificity of almost all human DUBs. Using a wheat cell-free protein synthesis system, 88 full-length recombinant human DUB proteins were prepared and termed the DUB array. In vitro DUB assays were performed with all of these recombinant DUBs, using eight linkage types of diubiquitins as substrates. As a result, 80 DUBs in the array showed DUB activities, and their linkage specificities were determined. These 80 DUBs included many biochemically uncharacterized DUBs in the past. In addition, taking advantage of these active DUB proteins, we applied the DUB array to evaluate the selectivities of DUB inhibitors. We successfully developed a high-throughput and semi-quantitative DUB assay based on AlphaScreen technology, and a model study using two commercially available DUB inhibitors revealed individual selectivities to 29 DUBs, as previously reported. In conclusion, the DUB array established here is a powerful tool for biochemical analyses and drug discovery for human DUBs.
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43
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Jang JH, Lee HM, Kim H, Cho JH. Molecular cloning and functional analysis of deubiquitinase CYLD in rainbow trout, Oncorhynchus mykiss. FISH & SHELLFISH IMMUNOLOGY 2020; 101:135-142. [PMID: 32224281 DOI: 10.1016/j.fsi.2020.03.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 06/10/2023]
Abstract
Deubiquitinase cylindromatosis (CYLD) inhibits MAPK and NF-κB activation pathways by deubiquitinating upstream regulatory factors. Although CYLD has been identified and actively studied in mammals, nothing is known about its putative function in fish. In this study, we identified the gene encoding CYLD (OmCYLD) from rainbow trout, Oncorhynchus mykiss, and examined its role during pathogenic infections. The deduced amino acid sequence of OmCYLD contains conserved CAP-Gly and USP domains. In RTH-149 cells, the expression of OmCYLD was increased by stimulation with Edwardsiella tarda and Streptococcus iniae. Gain-of-function and loss-of-function experiments showed that OmCYLD down-regulates the activation of MAPK and NF-κB and the expression of pro-inflammatory cytokines in E. tarda-stimulated RTH-149 cells. These findings suggest that OmCYLD might function like those of mammals to negatively regulate bacteria-triggered signaling pathway in fish.
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Affiliation(s)
- Ju Hye Jang
- Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Hyang Mi Lee
- Division of Applied Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Hyun Kim
- Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Ju Hyun Cho
- Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, South Korea; Division of Applied Life Science, Gyeongsang National University, Jinju, 52828, South Korea; Division of Life Science, Gyeongsang National University, Jinju, 52828, South Korea.
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44
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Mukherjee S, Kumar R, Tsakem Lenou E, Basrur V, Kontoyiannis DL, Ioakeimidis F, Mosialos G, Theiss AL, Flavell RA, Venuprasad K. Deubiquitination of NLRP6 inflammasome by Cyld critically regulates intestinal inflammation. Nat Immunol 2020; 21:626-635. [PMID: 32424362 DOI: 10.1038/s41590-020-0681-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 04/06/2020] [Indexed: 02/08/2023]
Abstract
The inflammasome NLRP6 plays a crucial role in regulating inflammation and host defense against microorganisms in the intestine. However, the molecular mechanisms by which NLRP6 function is inhibited to prevent excessive inflammation remain unclear. Here, we demonstrate that the deubiquitinase Cyld prevents excessive interleukin 18 (IL-18) production in the colonic mucosa by deubiquitinating NLRP6. We show that deubiquitination inhibited the NLRP6-ASC inflammasome complex and regulated the maturation of IL-18. Cyld deficiency in mice resulted in elevated levels of active IL-18 and severe colonic inflammation following Citrobacter rodentium infection. Further, in patients with ulcerative colitis, the concentration of active IL-18 was inversely correlated with CYLD expression. Thus, we have identified a novel regulatory mechanism that inhibits the NLRP6-IL-18 pathway in intestinal inflammation.
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Affiliation(s)
- Sandip Mukherjee
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ritesh Kumar
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Elviche Tsakem Lenou
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA.,Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - Dimitris L Kontoyiannis
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - Fotis Ioakeimidis
- Division of Immunology, Biomedical Sciences Research Center Alexander Fleming, Athens, Greece
| | - George Mosialos
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Arianne L Theiss
- Division of Gastroenterology and Hepatology, School of Medicine at the Anschutz Medical Campus, University of Colorado, Aurora, CO, USA
| | - Richard A Flavell
- Department of Immunobiology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA
| | - K Venuprasad
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas, TX, USA. .,Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA.
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45
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Dobson-Stone C, Hallupp M, Shahheydari H, Ragagnin AMG, Chatterton Z, Carew-Jones F, Shepherd CE, Stefen H, Paric E, Fath T, Thompson EM, Blumbergs P, Short CL, Field CD, Panegyres PK, Hecker J, Nicholson G, Shaw AD, Fullerton JM, Luty AA, Schofield PR, Brooks WS, Rajan N, Bennett MF, Bahlo M, Shankaracharya, Landers JE, Piguet O, Hodges JR, Halliday GM, Topp SD, Smith BN, Shaw CE, McCann E, Fifita JA, Williams KL, Atkin JD, Blair IP, Kwok JB. CYLD is a causative gene for frontotemporal dementia - amyotrophic lateral sclerosis. Brain 2020; 143:783-799. [PMID: 32185393 PMCID: PMC7089666 DOI: 10.1093/brain/awaa039] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 12/01/2019] [Accepted: 12/17/2019] [Indexed: 02/03/2023] Open
Abstract
Frontotemporal dementia and amyotrophic lateral sclerosis are clinically and pathologically overlapping disorders with shared genetic causes. We previously identified a disease locus on chromosome 16p12.1-q12.2 with genome-wide significant linkage in a large European Australian family with autosomal dominant inheritance of frontotemporal dementia and amyotrophic lateral sclerosis and no mutation in known amyotrophic lateral sclerosis or dementia genes. Here we demonstrate the segregation of a novel missense variant in CYLD (c.2155A>G, p.M719V) within the linkage region as the genetic cause of disease in this family. Immunohistochemical analysis of brain tissue from two CYLD p.M719V mutation carriers showed widespread glial CYLD immunoreactivity. Primary mouse neurons transfected with CYLDM719V exhibited increased cytoplasmic localization of TDP-43 and shortened axons. CYLD encodes a lysine 63 deubiquitinase and CYLD cutaneous syndrome, a skin tumour disorder, is caused by mutations that lead to reduced deubiquitinase activity. In contrast with CYLD cutaneous syndrome-causative mutations, CYLDM719V exhibited significantly increased lysine 63 deubiquitinase activity relative to the wild-type enzyme (paired Wilcoxon signed-rank test P = 0.005). Overexpression of CYLDM719V in HEK293 cells led to more potent inhibition of the cell signalling molecule NF-κB and impairment of autophagosome fusion to lysosomes, a key process in autophagy. Although CYLD mutations appear to be rare, CYLD's interaction with at least three other proteins encoded by frontotemporal dementia and/or amyotrophic lateral sclerosis genes (TBK1, OPTN and SQSTM1) suggests that it may play a central role in the pathogenesis of these disorders. Mutations in several frontotemporal dementia and amyotrophic lateral sclerosis genes, including TBK1, OPTN and SQSTM1, result in a loss of autophagy function. We show here that increased CYLD activity also reduces autophagy function, highlighting the importance of autophagy regulation in the pathogenesis of frontotemporal dementia and amyotrophic lateral sclerosis.
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Affiliation(s)
- Carol Dobson-Stone
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Marianne Hallupp
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
| | - Hamideh Shahheydari
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Audrey M G Ragagnin
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Zac Chatterton
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Francine Carew-Jones
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Claire E Shepherd
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Holly Stefen
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Esmeralda Paric
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Thomas Fath
- Dementia Research Centre and Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Elizabeth M Thompson
- SA Clinical Genetics Service, Women’s and Children’s Hospital, North Adelaide 5006, SA, Australia
- Adelaide Medical School, Faculty of Health Sciences, University of Adelaide, Adelaide SA 5005, Australia
| | - Peter Blumbergs
- Institute of Medical and Veterinary Science, Adelaide, SA 5000, Australia
| | - Cathy L Short
- Department of Neurology, The Queen Elizabeth Hospital, Woodville, SA 5011, Australia
| | - Colin D Field
- Adelaide Dementia Driving Clinic, Adelaide, SA 5041, Australia
| | - Peter K Panegyres
- Neurodegenerative Disorders Research Pty Ltd, West Perth, WA 6005, Australia
| | - Jane Hecker
- Department of General Medicine, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Garth Nicholson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Concord, NSW 2137, Australia
- Sydney Medical School, University of Sydney, Camperdown, NSW 2050, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW 2137, Australia
| | - Alex D Shaw
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Janice M Fullerton
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Agnes A Luty
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Peter R Schofield
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - William S Brooks
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia
| | - Neil Rajan
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Mark F Bennett
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, VIC 3084, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Shankaracharya
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - John E Landers
- University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Olivier Piguet
- The University of Sydney, Brain and Mind Centre and School of Psychology, Camperdown, NSW 2006, Australia
- ARC Centre of Excellence in Cognition and its Disorders, Sydney, NSW, Australia
| | - John R Hodges
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- ARC Centre of Excellence in Cognition and its Disorders, Sydney, NSW, Australia
| | - Glenda M Halliday
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Simon D Topp
- UK Dementia Research Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London SE5 9RX, UK
| | - Bradley N Smith
- UK Dementia Research Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London SE5 9RX, UK
| | - Christopher E Shaw
- UK Dementia Research Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King’s College London, London SE5 9RX, UK
| | - Emily McCann
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Jennifer A Fifita
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Julie D Atkin
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, Bundoora, VIC 3083, Australia
| | - Ian P Blair
- Centre for Motor Neuron Disease Research, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - John B Kwok
- The University of Sydney, Brain and Mind Centre and Central Clinical School, Faculty of Medicine and Health, Camperdown, NSW 2006, Australia
- Neuroscience Research Australia, Randwick, NSW 2031, Australia
- School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Functional analysis of deubiquitylating enzymes in tumorigenesis and development. Biochim Biophys Acta Rev Cancer 2019; 1872:188312. [DOI: 10.1016/j.bbcan.2019.188312] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 02/06/2023]
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47
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Insights into ubiquitin chain architecture using Ub-clipping. Nature 2019; 572:533-537. [PMID: 31413367 DOI: 10.1038/s41586-019-1482-y] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/17/2019] [Indexed: 01/17/2023]
Abstract
Protein ubiquitination is a multi-functional post-translational modification that affects all cellular processes. Its versatility arises from architecturally complex polyubiquitin chains, in which individual ubiquitin moieties may be ubiquitinated on one or multiple residues, and/or modified by phosphorylation and acetylation1-3. Advances in mass spectrometry have enabled the mapping of individual ubiquitin modifications that generate the ubiquitin code; however, the architecture of polyubiquitin signals has remained largely inaccessible. Here we introduce Ub-clipping as a methodology by which to understand polyubiquitin signals and architectures. Ub-clipping uses an engineered viral protease, Lbpro∗, to incompletely remove ubiquitin from substrates and leave the signature C-terminal GlyGly dipeptide attached to the modified residue; this simplifies the direct assessment of protein ubiquitination on substrates and within polyubiquitin. Monoubiquitin generated by Lbpro∗ retains GlyGly-modified residues, enabling the quantification of multiply GlyGly-modified branch-point ubiquitin. Notably, we find that a large amount (10-20%) of ubiquitin in polymers seems to exist as branched chains. Moreover, Ub-clipping enables the assessment of co-existing ubiquitin modifications. The analysis of depolarized mitochondria reveals that PINK1/parkin-mediated mitophagy predominantly exploits mono- and short-chain polyubiquitin, in which phosphorylated ubiquitin moieties are not further modified. Ub-clipping can therefore provide insight into the combinatorial complexity and architecture of the ubiquitin code.
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Zhang J, Zhou Q, Wang H, Huang M, Shi J, Han F, Cai W, Li Y, He T, Hu D. MicroRNA-130a has pro-fibroproliferative potential in hypertrophic scar by targeting CYLD. Arch Biochem Biophys 2019; 671:152-161. [PMID: 31283910 DOI: 10.1016/j.abb.2019.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/26/2019] [Accepted: 07/04/2019] [Indexed: 02/08/2023]
Abstract
Hypertrophic scars are dermal fibrosis diseases that protrude from the surface of the skin and irregularly extend to the periphery, seriously affecting the appearance and limb function of the patient. In this study, we found that microRNA-130a (miR-130a) was increased in hypertrophic scar tissues and derived primary fibroblasts, accompanied by up-regulation of collagen1/3 and α-SMA. Inhibition of miR-130a in hypertrophic scars fibroblasts suppressed the expression of collagen1/3 and α-SMA as well as the cell proliferation. Bioinformatics analysis combined with luciferase reporter gene assay results indicated that CYLD was a target gene of miR-130a, and the miR-130a mimic could reduce the level of CYLD. In contrast to miR-130a, the expression of CYLD was downregulated in hypertrophic scars and their derived fibroblasts. Overexpressing CYLD inhibited the expression of collagen 1/3 and α-SMA, slowed cell proliferation, and inhibited Akt activity. As expected, further study showed that the overexpression of CYLD could prevent the pro-fibroproliferative effects of miR-130a. Consistent with the in vitro results, the inhibitor of miR-130a effectively ameliorated excessive collagen deposition in bleomycin-induced skin fibrosis mouse model. Taken together, our results indicate that miR-130a promotes collagen secretion, myofibroblast transformation and cell proliferation by targeting CYLD and enhancing Akt activity. Therefore, the miR-130a/CYLD/Akt pathway may serve as a novel entry point for future skin fibrosis research.
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Affiliation(s)
- Jian Zhang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China
| | - Qin Zhou
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China
| | - Hongtao Wang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China
| | - Meiling Huang
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China
| | - Jihong Shi
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China
| | - Fu Han
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China
| | - Weixia Cai
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China
| | - Yan Li
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China
| | - Ting He
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China
| | - Dahai Hu
- Department of Burns and Cutaneous Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, 710032, PR China.
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Mussell A, Frangou C, Zhang J. Regulation of the Hippo signaling pathway by deubiquitinating enzymes in cancer. Genes Dis 2019; 6:335-341. [PMID: 31832513 PMCID: PMC6888741 DOI: 10.1016/j.gendis.2019.06.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/04/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022] Open
Abstract
Regulation of the Hippo signaling pathway is essential for normal organ growth and tissue homeostasis. The proteins that act to regulate this pathway are important for ensuring proper function and cellular location. Deubiquitinases (DUBs) are a family of proteases that act upon many proteins. While ubiquitinases add ubiquitin and target proteins for degradation, DUBs act by removing ubiquitin (Ub) moieties. Changes in ubiquitin chain topology results in the stabilization of proteins, membrane trafficking, and the alteration of cellular localization. While the roles of these proteins have been well established in a cancer setting, their convergence in cancer is still under investigation. In this review, we discuss the roles that DUBs play in the regulation of the Hippo signaling pathway for homeostasis and disease.
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Affiliation(s)
- Ashley Mussell
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14261, USA
| | - Costa Frangou
- Harvard TH Chan School of Public Health, Molecular and Integrative Physiological Sciences, Boston, MA 02115, USA
| | - Jianmin Zhang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY, 14261, USA
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50
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Differential Oligomerization of the Deubiquitinases USP25 and USP28 Regulates Their Activities. Mol Cell 2019; 74:421-435.e10. [PMID: 30926243 DOI: 10.1016/j.molcel.2019.02.029] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/13/2018] [Accepted: 02/20/2019] [Indexed: 12/12/2022]
Abstract
Deubiquitinases have emerged as promising drug targets for cancer therapy. The two DUBs USP25 and USP28 share high similarity but vary in their cellular functions. USP28 is known for its tumor-promoting role, whereas USP25 is a regulator of the innate immune system and, recently, a role in tumorigenesis was proposed. We solved the structures of the catalytic domains of both proteins and established substantial differences in their activities. While USP28 is a constitutively active dimer, USP25 presents an auto-inhibited tetramer. Our data indicate that the activation of USP25 is not achieved through substrate or ubiquitin binding. USP25 cancer-associated mutations lead to activation in vitro and in vivo, thereby providing a functional link between auto-inhibition and the cancer-promoting role of the enzyme. Our work led to the identification of significant differences between USP25 and USP28 and provided the molecular basis for the development of new and highly specific anti-cancer drugs.
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