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Tao Y, Xu X, Shen R, Miao X, He S. Roles of ubiquitin‑specific protease 13 in normal physiology and tumors (Review). Oncol Lett 2024; 27:58. [PMID: 38192665 PMCID: PMC10773187 DOI: 10.3892/ol.2023.14191] [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: 09/18/2023] [Accepted: 11/24/2023] [Indexed: 01/10/2024] Open
Abstract
Ubiquitin-specific protease 13 (USP13) is one of the most important deubiquitinases involved in various diseases. As deubiquitinases are components of the deubiquitination process, a significant post-translational modification, they are potential treatment targets for different diseases. With recent technological developments, the structure of USP13 and its pathological and physiological functions have been investigated. However, USP13 expression and function differ in various diseases, especially in tumors, and the associated mechanisms are complex and remain to be fully investigated. The present review summarized the recent discoveries and the current understanding of the USP13 function in tumors.
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Affiliation(s)
- Yun Tao
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
- Department of Clinical Laboratory, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Xiaohong Xu
- Department of Hematological Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Rong Shen
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Xiaobing Miao
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
| | - Song He
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu 226000, P.R. China
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2
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Chen W, Ji G, Wu R, Fang C, Lu H. Mass spectrometry-based candidate substrate and site identification of PTM enzymes. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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3
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Abstract
The combination of large-scale protein separation techniques, sophisticated mass spectrometry, and systems bioinformatics has led to the establishment of proteomics as a distinct discipline within the wider field of protein biochemistry. Both discovery proteomics and targeted proteomics are widely used in biological and biomedical research, whereby the analytical approaches can be broadly divided into proteoform-centric top-down proteomics versus peptide-centric bottom-up proteomics. This chapter outlines the scientific value of top-down proteomics and describes how fluorescence two-dimensional difference gel electrophoresis can be combined with the systematic analysis of crucial post-translational modifications. The concept of on-membrane digestion following the electrophoretic transfer of proteins and the usefulness of comparative two-dimensional immunoblotting are discussed.
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Affiliation(s)
- Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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4
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Dowling P, Bazou D. Identification of Ubiquitination-Associated Proteins Using 2D-DIGE. Methods Mol Biol 2023; 2596:83-96. [PMID: 36378432 DOI: 10.1007/978-1-0716-2831-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ubiquitination is a post-translational modification, in which a small regulatory protein (~8.6 kDa) is tagged as a single moiety or as a chain to target proteins. Ubiquitination is the most versatile cellular regulatory mechanism, essential to the physiological and pathophysiological cellular events that regulate protein turnover, gene transcription, cell cycle progression, DNA repair, apoptosis, viral budding, and receptor-mediated endocytosis. Changes and abnormalities within the ubiquitination process can result in a plethora of diseases, including various cancers. The ubiquitination process is tightly controlled in a stepwise manner by four enzymes: E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, E3 ubiquitin-ligating enzymes, and deubiquitinating proteases. Using fluorescence two-dimensional difference gel electrophoresis (2D-DIGE) to detect and quantitate cellular proteins associated with the ubiquitination process will facilitate the evaluation of this post-translational modification associated with the pathophysiological phenotype.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, Dublin, Ireland.
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5
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Elu N, Osinalde N, Ramirez J, Presa N, Rodriguez JA, Prieto G, Mayor U. Identification of substrates for human deubiquitinating enzymes (DUBs): An up-to-date review and a case study for neurodevelopmental disorders. Semin Cell Dev Biol 2022; 132:120-131. [PMID: 35042675 DOI: 10.1016/j.semcdb.2022.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 12/15/2022]
Abstract
Similar to the reversal of kinase-mediated protein phosphorylation by phosphatases, deubiquitinating enzymes (DUBs) oppose the action of E3 ubiquitin ligases and reverse the ubiquitination of proteins. A total of 99 human DUBs, classified in 7 families, allow in this way for a precise control of cellular function and homeostasis. Ubiquitination regulates a myriad of cellular processes, and is altered in many pathological conditions. Thus, ubiquitination-regulating enzymes are increasingly regarded as potential candidates for therapeutic intervention. In this context, given the predicted easier pharmacological control of DUBs relative to E3 ligases, a significant effort is now being directed to better understand the processes and substrates regulated by each DUB. Classical studies have identified specific DUB substrate candidates by traditional molecular biology techniques in a case-by-case manner. Lately, single experiments can identify thousands of ubiquitinated proteins at a specific cellular context and narrow down which of those are regulated by a given DUB, thanks to the development of new strategies to isolate and enrich ubiquitinated material and to improvements in mass spectrometry detection capabilities. Here we present an overview of both types of studies, discussing the criteria that, in our view, need to be fulfilled for a protein to be considered as a high-confidence substrate of a given DUB. Applying these criteria, we have manually reviewed the relevant literature currently available in a systematic manner, and identified 650 high-confidence substrates of human DUBs. We make this information easily accessible to the research community through an updated version of the DUBase website (https://ehubio.ehu.eus/dubase/). Finally, in order to illustrate how this information can contribute to a better understanding of the physiopathological role of DUBs, we place a special emphasis on a subset of these enzymes that have been associated with neurodevelopmental disorders.
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Affiliation(s)
- Nagore Elu
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, UPV/EHU, Vitoria-Gasteiz 01006, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Natalia Presa
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain
| | - Gorka Prieto
- Department of Communications Engineering, University of the Basque Country (UPV/EHU), Bilbao 48013, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa 48940, Spain; Ikerbasque, Basque Foundation for Science, Bilbao 48013, Spain.
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6
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Liu X, Balaraman K, Lynch CC, Hebron M, Shah PK, Hu S, Stevenson M, Wolf C, Moussa C. Inhibition of Ubiquitin-Specific Protease-13 Improves Behavioral Performance in Alpha-Synuclein Expressing Mice. Int J Mol Sci 2022; 23:ijms23158131. [PMID: 35897705 PMCID: PMC9330474 DOI: 10.3390/ijms23158131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 01/21/2023] Open
Abstract
Ubiquitin-Specific Protease-13 (USP13) promotes protein de-ubiquitination. USP13 levels are upregulated in post-mortem Parkinson's disease, whereas USP13 knockdown via shRNA reduces alpha-synuclein levels in animal models. We studied the role of USP13 in knockout mice expressing lentiviral human alpha-synuclein and investigated the impact of a small molecule inhibitor of USP13, BK50118-C, on alpha-synuclein pathology and animal behavior. Alpha-synuclein was expressed unilaterally in substantia nigra (SN) of USP13 deficient mice that were treated with a daily intraperitoneal injection of 100 mg/kg BK50118-C or DMSO for four consecutive weeks, and behavioral and functional assays were performed. Wild-type USP13+/+ mice expressing lentiviral human alpha-synuclein showed motor and behavioral defects that were not seen in partially (USP13+/-) or completely (USP13-/-) deficient USP13 mice. BK50118-C displayed a wide and favorable therapeutic dose range in vivo. Treatment with BK50118-C significantly reduced ubiquitinated alpha-synuclein, increased dopamine levels, and improved motor and behavioral symptoms in wild-type (USP13+/+), but not USP13 deficient, mice. These data suggest that USP13 is critical to the neuropathology of alpha-synuclein, whereas a novel small molecule inhibitor of USP13 is a potential therapeutic agent of alpha-synucleinopathies.
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Affiliation(s)
- Xiaoguang Liu
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
- Correspondence: (X.L.); (C.M.); Tel.: +1-202-687-7328 (C.M.); Fax: +1-202-687-7378 (C.M.)
| | - Kaluvu Balaraman
- Department of Chemistry, Georgetown University & Medicinal Chemistry Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; (K.B.); (C.C.L.); (C.W.)
| | - Ciarán C. Lynch
- Department of Chemistry, Georgetown University & Medicinal Chemistry Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; (K.B.); (C.C.L.); (C.W.)
| | - Michaeline Hebron
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
| | - Priya Ketankumar Shah
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
| | - Shicheng Hu
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
| | - Max Stevenson
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
| | - Christian Wolf
- Department of Chemistry, Georgetown University & Medicinal Chemistry Shared Resource, Georgetown University Medical Center, Washington, DC 20057, USA; (K.B.); (C.C.L.); (C.W.)
| | - Charbel Moussa
- Department of Neurology, Translational Neurotherapeutics Program, Laboratory for Dementia and Parkinsonism, Lewy Body Dementia Association, Research Center of Excellence, Georgetown University Medical Center, Washington, DC 20057, USA; (M.H.); (P.K.S.); (S.H.); (M.S.)
- Correspondence: (X.L.); (C.M.); Tel.: +1-202-687-7328 (C.M.); Fax: +1-202-687-7378 (C.M.)
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7
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Hu S, Bai S, Dai Y, Yang N, Li J, Zhang X, Wang F, Zhao B, Bao G, Chen Y, Wu X. Deubiquitination of MITF-M Regulates Melanocytes Proliferation and Apoptosis. Front Mol Biosci 2021; 8:692724. [PMID: 34179099 PMCID: PMC8221579 DOI: 10.3389/fmolb.2021.692724] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/01/2021] [Indexed: 11/29/2022] Open
Abstract
Microphthalmia-associated transcription factor-M (MITF-M) is the key gene in the proliferation and differentiation of melanocytes, which undergoes an array of post-translation modifications. As shown in our previous study, deubiquitinase USP13 is directly involved in melanogenesis. However, it is still ambiguous that the effect of USP13-mediated MITF-M expression on melanocytes proliferation and apoptosis. Herein, we found that MITF-M overexpressing melanocytes showed high cell proliferation, reduced apoptosis, and increased melanin levels. Besides, melanin-related genes, TYR, DCT, GPNMB, and PMEL, were significantly up-regulated in MITF-M overexpressing melanocytes. Furthermore, Exogenous USP13 significantly upregulated the endogenous MITF-M protein level, downregulated USP13 significantly inhibited MITF-M protein levels, without altering MITF-M mRNA expression. In addition, USP13 upregulation mitigated the MITF-M degradation and significantly increased the half-life of MITF-M. Also, USP13 stabilized the exogenous MITF protein levels. In conclusion, the MITF-M level was regulated by USP13 deubiquitinase in melanocytes, affecting melanocytes proliferation and apoptosis. This study provides the theoretical basis for coat color transformation that could be useful in the development of the new breed in fur animals.
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Affiliation(s)
- Shuaishuai Hu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shaocheng Bai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yingying Dai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naisu Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jiali Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiyu Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Fan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Bohao Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guolian Bao
- Animal Husbandry and Veterinary Research Institute Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
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8
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Wu Y, Zhang Y, Liu C, Zhang Y, Wang D, Wang S, Wu Y, Liu F, Li Q, Liu X, Zaky MY, Yan D, Liu S. Amplification of USP13 drives non-small cell lung cancer progression mediated by AKT/MAPK signaling. Biomed Pharmacother 2019; 114:108831. [PMID: 30986623 DOI: 10.1016/j.biopha.2019.108831] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/31/2022] Open
Abstract
USP13 is emerging as a potential target in cancer therapy. However, the effect of USP13 on tumor progression is controversial. Here we focused on non-small cell lung cancer (NSCLC), a common cancer with high mortality, and studied the role of USP13 in tumor growth. By analysis of multi-level genetic database, we found USP13 is high expressed in heart among healthy primary tissues and is most amplified in lung cancer. Clinical samples of NSCLC showed tumor exhibited high USP13 level compared with adjacent normal tissues. We further utilized lung adenocarcinoma A549 and squamous carcinoma H226 cells as cell model and investigated USP13 effect by USP13 knockdown. As a results, downregulation of USP13 dramatically inhibited A549 and H226 cell proliferation by AKT/MAPK signaling and suppressed tumor growth in nude mice. Collectively, we identified USP13 as a tumor promoter in NSCLC and provide a promising target in cancer therapy.
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Affiliation(s)
- Yue Wu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Yingqiu Zhang
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Congcong Liu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Yang Zhang
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Duchuang Wang
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Shanshan Wang
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Yueguang Wu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Fang Liu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Qiong Li
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Xiuxiu Liu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China
| | - Mohamed Y Zaky
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China; Molecular Physiology Division, Department of Zoology, Faculty of Science, Beni-Suef University, Egypt
| | - Dong Yan
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China.
| | - Shuyan Liu
- The Second Affiliated Hospital, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, PR China.
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Kalogeropoulos K, Treschow AF, Auf dem Keller U, Escalante T, Rucavado A, Gutiérrez JM, Laustsen AH, Workman CT. Protease Activity Profiling of Snake Venoms Using High-Throughput Peptide Screening. Toxins (Basel) 2019; 11:toxins11030170. [PMID: 30893860 PMCID: PMC6468401 DOI: 10.3390/toxins11030170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/13/2019] [Accepted: 03/15/2019] [Indexed: 01/22/2023] Open
Abstract
Snake venom metalloproteinases (SVMPs) and snake venom serine proteinases (SVSPs) are among the most abundant enzymes in many snake venoms, particularly among viperids. These proteinases are responsible for some of the clinical manifestations classically seen in viperid envenomings, including hemorrhage, necrosis, and coagulopathies. The objective of this study was to investigate the enzymatic activities of these proteins using a high-throughput peptide library to screen for the proteinase targets of the venoms of five viperid (Echis carinatus, Bothrops asper, Daboia russelii, Bitis arietans, Bitis gabonica) and one elapid (Naja nigricollis) species of high medical importance. The proteinase activities of these venoms were each tested against 360 peptide substrates, yielding 2160 activity profiles. A nonlinear regression model that accurately described the observed enzymatic activities was fitted to the experimental data, allowing for the comparison of cleavage rates across species. In this study, previously unknown protein targets of snake venom proteinases were identified, potentially implicating novel human and animal proteins that may be involved in the pathophysiology of viper envenomings. The functional relevance of these targets was further evaluated and discussed. These new findings may contribute to our understanding of the clinical manifestations and underlying biochemical mechanisms of snakebite envenoming by viperid species.
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Affiliation(s)
| | | | - Ulrich Auf dem Keller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Teresa Escalante
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica.
| | - Alexandra Rucavado
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica.
| | - José María Gutiérrez
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José 11501-2060, Costa Rica.
| | | | - Christopher T Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark.
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