1
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Zhang P, Liu D, Zang Y, Wang J, Liu Z, Zhu J, Li X, Ding Y. USP12 facilitates gastric cancer progression via stabilizing YAP. Cell Death Discov 2024; 10:174. [PMID: 38605077 PMCID: PMC11009230 DOI: 10.1038/s41420-024-01943-2] [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: 01/19/2024] [Revised: 03/29/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024] Open
Abstract
The dysregulation of Hippo signaling is a crucial factor driving the progression of gastric cancer, making the targeting of the Hippo pathway a promising therapeutic strategy. However, effective drugs targeting the Hippo/YAP axis remain unavailable. Thus, identifying potential therapeutic targets and mechanisms that inhibit the activity of the Hippo/YAP axis in gastric cancer is of paramount importance. The ubiquitination modification of the Hippo/YAP pathway plays a significant role in signaling transduction and cancer progression. In an effort to shed light on effective therapeutic targets, we conducted a screening using a deubiquitinase small interfering RNA library, leading to the identification of USP12 as an important deubiquitinase in the context of Hippo/YAP axis and the progression of gastric cancer. Our bioinformatic analysis further demonstrated a correlation between USP12 and poor survival, as well as a positive association with classical YAP target genes in gastric cancer samples. Notably, USP12 depletion was found to inhibit gastric cancer progression via the Hippo/YAP axis, whereas USP12 overexpression exhibited the opposite effect, promoting gastric cancer growth and enhancing YAP activity. Further studies through immuno-staining and immuno-precipitation assays indicated the nuclear localization of USP12 and its association with YAP to enhance YAP stability. Specifically, our findings revealed that USP12 could inhibit K48-linked poly-ubiquitination of YAP, predominantly at the K315 site. As a result, we have identified a novel regulatory mechanism involving USP12 and Hippo signaling in the progression of gastric cancer, with the potential for blockade of USP12 to materialize as a promising strategy for combating gastric cancer.
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Affiliation(s)
- Peng Zhang
- Department of General Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, PR China
| | - Dongyi Liu
- Department of Anaesthesiology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, PR China
| | - Yifeng Zang
- Department of General Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, PR China
| | - Jinqing Wang
- Department of General Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, PR China
| | - Ziping Liu
- Department of General Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, PR China.
| | - Jian Zhu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, 110000, Liaoning, PR China.
| | - Xin Li
- Xinxiang Key Laboratory of Tumor Migration and Invasion Precision Medicine, School of Medical Technology, Xinxiang Medical University, Xinxiang, 453003, Henan, PR China.
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Shenyang, 110000, Liaoning, PR China.
| | - Yinlu Ding
- Department of General Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033, Shandong, PR China.
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2
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Gao S, Wang Y, Xu Y, Liu L, Liu S. USP46 enhances tamoxifen resistance in breast cancer cells by stabilizing PTBP1 to facilitate glycolysis. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167011. [PMID: 38176460 DOI: 10.1016/j.bbadis.2023.167011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 12/10/2023] [Accepted: 12/27/2023] [Indexed: 01/06/2024]
Abstract
Tamoxifen (TAM) is the primary drug for treating estrogen receptor alpha-positive (ER+) breast cancer (BC). However, resistance to TAM can develop in some patients, limiting its therapeutic efficacy. The ubiquitin-specific protease (USP) family has been associated with the development, progression, and drug resistance of various cancers. To explore the role of USPs in TAM resistance in BC, we used qRT-PCR to compare USP expression between TAM-sensitive (MCF-7 and T47D) and TAM-resistant cells (MCF-7R and T47DR). We then modulated USP46 expression and examined its impact on cell proliferation, drug resistance (via CCK-8 and EdU experiments), glycolysis levels (using a glycolysis detection assay), protein interactions (confirmed by co-IP), and protein changes (analyzed through Western blotting). Our findings revealed that USP46 was significantly overexpressed in TAM-resistant BC cells, leading to the inhibition of the ubiquitin degradation of polypyrimidine tract-binding protein 1 (PTBP1). Overexpression of PTBP1 increased the PKM2/PKM1 ratio, promoted glycolysis, and intensified TAM resistance in BC cells. Knockdown of USP46 induced downregulation of PTBP1 protein by promoting its K48-linked ubiquitination, resulting in a decreased PKM2/PKM1 ratio, reduced glycolysis, and heightened TAM sensitivity in BC cells. In conclusion, this study highlights the critical role of the USP46/PTBP1/PKM2 axis in TAM resistance in BC. Targeted therapy against USP46 may represent a promising strategy to improve the prognosis of TAM-resistant patients.
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Affiliation(s)
- Shun Gao
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yuan Wang
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yingkun Xu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Liu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Shengchun Liu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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3
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Ng VH, Spencer Z, Neitzel LR, Nayak A, Loberg MA, Shen C, Kassel SN, Kroh HK, An Z, Anthony CC, Bryant JM, Lawson A, Goldsmith L, Benchabane H, Hansen AG, Li J, D'Souza S, Lebensohn AM, Rohatgi R, Weiss WA, Weiss VL, Williams C, Hong CC, Robbins DJ, Ahmed Y, Lee E. The USP46 complex deubiquitylates LRP6 to promote Wnt/β-catenin signaling. Nat Commun 2023; 14:6173. [PMID: 37798301 PMCID: PMC10556042 DOI: 10.1038/s41467-023-41836-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 09/20/2023] [Indexed: 10/07/2023] Open
Abstract
The relative abundance of Wnt receptors plays a crucial role in controlling Wnt signaling in tissue homeostasis and human disease. While the ubiquitin ligases that ubiquitylate Wnt receptors are well-characterized, the deubiquitylase that reverses these reactions remains unclear. Herein, we identify USP46, UAF1, and WDR20 (USP46 complex) as positive regulators of Wnt signaling in cultured human cells. We find that the USP46 complex is similarly required for Wnt signaling in Xenopus and zebrafish embryos. We demonstrate that Wnt signaling promotes the association between the USP46 complex and cell surface Wnt coreceptor, LRP6. Knockdown of USP46 decreases steady-state levels of LRP6 and increases the level of ubiquitylated LRP6. In contrast, overexpression of the USP46 complex blocks ubiquitylation of LRP6 by the ubiquitin ligases RNF43 and ZNFR3. Size exclusion chromatography studies suggest that the size of the USP46 cytoplasmic complex increases upon Wnt stimulation. Finally, we show that USP46 is essential for Wnt-dependent intestinal organoid viability, likely via its role in LRP6 receptor homeostasis. We propose a model in which the USP46 complex increases the steady-state level of cell surface LRP6 and facilitates the assembly of LRP6 into signalosomes via a pruning mechanism that removes sterically hindering ubiquitin chains.
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Affiliation(s)
- Victoria H Ng
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Zachary Spencer
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Leif R Neitzel
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Anmada Nayak
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Matthew A Loberg
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Chen Shen
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Sara N Kassel
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Heather K Kroh
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Zhenyi An
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Christin C Anthony
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Jamal M Bryant
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Amanda Lawson
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Lily Goldsmith
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Hassina Benchabane
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Amanda G Hansen
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
- STEMCELL Technologies, 1618 Station Street, Vancouver, BC, V6A 1B6, Canada
| | - Jingjing Li
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Starina D'Souza
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Andres M Lebensohn
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Rajat Rohatgi
- Departments of Biochemistry, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - William A Weiss
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, 94158, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Vivian L Weiss
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Charles Williams
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David J Robbins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20057, USA
| | - Yashi Ahmed
- Department of Molecular and Systems Biology and the Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.
| | - Ethan Lee
- Department of Cell & Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA.
- Program in Cancer Biology, Vanderbilt University, Nashville, TN, 37232, USA.
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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4
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Niu K, Shi Y, Lv Q, Wang Y, Chen J, Zhang W, Feng K, Zhang Y. Spotlights on ubiquitin-specific protease 12 (USP12) in diseases: from multifaceted roles to pathophysiological mechanisms. J Transl Med 2023; 21:665. [PMID: 37752518 PMCID: PMC10521459 DOI: 10.1186/s12967-023-04540-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/16/2023] [Indexed: 09/28/2023] Open
Abstract
Ubiquitination is one of the most significant post-translational modifications that regulate almost all physiological processes like cell proliferation, autophagy, apoptosis, and cell cycle progression. Contrary to ubiquitination, deubiquitination removes ubiquitin from targeted protein to maintain its stability and thus regulate cellular homeostasis. Ubiquitin-Specific Protease 12 (USP12) belongs to the biggest family of deubiquitinases named ubiquitin-specific proteases and has been reported to be correlated with various pathophysiological processes. In this review, we initially introduce the structure and biological functions of USP12 briefly and summarize multiple substrates of USP12 as well as the underlying mechanisms. Moreover, we discuss the influence of USP12 on tumorigenesis, tumor immune microenvironment (TME), disease, and related signaling pathways. This study also provides updated information on the roles and functions of USP12 in different types of cancers and other diseases, including prostate cancer, breast cancer, lung cancer, liver cancer, cardiac hypertrophy, multiple myeloma, and Huntington's disease. Generally, this review sums up the research advances of USP12 and discusses its potential clinical application value which deserves more exploration in the future.
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Affiliation(s)
- Kaiyi Niu
- Hepato-Pancreato-Biliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, Jiangsu Province, China
| | - Yanlong Shi
- Hepato-Pancreato-Biliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, Jiangsu Province, China
| | - Qingpeng Lv
- Hepato-Pancreato-Biliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, Jiangsu Province, China
| | - Yizhu Wang
- Hepato-Pancreato-Biliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, Jiangsu Province, China
| | - Jiping Chen
- Hepato-Pancreato-Biliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, Jiangsu Province, China
| | - Wenning Zhang
- Hepato-Pancreato-Biliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, Jiangsu Province, China
| | - Kung Feng
- Hepato-Pancreato-Biliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, Jiangsu Province, China
| | - Yewei Zhang
- Hepato-Pancreato-Biliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210003, Jiangsu Province, China.
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5
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Fu Y, Zhan X, You X, Nie D, Mai H, Chen Y, He S, Sheng J, Zeng Z, Li H, Li J, Hu S. USP12 promotes antiviral responses by deubiquitinating and stabilizing IFI16. PLoS Pathog 2023; 19:e1011480. [PMID: 37410794 PMCID: PMC10353808 DOI: 10.1371/journal.ppat.1011480] [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: 02/13/2023] [Revised: 07/18/2023] [Accepted: 06/13/2023] [Indexed: 07/08/2023] Open
Abstract
Deubiquitinating enzymes (DUBs) regulate antiviral immune response through targeting DNA sensor signaling pathway members. As one of the DNA sensors, interferon (IFN)-γ inducible protein 16 (IFI16) play a major role in response to virus infections through activating the canonical STING/TBK-1/IRF3 signaling pathway. Only a few studies discuss the function of DUBs in IFI16-mediated antiviral response. Ubiquitin-specific protease 12 (USP12), which is one of the major members of the USP family, participates in various biological functions. However, whether USP12 regulates the nucleic acid sensor to modulate antiviral immune responses has not yet been elucidated. In this study, we found that knockout or knockdown of USP12 impaired the HSV-1-induced expressions of IFN-β, CCL-5, IL-6, and downstream interferon-stimulated genes (ISGs). Moreover, USP12 deficiency increased HSV-1 replication and host susceptibility to HSV-1 infection. Mechanistically, USP12 inhibited the proteasome-dependent degradation of IFI16 through its deubiquitinase activity, thereby maintaining IFI16 stability and promoting IFI16-STING-IRF3- and p65-mediated antiviral signaling. Overall, our findings demonstrate an essential role of USP12 in DNA-sensing signaling and contribute to the understanding of deubiquitination-mediated regulation of innate antiviral responses.
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Affiliation(s)
- Yuling Fu
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Xiaoxia Zhan
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaolong You
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Dingnai Nie
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Haiyan Mai
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Yitian Chen
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Shitong He
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Junli Sheng
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Zhijie Zeng
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hongwei Li
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Jinlong Li
- Institute of Biotherapy, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Shengfeng Hu
- Institute of Molecular Immunology, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
- The Second Affiliated Hospital, The State Key Laboratory of Respiratory Disease, Guangdong Provincial Key Laboratory of Allergy & Clinical Immunology, Guangzhou Medical University, Guangzhou, China
- Department of Rheumatology and Clinical Immunology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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6
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Estavoyer B, Messmer C, Echbicheb M, Rudd CE, Milot E, Affar EB. Mechanisms orchestrating the enzymatic activity and cellular functions of deubiquitinases. J Biol Chem 2022; 298:102198. [PMID: 35764170 PMCID: PMC9356280 DOI: 10.1016/j.jbc.2022.102198] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 11/30/2022] Open
Abstract
Deubiquitinases (DUBs) are required for the reverse reaction of ubiquitination and act as major regulators of ubiquitin signaling processes. Emerging evidence suggests that these enzymes are regulated at multiple levels in order to ensure proper and timely substrate targeting and to prevent the adverse consequences of promiscuous deubiquitination. The importance of DUB regulation is highlighted by disease-associated mutations that inhibit or activate DUBs, deregulating their ability to coordinate cellular processes. Here, we describe the diverse mechanisms governing protein stability, enzymatic activity, and function of DUBs. In particular, we outline how DUBs are regulated by their protein domains and interacting partners. Intramolecular interactions can promote protein stability of DUBs, influence their subcellular localization, and/or modulate their enzymatic activity. Remarkably, these intramolecular interactions can induce self-deubiquitination to counteract DUB ubiquitination by cognate E3 ubiquitin ligases. In addition to intramolecular interactions, DUBs can also oligomerize and interact with a wide variety of cellular proteins, thereby forming obligate or facultative complexes that regulate their enzymatic activity and function. The importance of signaling and post-translational modifications in the integrated control of DUB function will also be discussed. While several DUBs are described with respect to the multiple layers of their regulation, the tumor suppressor BAP1 will be outlined as a model enzyme whose localization, stability, enzymatic activity, and substrate recognition are highly orchestrated by interacting partners and post-translational modifications.
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Affiliation(s)
- Benjamin Estavoyer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Clémence Messmer
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Mohamed Echbicheb
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada
| | - Christopher E Rudd
- Laboratory for Cell Signaling in Immunotherapy, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - Eric Milot
- Laboratory for Malignant Hematopoiesis and Epigenetic Regulation of Gene Expression, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada
| | - El Bachir Affar
- Laboratory for Cell Signaling and Cancer, Maisonneuve-Rosemont Hospital Research Center, H1T 2M4, Montréal, Québec, Canada; Department of Medicine, University of Montréal, Montréal H3C 3J7, Québec, Canada.
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7
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Lange SM, Armstrong LA, Kulathu Y. Deubiquitinases: From mechanisms to their inhibition by small molecules. Mol Cell 2021; 82:15-29. [PMID: 34813758 DOI: 10.1016/j.molcel.2021.10.027] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/21/2022]
Abstract
Deubiquitinases (DUBs) are specialized proteases that remove ubiquitin from substrates or cleave within ubiquitin chains to regulate ubiquitylation and therefore play important roles in eukaryotic biology. Dysregulation of DUBs is implicated in several human diseases, highlighting the importance of DUB function. In addition, many pathogenic bacteria and viruses encode and deploy DUBs to manipulate host immune responses and establish infectious diseases in humans and animals. Hence, therapeutic targeting of DUBs is an increasingly explored area that requires an in-depth mechanistic understanding of human and pathogenic DUBs. In this review, we summarize the multiple layers of regulation that control autoinhibition, activation, and substrate specificity of DUBs. We discuss different strategies to inhibit DUBs and the progress in developing selective small-molecule DUB inhibitors. Finally, we propose a classification system of DUB inhibitors based on their mode of action.
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Affiliation(s)
- Sven M Lange
- 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
| | - Yogesh Kulathu
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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8
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USP12 promotes CD4 + T cell responses through deubiquitinating and stabilizing BCL10. Cell Death Differ 2021; 28:2857-2870. [PMID: 33941870 PMCID: PMC8481463 DOI: 10.1038/s41418-021-00787-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 04/07/2021] [Accepted: 04/15/2021] [Indexed: 02/07/2023] Open
Abstract
Deubiquitinases (DUBs) regulate diverse biological processes and represent a novel class of drug targets. However, the biological function of only a small fraction of DUBs, especially in adaptive immune response regulation, is well-defined. In this study, we identified DUB ubiquitin-specific peptidase 12 (USP12) as a critical regulator of CD4+ T cell activation. USP12 plays an intrinsic role in promoting the CD4+ T cell phenotype, including differentiation, activation, and proliferation. Although USP12-deficient CD4+ T cells protected mice from autoimmune diseases, the immune response against bacterial infection was subdued. USP12 stabilized B cell lymphoma/leukemia 10 (BCL10) by deubiquitinating, and thereby activated the NF-κB signaling pathway. Interestingly, this USP12 regulatory mechanism was identified in CD4+ T cells, but not in CD8+ T cells. Our study results showed that USP12 activated CD4+ T cell signaling, and targeting USP12 might help develop therapeutic interventions for treating inflammatory diseases or pathogen infections.
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9
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Olazabal-Herrero A, Bilbao-Arribas M, Carlevaris O, Sendino M, Varela-Martinez E, Jugo BM, Berra E, Rodriguez JA. The dystrophia myotonica WD repeat-containing protein DMWD and WDR20 differentially regulate USP12 deubiquitinase. FEBS J 2021; 288:5943-5963. [PMID: 33844468 DOI: 10.1111/febs.15875] [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: 11/13/2020] [Revised: 03/05/2021] [Accepted: 04/09/2021] [Indexed: 11/26/2022]
Abstract
Despite its potential clinical relevance, the product of the DMWD (dystrophia myotonica, WD repeat containing) gene is a largely uncharacterized protein. The DMWD amino acid sequence is similar to that of WDR20, a known regulator of the USP12 and USP46 deubiquitinases (DUBs). Here, we apply a combination of in silico and experimental methods to investigate several aspects of DMWD biology. Molecular evolution and phylogenetic analyses reveal that WDR20 and DMWD, similar to USP12 and USP46, arose by duplication of a common ancestor during the whole genome duplication event in the vertebrate ancestor lineage. The analysis of public human gene expression datasets suggests that DMWD expression is positively correlated with USP12 expression in normal tissues and negatively correlated with WDR20 expression in tumors. Strikingly, a survey of the annotated interactome for DMWD and WDR20 reveals a largely nonoverlapping set of interactors for these proteins. Experimentally, we first confirmed that DMWD binds both USP12 and USP46 through direct coimmunoprecipitation of epitope-tagged proteins. We found that DMWD and WDR20 share the same binding interface in USP12, suggesting that their interaction with the DUB may be mutually exclusive. Finally, we show that both DMWD and WDR20 promote USP12 enzymatic activity, but they differentially modulate the subcellular localization of the DUB. Altogether, our findings suggest a model whereby mutually exclusive binding of DMWD and WDR20 to USP12 may lead to formation of deubiquitinase complexes with distinct subcellular localization, potentially targeting different substrate repertoires.
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Affiliation(s)
- Anne Olazabal-Herrero
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Martin Bilbao-Arribas
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Onintza Carlevaris
- Cell Signaling and Metabolism Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia, Spain
| | - Maria Sendino
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Endika Varela-Martinez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Begoña M Jugo
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Edurne Berra
- Cell Signaling and Metabolism Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia, Spain.,CIBERONC, Madrid, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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10
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Structural basis of FANCD2 deubiquitination by USP1-UAF1. Nat Struct Mol Biol 2021; 28:356-364. [PMID: 33795880 DOI: 10.1038/s41594-021-00576-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/22/2021] [Indexed: 12/19/2022]
Abstract
Ubiquitin-specific protease 1 (USP1) acts together with the cofactor UAF1 during DNA repair processes to specifically remove monoubiquitin signals. One substrate of the USP1-UAF1 complex is the monoubiquitinated FANCI-FANCD2 heterodimer, which is involved in the repair of DNA interstrand crosslinks via the Fanconi anemia pathway. Here we determine structures of human USP1-UAF1 with and without ubiquitin and bound to monoubiquitinated FANCI-FANCD2. The crystal structures of USP1-UAF1 reveal plasticity in USP1 and key differences to USP12-UAF1 and USP46-UAF1, two related proteases. A cryo-EM reconstruction of USP1-UAF1 in complex with monoubiquitinated FANCI-FANCD2 highlights a highly orchestrated deubiquitination process, with USP1-UAF1 driving conformational changes in the substrate. An extensive interface between UAF1 and FANCI, confirmed by mutagenesis and biochemical assays, provides a molecular explanation for the requirement of both proteins, despite neither being directly involved in catalysis. Overall, our data provide molecular details of USP1-UAF1 regulation and substrate recognition.
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Deubiquitylating enzymes in neuronal health and disease. Cell Death Dis 2021; 12:120. [PMID: 33483467 PMCID: PMC7822931 DOI: 10.1038/s41419-020-03361-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022]
Abstract
Ubiquitylation and deubiquitylation play a pivotal role in protein homeostasis (proteostasis). Proteostasis shapes the proteome landscape in the human brain and its impairment is linked to neurodevelopmental and neurodegenerative disorders. Here we discuss the emerging roles of deubiquitylating enzymes in neuronal function and survival. We provide an updated perspective on the genetics, physiology, structure, and function of deubiquitylases in neuronal health and disease. ![]()
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Regulation of Deubiquitinating Enzymes by Post-Translational Modifications. Int J Mol Sci 2020; 21:ijms21114028. [PMID: 32512887 PMCID: PMC7312083 DOI: 10.3390/ijms21114028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 01/04/2023] Open
Abstract
Ubiquitination and deubiquitination play a critical role in all aspects of cellular processes, and the enzymes involved are tightly regulated by multiple factors including posttranslational modifications like most other proteins. Dysfunction or misregulation of these enzymes could have dramatic physiological consequences, sometimes leading to diseases. Therefore, it is important to have a clear understanding of these regulatory processes. Here, we have reviewed the posttranslational modifications of deubiquitinating enzymes and their consequences on the catalytic activity, stability, abundance, localization, and interaction with the partner proteins.
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