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Kim YJ, Lee HJ, Kim KH, Cho SP, Jung JY. OTUD7B knockdown inhibits proliferation and autophagy through AKT/mTOR signaling pathway in human prostate cancer cell. Discov Oncol 2024; 15:247. [PMID: 38935308 PMCID: PMC11211289 DOI: 10.1007/s12672-024-01073-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Prostate cancer (PCa) is the second leading disease of cancer-related death in men around the world, and it is almost impossible to treat advanced PCa. OTUD7B is a member of the deubiquitinase family that undergoes a post-translational transformation process, which is essential for cell stability and signaling and is known to play a critical role in cancer. However, its role in PCa has not been discovered. The aim of the study was to investigate the expression and mechanism of OTUD7B in PCa cells. According to the database, high OTUD7B expression showed a poor prognosis. Therefore, we downregulated OTUD7B using siRNA and confirmed the role of OTUD7B in PC3 prostate cancer cells. OTUD7B knockdown effectively induced apoptosis and inhibited the proliferation in PC3 cells. OTUD7B knockdown inhibited autophagy through AKT/mTOR signaling. We also confirmed the relationship between AKT/mTOR signaling and autophagy through rapamycin, an mTOR inhibitor. Taken together, OTUD7B promotes the proliferation, and autophagy, and inhibits apoptosis of prostate cancer cells via the AKT/mTOR signaling pathway.
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Affiliation(s)
- Yae Ji Kim
- Department of Veterinary Medicine, Institute of Veterinary Science, College of Veterinary Medicine, Chungnam National University, 220 Gung-Dong, Yusung-Gu, Daejeon, 34134, Republic of Korea
| | - Hui Ju Lee
- Department of Veterinary Medicine, Institute of Veterinary Science, College of Veterinary Medicine, Chungnam National University, 220 Gung-Dong, Yusung-Gu, Daejeon, 34134, Republic of Korea
| | - Kyung Hyun Kim
- Department of Veterinary Medicine, Institute of Veterinary Science, College of Veterinary Medicine, Chungnam National University, 220 Gung-Dong, Yusung-Gu, Daejeon, 34134, Republic of Korea
| | - Sung Pil Cho
- Department of Veterinary Medicine, Institute of Veterinary Science, College of Veterinary Medicine, Chungnam National University, 220 Gung-Dong, Yusung-Gu, Daejeon, 34134, Republic of Korea
| | - Ju Young Jung
- Department of Veterinary Medicine, Institute of Veterinary Science, College of Veterinary Medicine, Chungnam National University, 220 Gung-Dong, Yusung-Gu, Daejeon, 34134, Republic of Korea.
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Foster BM, Wang Z, Schmidt CK. DoUBLing up: ubiquitin and ubiquitin-like proteases in genome stability. Biochem J 2024; 481:515-545. [PMID: 38572758 PMCID: PMC11088880 DOI: 10.1042/bcj20230284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Maintaining stability of the genome requires dedicated DNA repair and signalling processes that are essential for the faithful duplication and propagation of chromosomes. These DNA damage response (DDR) mechanisms counteract the potentially mutagenic impact of daily genotoxic stresses from both exogenous and endogenous sources. Inherent to these DNA repair pathways is the activity of protein factors that instigate repair processes in response to DNA lesions. The regulation, coordination, and orchestration of these DDR factors is carried out, in a large part, by post-translational modifications, such as phosphorylation, ubiquitylation, and modification with ubiquitin-like proteins (UBLs). The importance of ubiquitylation and UBLylation with SUMO in DNA repair is well established, with the modified targets and downstream signalling consequences relatively well characterised. However, the role of dedicated erasers for ubiquitin and UBLs, known as deubiquitylases (DUBs) and ubiquitin-like proteases (ULPs) respectively, in genome stability is less well established, particularly for emerging UBLs such as ISG15 and UFM1. In this review, we provide an overview of the known regulatory roles and mechanisms of DUBs and ULPs involved in genome stability pathways. Expanding our understanding of the molecular agents and mechanisms underlying the removal of ubiquitin and UBL modifications will be fundamental for progressing our knowledge of the DDR and likely provide new therapeutic avenues for relevant human diseases, such as cancer.
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Affiliation(s)
- Benjamin M. Foster
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Zijuan Wang
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
| | - Christine K. Schmidt
- Manchester Cancer Research Centre (MCRC), Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, 555 Wilmslow Road, Manchester M20 4GJ, U.K
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3
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Gao ST, Xin X, Wang ZY, Hu YY, Feng Q. USP5: Comprehensive insights into structure, function, biological and disease-related implications, and emerging therapeutic opportunities. Mol Cell Probes 2024; 73:101944. [PMID: 38049041 DOI: 10.1016/j.mcp.2023.101944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023]
Abstract
Ubiquitin specific protease 5 (USP5) is a vital deubiquitinating enzyme that regulates various physiological functions by removing ubiquitin chains from target proteins. This review provides an overview of the structural and functional characteristics of USP5. Additionally, we discuss the role of USP5 in regulating diverse cellular processes, including cell proliferation, apoptosis, DNA double-strand damage, methylation, heat stress, and protein quality control, by targeting different substrates. Furthermore, we describe the involvement of USP5 in several pathological conditions such as tumors, pathological pain, developmental abnormalities, inflammatory diseases, and virus infection. Finally, we introduce newly developed inhibitors of USP5. In conclusion, investigating the novel functions and substrates of USP5, elucidating the underlying mechanisms of USP5-substrate interactions, intensifying the development of inhibitors, and exploring the upstream regulatory mechanisms of USP5 in detail can provide a new theoretical basis for the treatment of various diseases, including cancer, which is a promising research direction with considerable potential. Overall, USP5 plays a critical role in regulating various physiological and pathological processes, and investigating its novel functions and regulatory mechanisms may have significant implications for the development of therapeutic strategies for cancer and other diseases.
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Affiliation(s)
- Si-Ting Gao
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xin Xin
- Key Laboratory of Liver and Kidney Diseases, Shanghai University of Traditional Chinese Medicine, Ministry of Education, Shanghai, China
| | - Zhuo-Yuan Wang
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi-Yang Hu
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Key Laboratory of Liver and Kidney Diseases, Shanghai University of Traditional Chinese Medicine, Ministry of Education, Shanghai, China; Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shanghai, China.
| | - Qin Feng
- Institute of Liver Diseases, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China; Key Laboratory of Liver and Kidney Diseases, Shanghai University of Traditional Chinese Medicine, Ministry of Education, Shanghai, China; Central Laboratory, ShuGuang Hospital Affiliated to Shanghai University of Chinese Traditional Medicine, Shanghai, China; Shanghai Key Laboratory of Traditional Chinese Clinical Medicine, Shanghai, China.
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4
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Li J, Zhang B, Feng Z, An D, Zhou Z, Wan C, Hu Y, Sun Y, Wang Y, Liu X, Wei W, Yang X, Meng J, Che M, Sheng Y, Wu B, Wen L, Huang F, Li Y, Yang K. Stabilization of KPNB1 by deubiquitinase USP7 promotes glioblastoma progression through the YBX1-NLGN3 axis. J Exp Clin Cancer Res 2024; 43:28. [PMID: 38254206 DOI: 10.1186/s13046-024-02954-8] [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: 09/17/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most common malignant tumor of the central nervous system. It is an aggressive tumor characterized by rapid proliferation, diffuse tumor morphology, and poor prognosis. Unfortunately, current treatments, such as surgery, radiotherapy, and chemotherapy, are unable to achieve good outcomes. Therefore, there is an urgent need to explore new treatment targets. A detailed mechanistic exploration of the role of the nuclear pore transporter KPNB1 in GBM is lacking. This study demonstrated that KPNB1 regulated GBM progression through a transcription factor YBX1 to promote the expression of post-protrusion membrane protein NLGN3. This regulation was mediated by the deubiquitinating enzyme USP7. METHODS A tissue microarray was used to measure the expression of KPNB1 and USP7 in glioma tissues. The effects of KPNB1 knockdown on the tumorigenic properties of glioma cells were characterized by colony formation assays, Transwell migration assay, EdU proliferation assays, CCK-8 viability assays, and apoptosis analysis using flow cytometry. Transcriptome sequencing identified NLGN3 as a downstream molecule that is regulated by KPNB1. Mass spectrometry and immunoprecipitation were performed to analyze the potential interaction between KPNB1 and YBX1. Moreover, the nuclear translocation of YBX1 was determined with nuclear-cytoplasmic fractionation and immunofluorescence staining, and chromatin immunoprecipitation assays were conducted to study DNA binding with YBX1. Ubiquitination assays were performed to determine the effects of USP7 on KPNB1 stability. The intracranial orthotopic tumor model was used to detect the efficacy in vivo. RESULTS In this study, we found that the nuclear receptor KPNB1 was highly expressed in GBM and could mediate the nuclear translocation of macromolecules to promote GBM progression. Knockdown of KPNB1 inhibited the progression of GBM, both in vitro and in vivo. In addition, we found that KPNB1 could regulate the downstream expression of Neuroligin-3 (NLGN3) by mediating the nuclear import of transcription factor YBX1, which could bind to the NLGN3 promoter. NLGN3 was necessary and sufficient to promote glioma cell growth. Furthermore, we found that deubiquitinase USP7 played a critical role in stabilizing KPNB1 through deubiquitination. Knockdown of USP7 expression or inhibition of its activity could effectively impair GBM progression. In vivo experiments also demonstrated the promoting effects of USP7, KPNB1, and NLGN3 on GBM progression. Overall, our results suggested that KPNB1 stability was enhanced by USP7-mediated deubiquitination, and the overexpression of KPNB1 could promote GBM progression via the nuclear translocation of YBX1 and the subsequent increase in NLGN3 expression. CONCLUSION This study identified a novel and targetable USP7/KPNB1/YBX1/NLGN3 signaling axis in GBM cells.
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Affiliation(s)
- Jie Li
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bin Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zishan Feng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Dandan An
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhiyuan Zhou
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Chao Wan
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yan Hu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yajie Sun
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yijun Wang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xixi Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Wenwen Wei
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiao Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jingshu Meng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Mengjie Che
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yuhan Sheng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bian Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lu Wen
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Fang Huang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yan Li
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Kunyu Yang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Institute of Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
- Hubei Key Laboratory of Precision Radiation Oncology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Chen S, Zhou B, Huang W, Li Q, Yu Y, Kuang X, Huang H, Wang W, Xie P. The deubiquitinating enzyme USP44 suppresses hepatocellular carcinoma progression by inhibiting Hedgehog signaling and PDL1 expression. Cell Death Dis 2023; 14:830. [PMID: 38097536 PMCID: PMC10721641 DOI: 10.1038/s41419-023-06358-y] [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: 07/27/2023] [Revised: 11/22/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the deadliest malignancies in the world. Research into the key genes that maintain the malignant behavior of cancer cells is crucial for the treatment of HCC. Here, we identified ubiquitin-specific peptidase 44 (USP44), a member of the deubiquitinase family, as a novel regulator of HCC progression. The tumor suppressive function of USP44 was evaluated in a series of in vitro and in vivo experiments. Through quantitative proteomics examination, we demonstrated that USP44 inhibits HCC PDL1 expression by downregulating the Hedgehog (Hh) signaling pathway. Mechanistically, we found that USP44 directly interacts with Itch, an E3 ligase involved in Hh signaling, and promotes the deubiquitination and stabilization of Itch. These events result in the proteasomal degradation of Gli1 and subsequent inactivation of Hh signaling, which ultimately suppresses PDL1 expression and the progression of HCC. Furthermore, the HCC tissue microarray was analyzed by immunohistochemistry to evaluate the pathological relevance of the USP44/Itch/Gli1/PDL1 axis. Finally, the Gli1 inhibitor GANT61 was found to act in synergy with anti-PDL1 therapy. Overall, USP44 can act as a suppressive gene in HCC by modulating Hh signaling, and co-inhibition of Gli1 and PDL1 might be an effective novel combination strategy for treating HCC patients.
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Affiliation(s)
- Sisi Chen
- Department of Neurology, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
| | - Binghai Zhou
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, PR China
| | - Wei Huang
- Department of Neurology, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
| | - Qing Li
- Department of Pathology, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
| | - Ye Yu
- Department of Neurology, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
| | - Xiuqing Kuang
- Department of Physical Examination, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
| | - Huabin Huang
- Department of Medical Imaging, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China
| | - Wei Wang
- Department of Neurology, Second Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, PR China.
| | - Peiyi Xie
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, 200032, PR China.
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6
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Wang L, Wang J, Ma X, Ju G, Shi C, Wang W, Wu J. USP35 promotes HCC development by stabilizing ABHD17C and activating the PI3K/AKT signaling pathway. Cell Death Discov 2023; 9:421. [PMID: 37993419 PMCID: PMC10665393 DOI: 10.1038/s41420-023-01714-5] [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: 08/07/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023] Open
Abstract
S-palmitoylation is a reversible protein lipidation that controls the subcellular localization and function of targeted proteins, including oncogenes such as N-RAS. The depalmitoylation enzyme family ABHD17s can remove the S-palmitoylation from N-RAS to facilitate cancer development. We previously showed that ABHD17C has oncogenic roles in hepatocellular carcinoma (HCC) cells, and its mRNA stability is controlled by miR-145-5p. However, it is still unclear whether ABHD17C is regulated at the post-translational level. In the present study, we identified multiple ubiquitin-specific proteases (USPs) that can stabilize ABHD17C by inhibiting the ubiquitin-proteasome-mediated degradation. Among them, USP35 is the most potent stabilizer of ABHD17C. We found a positive correlation between the elevated expression levels of USP35 and ABHD17C, together with their association with increased PI3K/AKT pathway activity in HCCs. USP35 knockdown caused decreased ABHD17C protein level, impaired PI3K/AKT pathway, reduced proliferation, cell cycle arrest, increased apoptosis, and mitigated migration and invasion. USP35 can interact with and stabilize ABHD17C by inhibiting its ubiquitination. Overexpression of ABHD17C can rescue the defects caused by USP35 knockdown in HCC cells. In support of these in vitro observations, xenograft assay data also showed that USP35 deficiency repressed HCC development in vivo, characterized by reduced proliferation and disrupted PI3K/AKT signaling. Together, these findings demonstrate that USP35 may promote HCC development by stabilization of ABHD17C and activation of the PI3K/AKT pathway.
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Affiliation(s)
- Linpei Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Fujian Medical University, 362000, Quanzhou, Fujian Province, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, Zhejiang Province, China
| | - Jiawei Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Fujian Medical University, 362000, Quanzhou, Fujian Province, China
| | - Xiaoqiu Ma
- Department of Health Medicine, The 910th Hospital of People's Liberation Army, 362000, Quanzhou, Fujian Province, China
| | - Guomin Ju
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, Zhejiang Province, China
| | - Chunfeng Shi
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Fujian Medical University, 362000, Quanzhou, Fujian Province, China
| | - Wei Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Fujian Medical University, 362000, Quanzhou, Fujian Province, China.
| | - Jian Wu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, Zhejiang Province, China.
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Li X, Yang F, He N, Zhang M, Lv Y, Yu Y, Dong Q, Hou X, Hao Y, An Z, Zhang H, Yang Z, Zhai H, Guo D, Cao Z, Jiang VC, Chen Y. YM155 inhibits neuroblastoma growth through degradation of MYCN: A new role as a USP7 inhibitor. Eur J Pharm Sci 2023; 181:106343. [PMID: 36436754 DOI: 10.1016/j.ejps.2022.106343] [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] [Received: 05/31/2022] [Revised: 10/27/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022]
Abstract
Amplification of the MYCN gene (MNA) is observed in approximately 25 to 35% of neuroblastoma patients, and is a well-recognized marker of tumor aggressiveness and poor outcome. Targeting MYCN is a novel therapy strategy to induce tumor regression. Here, we discovered that a BIRC5/Survivin inhibitor, YM155, specifically inhibits MNA neuroblastoma cell growth in vitro. We found that YM155 promotes MYCN degradation in MNA cells. Further, we found that YM155 inhibits USP7 deubiquitinase activity in vitro, using Ub-aminomethylcoumarin (Ub-AMC) as substrate. Results from in vivo studies further demonstrated that YM155 significantly inhibited the tumor growth in MNA neuroblastoma xenograft model. Our data support a novel mechanism of action of YM155 in inhibition of growth of cancer cells through inducing MYCN degradation by inibition of activity of deubiquitinase like USP7.
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Affiliation(s)
- Xiang Li
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Feili Yang
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Na He
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Ming Zhang
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Yan Lv
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Yue Yu
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Qian Dong
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Xiaofu Hou
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Yanbing Hao
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Zhida An
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Haiwen Zhang
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Zhen Yang
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Heiyan Zhai
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Dagang Guo
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Zhixiang Cao
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Vernon C Jiang
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA
| | - Yiyou Chen
- Cothera Bioscience, Inc., 155 Bovet Road, Suite 660, San Mateo, CA 94402, USA.
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8
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Tan L, Shan H, Han C, Zhang Z, Shen J, Zhang X, Xiang H, Lu K, Qi C, Li Y, Zhuang G, Chen G, Tan L. Discovery of Potent OTUB1/USP8 Dual Inhibitors Targeting Proteostasis in Non-Small-Cell Lung Cancer. J Med Chem 2022; 65:13645-13659. [PMID: 36221183 DOI: 10.1021/acs.jmedchem.2c00408] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deubiquitinating enzymes (DUBs) are key regulatory components of the ubiquitination system. Many DUBs have been revealed to play key roles in normal physiology and diseases. However, only very limited DUB members have well-characterized inhibitors. OTUB1 and USP8 are two DUBs reported to promote both immune evasion and tumorigenesis in tumor models, yet their targeted inhibitors are in the early stages of development. Here, we describe the lead identification and optimization of an OTUB1/USP8 dual inhibitor, 61, which exhibits highly potent and selective inhibition of both targets with subnanomolar IC50s in vitro. By inhibiting both DUBs, 61 phenocopies the double knockdown of OTUB1/USP8 and exerts pronounced antiproliferative effects in H1975 and other non-small-cell lung cancer (NSCLC) cell lines. Moreover, 61 efficaciously mitigates tumor growth in vivo. Collectively, our results provide a useful tool for pharmacological perturbation of OTUB1/USP8 and introduce a promising therapeutic strategy of dual DUB inhibition for treating NSCLC.
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Affiliation(s)
- Lingli Tan
- School of Pharmacy, Fudan University, Shanghai 201203, China.,Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hengyue Shan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Han
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenfeng Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiali Shen
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Huaijiang Xiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuankuan Lu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunting Qi
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Ying Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Guanglei Zhuang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Gang Chen
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Li Tan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
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9
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Murgai A, Sosič I, Gobec M, Lemnitzer P, Proj M, Wittenburg S, Voget R, Gütschow M, Krönke J, Steinebach C. Targeting the deubiquitinase USP7 for degradation with PROTACs. Chem Commun (Camb) 2022; 58:8858-8861. [PMID: 35852517 PMCID: PMC9710854 DOI: 10.1039/d2cc02094g] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeting deubiquitinating enzymes (DUBs) has emerged as a promising therapeutic approach in several human cancers and other diseases. DUB inhibitors are exciting pharmacological tools but often exhibit limited cellular potency. Here we report PROTACs based on a ubiquitin-specific protease 7 (USP7) inhibitor scaffold to degrade USP7. By investigating several linker and E3 ligand types, including novel cereblon recruiters, we discovered a highly selective USP7 degrader tool compound that induced apoptosis of USP7-dependent cancer cells. This work represents one of the first DUB degraders and unlocks a new drug target class for protein degradation.
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Affiliation(s)
- Arunima Murgai
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany. .,German Cancer Consortium (DKTK) partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Martina Gobec
- Faculty of Pharmacy, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Patricia Lemnitzer
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Matic Proj
- Faculty of Pharmacy, University of Ljubljana, SI-1000, Ljubljana, Slovenia
| | - Sophie Wittenburg
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany.
| | - Rabea Voget
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany.
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany.
| | - Jan Krönke
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany. .,German Cancer Consortium (DKTK) partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121, Bonn, Germany.
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10
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Mahajan S, Majumder A, Stewart PA, Chen YA, Adhikari E, Fang B, Yang Y, Lawrence H, Kinose F, Koomen JM, Haura EB. Deubiquitinase Vulnerabilities Identified through Activity-Based Protein Profiling in Non-Small Cell Lung Cancer. ACS Chem Biol 2022; 17:776-784. [PMID: 35311290 PMCID: PMC11071078 DOI: 10.1021/acschembio.2c00018] [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] [Indexed: 01/26/2023]
Abstract
To aid in the prioritization of deubiquitinases (DUBs) as anticancer targets, we developed an approach combining activity-based protein profiling (ABPP) with mass spectrometry in both non-small cell lung cancer (NSCLC) tumor tissues and cell lines along with analysis of available RNA interference and CRISPR screens. We identified 67 DUBs in NSCLC tissues, 17 of which were overexpressed in adenocarcinoma or squamous cell histologies and 12 of which scored as affecting lung cancer cell viability in RNAi or CRISPR screens. We used the CSN5 inhibitor, which targets COPS5/CSN5, as a tool to understand the biological significance of one of these 12 DUBs, COPS6, in lung cancer. Our study provides a powerful resource to interrogate the role of DUB signaling biology and nominates druggable targets for the treatment of lung cancer subtypes.
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11
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Vere G, Alam MR, Farrar S, Kealy R, Kessler BM, O’Brien DP, Pinto-Fernández A. Targeting the Ubiquitylation and ISGylation Machinery for the Treatment of COVID-19. Biomolecules 2022; 12:biom12020300. [PMID: 35204803 PMCID: PMC8869442 DOI: 10.3390/biom12020300] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022] Open
Abstract
Ubiquitylation and ISGylation are protein post-translational modifications (PTMs) and two of the main events involved in the activation of pattern recognition receptor (PRRs) signals allowing the host defense response to viruses. As with similar viruses, SARS-CoV-2, the virus causing COVID-19, hijacks these pathways by removing ubiquitin and/or ISG15 from proteins using a protease called PLpro, but also by interacting with enzymes involved in ubiquitin/ISG15 machinery. These enable viral replication and avoidance of the host immune system. In this review, we highlight potential points of therapeutic intervention in ubiquitin/ISG15 pathways involved in key host-pathogen interactions, such as PLpro, USP18, TRIM25, CYLD, A20, and others that could be targeted for the treatment of COVID-19, and which may prove effective in combatting current and future vaccine-resistant variants of the disease.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
| | - Md Rashadul Alam
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Sam Farrar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
| | - Rachel Kealy
- Environmental Futures & Big Data Impact Lab, University of Exeter, Stocker Rd., Exeter EX4 4PY, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
| | - Darragh P. O’Brien
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Correspondence: (D.P.O.); (A.P.-F.)
| | - Adán Pinto-Fernández
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK; (G.V.); (M.R.A.); (S.F.); (B.M.K.)
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
- Correspondence: (D.P.O.); (A.P.-F.)
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12
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OTUB2 Promotes Proliferation and Migration of Hepatocellular Carcinoma Cells by PJA1 Deubiquitylation. Cell Mol Bioeng 2022; 15:281-292. [PMID: 35611163 PMCID: PMC9124278 DOI: 10.1007/s12195-022-00720-4] [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: 06/24/2021] [Accepted: 01/12/2022] [Indexed: 02/03/2023] Open
Abstract
Introduction Recent studies have revealed that several deubiquitinating enzymes (DUBs) play important roles in hepatocellular carcinoma (HCC) progression, but the roles of Otubain 2 (OTUB2) in HCC remain obscure. Methods In this study, we investigated the expression of OTUB2 in HCC based on clinical samples and a public online database (ENCORI), and its roles and working mechanisms were further explored by in vitro experiments. Results It was found that the expression of OTUB2 was significantly up-regulated in HCC tissues, and correlated with poor prognosis of HCC patients. Functionally, the overexpression of OTUB2 could promote malignant proliferation and metastasis of HCC cells, while knockdown of OTUB2 exerted the opposite results. Using two bioinformatics tools, PJA1 was identified as a potential gene regulated by OTUB2. Mechanistically, it was found that OTUB2 promoted the stabilization of PJA1 by deubiquitylation, based on immunoprecipitation (IP) and cycloheximide (CHX) assays. Moreover, the suppressive effects of OTUB2 depletion on the malignant phenotypes of HCC cells could be reversed by overexpressing PJA1. Conclusion In conclusion, our study indicated that OTUB2 could promote the malignant proliferation and migration of HCC cells by increasing the stability of PJA1 via deubiquitylation.
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13
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Varca AC, Casalena D, Chan WC, Hu B, Magin RS, Roberts RM, Liu X, Zhu H, Seo HS, Dhe-Paganon S, Marto JA, Auld D, Buhrlage SJ. Identification and validation of selective deubiquitinase inhibitors. Cell Chem Biol 2021; 28:1758-1771.e13. [PMID: 34129829 PMCID: PMC9473745 DOI: 10.1016/j.chembiol.2021.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/11/2021] [Accepted: 05/19/2021] [Indexed: 12/17/2022]
Abstract
Deubiquitinating enzymes (DUBs) are a class of isopeptidases that regulate ubiquitin dynamics through catalytic cleavage of ubiquitin from protein substrates and ubiquitin precursors. Despite growing interest in DUB biological function and potential as therapeutic targets, few selective small-molecule inhibitors and no approved drugs currently exist. To identify chemical scaffolds targeting specific DUBs and establish a broader framework for future inhibitor development across the gene family, we performed high-throughput screening of a chemically diverse small-molecule library against eight different DUBs, spanning three well-characterized DUB families. Promising hit compounds were validated in a series of counter-screens and orthogonal assays, as well as further assessed for selectivity across expanded panels of DUBs. Through these efforts, we have identified multiple highly selective DUB inhibitors and developed a roadmap for rapidly identifying and validating selective inhibitors of related enzymes.
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Affiliation(s)
- Anthony C Varca
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Dominick Casalena
- FAST Lab, Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bin Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert S Magin
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Rebekka M Roberts
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - He Zhu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Douglas Auld
- FAST Lab, Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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14
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Tyagi A, Haq S, Ramakrishna S. Redox regulation of DUBs and its therapeutic implications in cancer. Redox Biol 2021; 48:102194. [PMID: 34814083 PMCID: PMC8608616 DOI: 10.1016/j.redox.2021.102194] [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: 10/29/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
Reactive oxygen species (ROS) act as a double-edged sword in cancer, where low levels of ROS are beneficial but excessive accumulation leads to cancer progression. Elevated levels of ROS in cancer are counteracted by the antioxidant defense system. An imbalance between ROS generation and the antioxidant system alters gene expression and cellular signaling, leading to cancer progression or death. Post-translational modifications, such as ubiquitination, phosphorylation, and SUMOylation, play a critical role in the maintenance of ROS homeostasis by controlling ROS production and clearance. Recent evidence suggests that deubiquitinating enzymes (DUBs)-mediated ubiquitin removal from substrates is regulated by ROS. ROS-mediated oxidation of the catalytic cysteine (Cys) of DUBs, leading to their reversible inactivation, has emerged as a key mechanism regulating DUB-controlled cellular events. A better understanding of the mechanism by which DUBs are susceptible to ROS and exploring the ways to utilize ROS to pharmacologically modulate DUB-mediated signaling pathways might provide new insight for anticancer therapeutics. This review assesses the recent findings regarding ROS-mediated signaling in cancers, emphasizes DUB regulation by oxidation, highlights the relevant recent findings, and proposes directions of future research based on the ROS-induced modifications of DUB activity.
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Affiliation(s)
- Apoorvi Tyagi
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Saba Haq
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul, 04763, South Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul, 04763, South Korea; College of Medicine, Hanyang University, Seoul, 04763, South Korea.
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15
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Panyain N, Godinat A, Thawani AR, Lachiondo-Ortega S, Mason K, Elkhalifa S, Smith LM, Harrigan JA, Tate EW. Activity-based protein profiling reveals deubiquitinase and aldehyde dehydrogenase targets of a cyanopyrrolidine probe. RSC Med Chem 2021; 12:1935-1943. [PMID: 34820624 PMCID: PMC8597422 DOI: 10.1039/d1md00218j] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/11/2021] [Indexed: 11/21/2022] Open
Abstract
Ubiquitin carboxy-terminal hydrolase L1 (UCHL1), a deubiquitinating enzyme (DUB), is a potential drug target in various cancers, and liver and lung fibrosis. However, bona fide functions and substrates of UCHL1 remain poorly understood. Herein, we report the characterization of UCHL1 covalent inhibitor MT16-001 based on a thiazole cyanopyrrolidine scaffold. In combination with chemical proteomics, a closely related activity-based probe (MT16-205) was used to generate a comprehensive quantitative profile for on- and off-targets at endogenous cellular abundance. Both compounds are selective for UCHL1 over other DUBs in intact cells but also engage a range of other targets with good selectivity over the wider proteome, including aldehyde dehydrogenases, redox-sensitive Parkinson's disease related protein PARK7, and glutamine amidotransferase. Taken together, these results underline the importance of robust profiling of activity-based probes as chemical tools and highlight the cyanopyrrolidine warhead as a versatile platform for liganding diverse classes of protein with reactive cysteine residues which can be used for further inhibitor screening, and as a starting point for inhibitor development.
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Affiliation(s)
- Nattawadee Panyain
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
| | - Aurélien Godinat
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
| | - Aditya Raymond Thawani
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
| | - Sofía Lachiondo-Ortega
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
| | - Katie Mason
- Mission Therapeutics Ltd, The Glenn Berge Building, Babraham Research Campus Babraham Cambridge CB22 3FH UK
| | - Sarah Elkhalifa
- Mission Therapeutics Ltd, The Glenn Berge Building, Babraham Research Campus Babraham Cambridge CB22 3FH UK
| | - Lisa M Smith
- Mission Therapeutics Ltd, The Glenn Berge Building, Babraham Research Campus Babraham Cambridge CB22 3FH UK
| | - Jeanine A Harrigan
- Mission Therapeutics Ltd, The Glenn Berge Building, Babraham Research Campus Babraham Cambridge CB22 3FH UK
| | - Edward W Tate
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London W12 0BZ UK
- The Francis Crick Institute London NW1 1AT UK
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16
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Inhibition of USP28 overcomes Cisplatin-resistance of squamous tumors by suppression of the Fanconi anemia pathway. Cell Death Differ 2021; 29:568-584. [PMID: 34611298 PMCID: PMC8901929 DOI: 10.1038/s41418-021-00875-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
Squamous cell carcinomas (SCC) frequently have an exceptionally high mutational burden. As consequence, they rapidly develop resistance to platinum-based chemotherapy and overall survival is limited. Novel therapeutic strategies are therefore urgently required. SCC express ∆Np63, which regulates the Fanconi Anemia (FA) DNA-damage response in cancer cells, thereby contributing to chemotherapy-resistance. Here we report that the deubiquitylase USP28 is recruited to sites of DNA damage in cisplatin-treated cells. ATR phosphorylates USP28 and increases its enzymatic activity. This phosphorylation event is required to positively regulate the DNA damage repair in SCC by stabilizing ∆Np63. Knock-down or inhibition of USP28 by a specific inhibitor weakens the ability of SCC to cope with DNA damage during platin-based chemotherapy. Hence, our study presents a novel mechanism by which ∆Np63 expressing SCC can be targeted to overcome chemotherapy resistance. Limited treatment options and low response rates to chemotherapy are particularly common in patients with squamous cancer. The SCC specific transcription factor ∆Np63 enhances the expression of Fanconi Anemia genes, thereby contributing to recombinational DNA repair and Cisplatin resistance. Targeting the USP28-∆Np63 axis in SCC tones down this DNA damage response pathways, thereby sensitizing SCC cells to cisplatin treatment.
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17
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Wang Y, Wang F. Post-Translational Modifications of Deubiquitinating Enzymes: Expanding the Ubiquitin Code. Front Pharmacol 2021; 12:685011. [PMID: 34177595 PMCID: PMC8224227 DOI: 10.3389/fphar.2021.685011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
Post-translational modifications such as ubiquitination play important regulatory roles in several biological processes in eukaryotes. This process could be reversed by deubiquitinating enzymes (DUBs), which remove conjugated ubiquitin molecules from target substrates. Owing to their role as essential enzymes in regulating all ubiquitin-related processes, the abundance, localization, and catalytic activity of DUBs are tightly regulated. Dysregulation of DUBs can cause dramatic physiological consequences and a variety of disorders such as cancer, and neurodegenerative and inflammatory diseases. Multiple factors, such as transcription and translation of associated genes, and the presence of accessory domains, binding proteins, and inhibitors have been implicated in several aspects of DUB regulation. Beyond this level of regulation, emerging studies show that the function of DUBs can be regulated by a variety of post-translational modifications, which significantly affect the abundance, localization, and catalytic activity of DUBs. The most extensively studied post-translational modification of DUBs is phosphorylation. Besides phosphorylation, ubiquitination, SUMOylation, acetylation, oxidation, and hydroxylation are also reported in DUBs. In this review, we summarize the current knowledge on the regulatory effects of post-translational modifications of DUBs.
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Affiliation(s)
- Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Feng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, China
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18
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Vere G, Kealy R, Kessler BM, Pinto-Fernandez A. Ubiquitomics: An Overview and Future. Biomolecules 2020; 10:E1453. [PMID: 33080838 PMCID: PMC7603029 DOI: 10.3390/biom10101453] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
Covalent attachment of ubiquitin, a small globular polypeptide, to protein substrates is a key post-translational modification that determines the fate, function, and turnover of most cellular proteins. Ubiquitin modification exists as mono- or polyubiquitin chains involving multiple ways how ubiquitin C-termini are connected to lysine, perhaps other amino acid side chains, and N-termini of proteins, often including branching of the ubiquitin chains. Understanding this enormous complexity in protein ubiquitination, the so-called 'ubiquitin code', in combination with the ∼1000 enzymes involved in controlling ubiquitin recognition, conjugation, and deconjugation, calls for novel developments in analytical techniques. Here, we review different headways in the field mainly driven by mass spectrometry and chemical biology, referred to as "ubiquitomics", aiming to understand this system's biological diversity.
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Affiliation(s)
- George Vere
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
| | - Rachel Kealy
- St Anne’s College, University of Oxford, Oxford OX2 6HS, UK;
| | - Benedikt M. Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Chinese Academy of Medical Sciences Oxford Institute (CAMS), Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK; (G.V.); (B.M.K.)
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19
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Proteomics-Based Identification of DUB Substrates Using Selective Inhibitors. Cell Chem Biol 2020; 28:78-87.e3. [PMID: 33007217 DOI: 10.1016/j.chembiol.2020.09.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/16/2020] [Accepted: 09/09/2020] [Indexed: 01/04/2023]
Abstract
Deubiquitinating enzymes (DUBs) catalyze the removal of ubiquitin, thereby reversing the activity of E3 ubiquitin ligases and are central to the control of protein abundance and function. Despite the growing interest in DUBs as therapeutic targets, cellular functions for DUBs remain largely unknown and technical challenges often preclude the identification of DUB substrates in a comprehensive manner. Here, we demonstrate that treatment with potent DUB inhibitors coupled to mass spectrometry-based proteomics can identify DUB substrates at a proteome-wide scale. We applied this approach to USP7, a DUB widely investigated as a therapeutic target and identified many known substrates and additional targets. We demonstrate that USP7 substrates are enriched for DNA repair enzymes and E3 ubiquitin ligases. This work provides not only a comprehensive annotation of USP7 substrates, but a general protocol widely applicable to other DUBs, which is critical for translational development of DUB targeted agents.
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20
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Dwane L, O'Connor AE, Das S, Moran B, Mulrane L, Pinto-Fernandez A, Ward E, Blümel AM, Cavanagh BL, Mooney B, Dirac AM, Jirström K, Kessler BM, Ní Chonghaile T, Bernards R, Gallagher WM, O'Connor DP. A Functional Genomic Screen Identifies the Deubiquitinase USP11 as a Novel Transcriptional Regulator of ERα in Breast Cancer. Cancer Res 2020; 80:5076-5088. [PMID: 33004351 DOI: 10.1158/0008-5472.can-20-0214] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/26/2020] [Accepted: 09/15/2020] [Indexed: 01/23/2023]
Abstract
Approximately 70% of breast cancers express estrogen receptor α (ERα) and depend on this key transcriptional regulator for proliferation and differentiation. While patients with this disease can be treated with targeted antiendocrine agents, drug resistance remains a significant issue, with almost half of patients ultimately relapsing. Elucidating the mechanisms that control ERα function may further our understanding of breast carcinogenesis and reveal new therapeutic opportunities. Here, we investigated the role of deubiquitinases (DUB) in regulating ERα in breast cancer. An RNAi loss-of-function screen in breast cancer cells targeting all DUBs identified USP11 as a regulator of ERα transcriptional activity, which was further validated by assessment of direct transcriptional targets of ERα. USP11 expression was induced by estradiol, an effect that was blocked by tamoxifen and not observed in ERα-negative cells. Mass spectrometry revealed a significant change to the proteome and ubiquitinome in USP11-knockdown (KD) cells in the presence of estradiol. RNA sequencing in LCC1 USP11-KD cells revealed significant suppression of cell-cycle-associated and ERα target genes, phenotypes that were not observed in LCC9 USP11-KD, antiendocrine-resistant cells. In a breast cancer patient cohort coupled with in silico analysis of publicly available cohorts, high expression of USP11 was significantly associated with poor survival in ERα-positive (ERα+) patients. Overall, this study highlights a novel role for USP11 in the regulation of ERα activity, where USP11 may represent a prognostic marker in ERα+ breast cancer. SIGNIFICANCE: A newly identified role for USP11 in ERα transcriptional activity represents a novel mechanism of ERα regulation and a pathway to be exploited for the management of ER-positive breast cancer.
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Affiliation(s)
- Lisa Dwane
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons Ireland, Dublin, Ireland
| | - Aisling E O'Connor
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Sudipto Das
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons Ireland, Dublin, Ireland
| | - Bruce Moran
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Laoighse Mulrane
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Adan Pinto-Fernandez
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford, United Kingdom
| | - Elspeth Ward
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons Ireland, Dublin, Ireland
| | - Anna M Blümel
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons Ireland, Dublin, Ireland
| | - Brenton L Cavanagh
- Cellular and Molecular Imaging Core, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Brian Mooney
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons Ireland, Dublin, Ireland
| | - Annette M Dirac
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Karin Jirström
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Headington, Oxford, United Kingdom
| | - Tríona Ní Chonghaile
- Department of Physiology and Medical Physics, Royal College of Surgeons Ireland, Dublin, Ireland
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - William M Gallagher
- Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Darran P O'Connor
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons Ireland, Dublin, Ireland.
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21
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Gu H, Jan Fada B. Specificity in Ubiquitination Triggered by Virus Infection. Int J Mol Sci 2020; 21:ijms21114088. [PMID: 32521668 PMCID: PMC7313089 DOI: 10.3390/ijms21114088] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
Ubiquitination is a prominent posttranslational modification, in which the ubiquitin moiety is covalently attached to a target protein to influence protein stability, interaction partner and biological function. All seven lysine residues of ubiquitin, along with the N-terminal methionine, can each serve as a substrate for further ubiquitination, which effectuates a diverse combination of mono- or poly-ubiquitinated proteins with linear or branched ubiquitin chains. The intricately composed ubiquitin codes are then recognized by a large variety of ubiquitin binding domain (UBD)-containing proteins to participate in the regulation of various pathways to modulate the cell behavior. Viruses, as obligate parasites, involve many aspects of the cell pathways to overcome host defenses and subjugate cellular machineries. In the virus-host interactions, both the virus and the host tap into the rich source of versatile ubiquitination code in order to compete, combat, and co-evolve. Here, we review the recent literature to discuss the role of ubiquitin system as the infection progresses in virus life cycle and the importance of ubiquitin specificity in the regulation of virus-host relation.
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22
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Interaction of Deubiquitinase 2A-DUB/MYSM1 with DNA Repair and Replication Factors. Int J Mol Sci 2020; 21:ijms21113762. [PMID: 32466590 PMCID: PMC7312997 DOI: 10.3390/ijms21113762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023] Open
Abstract
The deubiquitination of histone H2A on lysine 119 by 2A-DUB/MYSM1, BAP1, USP16, and other enzymes is required for key cellular processes, including transcriptional activation, apoptosis, and cell cycle control, during normal hematopoiesis and tissue development, and in tumor cells. Based on our finding that MYSM1 colocalizes with γH2AX foci in human peripheral blood mononuclear cells, leukemia cells, and melanoma cells upon induction of DNA double-strand breaks with topoisomerase inhibitor etoposide, we applied a mass spectrometry-based proteomics approach to identify novel 2A-DUB/MYSM1 interaction partners in DNA-damage responses. Differential display of MYSM1 binding proteins significantly enriched after exposure of 293T cells to etoposide revealed an interacting network of proteins involved in DNA damage and replication, including factors associated with poor melanoma outcome. In the context of increased DNA-damage in a variety of cell types in Mysm1-deficient mice, in bone marrow cells upon aging and in UV-exposed Mysm1-deficient skin, our current mass spectrometry data provide additional evidence for an interaction between MYSM1 and key DNA replication and repair factors, and indicate a potential function of 2A-DUB/MYSM1 in DNA repair processes.
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23
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N-benzylpiperidinol derivatives as novel USP7 inhibitors: Structure-activity relationships and X-ray crystallographic studies. Eur J Med Chem 2020; 199:112279. [PMID: 32497973 DOI: 10.1016/j.ejmech.2020.112279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/25/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
USP7 as a deubiquitinase plays important roles in regulating the stability of some oncoproteins including MDM2 and DNMT1, and thus represents a potential anticancer target. Through comparative analysis of USP7 co-crystal structures in complex with the reported piperidinol inhibitors, we noticed that the USP7 Phe409 sub-site might have good adaptability to the ligands. Based on this observation, 55 N-aromatic and N-benzyl piperidinol derivatives were designed, synthesized and biologically evaluated, among which compound L55 was identified as a highly selective and potent USP7 inhibitor (IC50 = 40.8 nM, KD = 78.3 nM). X-ray crystallographic studies revealed that L55 bound to USP7 with a new pose that was very different from the previously reported inhibitors. The results of cellular assays showed that L55 had strong antitumor activity against LNCaP (IC50 = 29.6 nM) and RS4; 11 (IC50 = 41.6 nM) cells, probably through inducing cell death and restricting G0/G1 and S phases. Moreover, L55 dose-dependently reduced the protein levels of MDM2 and DNMT1 and increased the protein levels of p53 and p21. These findings could have valuable implications for designing novel structural classes of USP7 inhibitors.
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24
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Sarodaya N, Karapurkar J, Kim KS, Hong SH, Ramakrishna S. The Role of Deubiquitinating Enzymes in Hematopoiesis and Hematological Malignancies. Cancers (Basel) 2020; 12:E1103. [PMID: 32354135 PMCID: PMC7281754 DOI: 10.3390/cancers12051103] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/11/2020] [Accepted: 04/26/2020] [Indexed: 12/24/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are responsible for the production of blood cells throughout the human lifespan. Single HSCs can give rise to at least eight distinct blood-cell lineages. Together, hematopoiesis, erythropoiesis, and angiogenesis coordinate several biological processes, i.e., cellular interactions during development and proliferation, guided migration, lineage programming, and reprogramming by transcription factors. Any dysregulation of these processes can result in hematological disorders and/or malignancies. Several studies of the molecular mechanisms governing HSC maintenance have demonstrated that protein regulation by the ubiquitin proteasomal pathway is crucial for normal HSC function. Recent studies have shown that reversal of ubiquitination by deubiquitinating enzymes (DUBs) plays an equally important role in hematopoiesis; however, information regarding the biological function of DUBs is limited. In this review, we focus on recent discoveries about the physiological roles of DUBs in hematopoiesis, erythropoiesis, and angiogenesis and discuss the DUBs associated with common hematological disorders and malignancies, which are potential therapeutic drug targets.
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Affiliation(s)
- Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (J.K.); (K.-S.K.)
| | - Janardhan Karapurkar
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (J.K.); (K.-S.K.)
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (J.K.); (K.-S.K.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Seok-Ho Hong
- Department of Internal Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (J.K.); (K.-S.K.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
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25
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Schauer NJ, Liu X, Magin RS, Doherty LM, Chan WC, Ficarro SB, Hu W, Roberts RM, Iacob RE, Stolte B, Giacomelli AO, Perera S, McKay K, Boswell SA, Weisberg EL, Ray A, Chauhan D, Dhe-Paganon S, Anderson KC, Griffin JD, Li J, Hahn WC, Sorger PK, Engen JR, Stegmaier K, Marto JA, Buhrlage SJ. Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism. Sci Rep 2020; 10:5324. [PMID: 32210275 PMCID: PMC7093416 DOI: 10.1038/s41598-020-62076-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Ubiquitin specific peptidase 7 (USP7) is a deubiquitinating enzyme (DUB) that removes ubiquitin tags from specific protein substrates in order to alter their degradation rate and sub-cellular localization. USP7 has been proposed as a therapeutic target in several cancers because it has many reported substrates with a role in cancer progression, including FOXO4, MDM2, N-Myc, and PTEN. The multi-substrate nature of USP7, combined with the modest potency and selectivity of early generation USP7 inhibitors, has presented a challenge in defining predictors of response to USP7 and potential patient populations that would benefit most from USP7-targeted drugs. Here, we describe the structure-guided development of XL177A, which irreversibly inhibits USP7 with sub-nM potency and selectivity across the human proteome. Evaluation of the cellular effects of XL177A reveals that selective USP7 inhibition suppresses cancer cell growth predominantly through a p53-dependent mechanism: XL177A specifically upregulates p53 transcriptional targets transcriptome-wide, hotspot mutations in TP53 but not any other genes predict response to XL177A across a panel of ~500 cancer cell lines, and TP53 knockout rescues XL177A-mediated growth suppression of TP53 wild-type (WT) cells. Together, these findings suggest TP53 mutational status as a biomarker for response to USP7 inhibition. We find that Ewing sarcoma and malignant rhabdoid tumor (MRT), two pediatric cancers that are sensitive to other p53-dependent cytotoxic drugs, also display increased sensitivity to XL177A.
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Affiliation(s)
- Nathan J Schauer
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Xiaoxi Liu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Robert S Magin
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Laura M Doherty
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Wai Cheung Chan
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wanyi Hu
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rebekka M Roberts
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Björn Stolte
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital, LMU Munich, Munich, Germany
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Andrew O Giacomelli
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | - Kyle McKay
- Department of Chemistry, University of Vermont, Burlington, VT, USA
| | - Sarah A Boswell
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Arghya Ray
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Dharminder Chauhan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ken C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- The LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James D Griffin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jianing Li
- Department of Chemistry, University of Vermont, Burlington, VT, USA
| | - William C Hahn
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Peter K Sorger
- Department of Systems Biology and Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Boston Children's Hospital, Boston, MA, USA
- The Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Oncologic Pathology and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sara J Buhrlage
- Department of Cancer Biology and the Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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26
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Mustachio LM, Roszik J, Farria A, Dent SYR. Targeting the SAGA and ATAC Transcriptional Coactivator Complexes in MYC-Driven Cancers. Cancer Res 2020; 80:1905-1911. [PMID: 32094302 DOI: 10.1158/0008-5472.can-19-3652] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/28/2020] [Accepted: 02/19/2020] [Indexed: 12/26/2022]
Abstract
Targeting epigenetic regulators, such as histone-modifying enzymes, provides novel strategies for cancer therapy. The GCN5 lysine acetyltransferase (KAT) functions together with MYC both during normal development and in oncogenesis. As transcription factors, MYC family members are difficult to target with small-molecule inhibitors, but the acetyltransferase domain and the bromodomain in GCN5 might provide alternative targets for disruption of MYC-driven functions. GCN5 is part of two distinct multiprotein histone-modifying complexes, SAGA and ATAC. This review summarizes key findings on the roles of SAGA and ATAC in embryo development and in cancer to better understand the functional relationships of these complexes with MYC family members, as well as their future potential as therapeutic targets.
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Affiliation(s)
- Lisa Maria Mustachio
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Aimee Farria
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sharon Y R Dent
- Departments of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
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27
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Ballar Kirmizibayrak P, Erbaykent-Tepedelen B, Gozen O, Erzurumlu Y. Divergent Modulation of Proteostasis in Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:117-151. [PMID: 32274755 DOI: 10.1007/978-3-030-38266-7_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteostasis regulates key cellular processes such as cell proliferation, differentiation, transcription, and apoptosis. The mechanisms by which proteostasis is regulated are crucial and the deterioration of cellular proteostasis has been significantly associated with tumorigenesis since it specifically targets key oncoproteins and tumor suppressors. Prostate cancer (PCa) is the second most common cause of cancer death in men worldwide. Androgens mediate one of the most central signaling pathways in all stages of PCa via the androgen receptor (AR). In addition to their regulation by hormones, PCa cells are also known to be highly secretory and are particularly prone to ER stress as proper ER function is essential. Alterations in various complex signaling pathways and cellular processes including cell cycle control, transcription, DNA repair, apoptosis, cell adhesion, epithelial-mesenchymal transition (EMT), and angiogenesis are critical factors influencing PCa development through key molecular changes mainly by posttranslational modifications in PCa-related proteins, including AR, NKX3.1, PTEN, p53, cyclin D1, and p27. Several ubiquitin ligases like MDM2, Siah2, RNF6, CHIP, and substrate-binding adaptor SPOP; deubiquitinases such as USP7, USP10, USP26, and USP12 are just some of the modifiers involved in the regulation of these key proteins via ubiquitin-proteasome system (UPS). Some ubiquitin-like modifiers, especially SUMOs, have been also closely associated with PCa. On the other hand, the proteotoxicity resulting from misfolded proteins and failure of ER adaptive capacity induce unfolded protein response (UPR) that is an indispensable signaling mechanism for PCa development. Lastly, ER-associated degradation (ERAD) also plays a crucial role in prostate tumorigenesis. In this section, the relationship between prostate cancer and proteostasis will be discussed in terms of UPS, UPR, SUMOylation, ERAD, and autophagy.
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Affiliation(s)
| | | | - Oguz Gozen
- Faculty of Medicine, Department of Physiology, Ege University, Izmir, Turkey
| | - Yalcin Erzurumlu
- Faculty of Pharmacy, Department of Biochemistry, Suleyman Demirel University, Isparta, Turkey
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28
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Banerjee S, Wei T, Wang J, Lee JJ, Gutierrez HL, Chapman O, Wiley SE, Mayfield JE, Tandon V, Juarez EF, Chavez L, Liang R, Sah RL, Costello C, Mesirov JP, de la Vega L, Cooper KL, Dixon JE, Xiao J, Lei X. Inhibition of dual-specificity tyrosine phosphorylation-regulated kinase 2 perturbs 26S proteasome-addicted neoplastic progression. Proc Natl Acad Sci U S A 2019; 116:24881-24891. [PMID: 31754034 PMCID: PMC6900511 DOI: 10.1073/pnas.1912033116] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dependence on the 26S proteasome is an Achilles' heel for triple-negative breast cancer (TNBC) and multiple myeloma (MM). The therapeutic proteasome inhibitor, bortezomib, successfully targets MM but often leads to drug-resistant disease relapse and fails in breast cancer. Here we show that a 26S proteasome-regulating kinase, DYRK2, is a therapeutic target for both MM and TNBC. Genome editing or small-molecule mediated inhibition of DYRK2 significantly reduces 26S proteasome activity, bypasses bortezomib resistance, and dramatically delays in vivo tumor growth in MM and TNBC thereby promoting survival. We further characterized the ability of LDN192960, a potent and selective DYRK2-inhibitor, to alleviate tumor burden in vivo. The drug docks into the active site of DYRK2 and partially inhibits all 3 core peptidase activities of the proteasome. Our results suggest that targeting 26S proteasome regulators will pave the way for therapeutic strategies in MM and TNBC.
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Affiliation(s)
- Sourav Banerjee
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Tiantian Wei
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871 Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
| | - Jue Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
| | - Jenna J Lee
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Haydee L Gutierrez
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Owen Chapman
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Sandra E Wiley
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Joshua E Mayfield
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Vasudha Tandon
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093
| | - Edwin F Juarez
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Lukas Chavez
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - Ruqi Liang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871 Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
| | - Robert L Sah
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
| | - Caitlin Costello
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
- Division of Blood and Marrow Transplant, University of California San Diego, La Jolla, CA 92093
| | - Jill P Mesirov
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093
| | - Laureano de la Vega
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee, DD1 9SY, United Kingdom
| | - Kimberly L Cooper
- Division of Biological Sciences, Section of Cellular and Developmental Biology, University of California San Diego, La Jolla, CA 92093
| | - Jack E Dixon
- Department of Pharmacology, University of California San Diego, La Jolla, CA 92093;
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Junyu Xiao
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, 100871 Beijing, China;
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
| | - Xiaoguang Lei
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China;
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, 100871 Beijing, China
- Department of Chemical Biology, Synthetic and Functional Biomolecules Center, Peking University, 100871 Beijing, China
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29
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Fukui S, Nagasaka K, Miyagawa Y, Kikuchi-Koike R, Kawata Y, Kanda R, Ichinose T, Sugihara T, Hiraike H, Wada-Hiraike O, Sasajima Y, Ayabe T. The proteasome deubiquitinase inhibitor bAP15 downregulates TGF-β/Smad signaling and induces apoptosis via UCHL5 inhibition in ovarian cancer. Oncotarget 2019; 10:5932-5948. [PMID: 31666925 PMCID: PMC6800272 DOI: 10.18632/oncotarget.27219] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/10/2019] [Indexed: 02/06/2023] Open
Abstract
The ubiquitin-proteasome pathway plays an important role in the regulation of cellular proteins. As an alternative to the proteasome itself, recent research has focused on methods to modulate the regulation of deubiquitinating enzymes (DUBs) upstream of the proteasome, identifying DUBs as novel therapeutic targets in breast, endometrial, and prostate cancers, along with multiple myeloma. bAP15, an inhibitor of the 19S proteasome DUBs UCHL5 and USP14, results in cell growth inhibition in several human cancers; however, the mechanism remains poorly understood in ovarian cancer. Here, we found that aberrant UCHL5 expression predicted shorter progression-free survival (PFS) in a cohort of 1435 patients with ovarian cancer described in the Gene Expression Omnibus and The Cancer Genome Atlas databases. The subgroup of patients with TP53 mutations was significantly more likely to exhibit poor PFS (p <0.001). Moreover, we found bAP15 could suppress TP53-mutant ovarian cancer cell survival by regulating TGF-β signaling through inhibiting UCHL5 expression and dephosphorylating Smad2, consequently inducing apoptosis. bAP15 (2.5 and 5.0 mg/kg) also exerted significant anti-tumor effect on nude mice bearing subcutaneous SKOV3 xenografts. As activated TGF-β signaling is involved in ovarian cancer progression, these findings suggest that UCHL5 inhibition offers potential opportunities for a novel targeted therapy against TGF-β-activated ovarian cancer.
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Affiliation(s)
- Shiho Fukui
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Kazunori Nagasaka
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Yuko Miyagawa
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Ryoko Kikuchi-Koike
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Yoshiko Kawata
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Ranka Kanda
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Takayuki Ichinose
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Takeru Sugihara
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Haruko Hiraike
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Osamu Wada-Hiraike
- Department of Obstetrics and Gynecology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yuko Sasajima
- Department of Pathology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
| | - Takuya Ayabe
- Department of Obstetrics and Gynecology, Teikyo University School of Medicine, Itabashi-ku, Tokyo 173-8605, Japan
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30
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Pinto-Fernández A, Davis S, Schofield AB, Scott HC, Zhang P, Salah E, Mathea S, Charles PD, Damianou A, Bond G, Fischer R, Kessler BM. Comprehensive Landscape of Active Deubiquitinating Enzymes Profiled by Advanced Chemoproteomics. Front Chem 2019; 7:592. [PMID: 31555637 PMCID: PMC6727631 DOI: 10.3389/fchem.2019.00592] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/09/2019] [Indexed: 12/11/2022] Open
Abstract
Enzymes that bind and process ubiquitin, a small 76-amino-acid protein, have been recognized as pharmacological targets in oncology, immunological disorders, and neurodegeneration. Mass spectrometry technology has now reached the capacity to cover the proteome with enough depth to interrogate entire biochemical pathways including those that contain DUBs and E3 ligase substrates. We have recently characterized the breast cancer cell (MCF7) deep proteome by detecting and quantifying ~10,000 proteins, and within this data set, we can detect endogenous expression of 65 deubiquitylating enzymes (DUBs), whereas matching transcriptomics detected 78 DUB mRNAs. Since enzyme activity provides another meaningful layer of information in addition to the expression levels, we have combined advanced mass spectrometry technology, pre-fractionation, and more potent/selective ubiquitin active-site probes with propargylic-based electrophiles to profile 74 DUBs including distinguishable isoforms for 5 DUBs in MCF7 crude extract material. Competition experiments with cysteine alkylating agents and pan-DUB inhibitors combined with probe labeling revealed the proportion of active cellular DUBs directly engaged with probes by label-free quantitative (LFQ) mass spectrometry. This demonstrated that USP13, 39, and 40 are non-reactive to probe, indicating restricted enzymatic activity under these cellular conditions. Our extended chemoproteomics workflow increases depth of covering the active DUBome, including isoform-specific resolution, and provides the framework for more comprehensive cell-based small-molecule DUB selectivity profiling.
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Affiliation(s)
- Adán Pinto-Fernández
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Simon Davis
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Abigail B Schofield
- University of Oxford, Oxford, United Kingdom.,Christ Church, University of Oxford, Oxford, United Kingdom
| | - Hannah C Scott
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Ping Zhang
- University of Oxford, Oxford, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Eidarus Salah
- University of Oxford, Oxford, United Kingdom.,Department of Chemistry, University of Oxford, Oxford, United Kingdom.,Structural Genomics Consortium (United Kingdom), Oxford, United Kingdom
| | - Sebastian Mathea
- Structural Genomics Consortium (United Kingdom), Oxford, United Kingdom.,Institute of Pharmaceutical Chemistry, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Philip D Charles
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andreas Damianou
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gareth Bond
- University of Oxford, Oxford, United Kingdom.,Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- University of Oxford, Oxford, United Kingdom.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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31
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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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32
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Elu N, Osinalde N, Beaskoetxea J, Ramirez J, Lectez B, Aloria K, Rodriguez JA, Arizmendi JM, Mayor U. Detailed Dissection of UBE3A-Mediated DDI1 Ubiquitination. Front Physiol 2019; 10:534. [PMID: 31130875 PMCID: PMC6509411 DOI: 10.3389/fphys.2019.00534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
The ubiquitin E3 ligase UBE3A has been widely reported to interact with the proteasome, but it is still unclear how this enzyme regulates by ubiquitination the different proteasomal subunits. The proteasome receptor DDI1 has been identified both in Drosophila photoreceptor neurons and in human neuroblastoma cells in culture as a direct substrate of UBE3A. Here, we further characterize this regulation, by identifying the UBE3A-dependent ubiquitination sites and ubiquitin chains formed on DDI1. Additionally, we found one deubiquitinating enzyme that is capable of reversing the action of UBE3A on DDI1. The complete characterization of the ubiquitination pathway of an UBE3A substrate is important due to the role of this E3 ligase in rare neurological disorders as Angelman syndrome.
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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, Spain
| | - Nerea Osinalde
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - Javier Beaskoetxea
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Juanma Ramirez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Benoit Lectez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Kerman Aloria
- Proteomics Core Facility-SGIKER, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jose Antonio Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Jesus M Arizmendi
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Ugo Mayor
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain.,Ikerbasque - Basque Foundation for Science, Bilbao, Spain
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33
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Kabra A, Benson CA, Li Y. Backbone 1H, 13C, and 15N resonance assignments of deubiquitinase A in non-phosphorylated and phosphorylated forms. BIOMOLECULAR NMR ASSIGNMENTS 2019; 13:37-42. [PMID: 30232733 PMCID: PMC6424661 DOI: 10.1007/s12104-018-9847-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Ubiquitination is one of the most prevalent forms of post-translational modifications that are important for regulating many cellular processes in eukaryotes. Deubiquitinases are proteases that hydrolyze the isopeptide or peptide bonds formed between ubiquitin and the target proteins or within a polyubiquitin chain. Deubiquitinase A (DUBA) is a deubiquitinase known to be a negative regulator of innate immune responses in humans by suppressing production of type I interferons (INF-I). Excess INF-I production has been associated with autoimmune diseases. Phosphorylation of a single serine residue at position 177 is essential for the protease activity of DUBA. The structural and mechanistic basis of DUBA activation by phosphorylation and substrate specificity is not well understood. Here, we report the backbone resonance assignments of the isoform 2 of DUBA in both non-phosphorylated and phosphorylated forms. The reported assignments form the basis for future NMR studies on the structural and dynamical properties of both active and inactive forms of DUBA.
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Affiliation(s)
- Ashish Kabra
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, KY, 40208, USA
| | - Catherine A Benson
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, KY, 40208, USA
| | - Ying Li
- Department of Chemistry, University of Louisville, 2320 South Brook Street, Louisville, KY, 40208, USA.
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34
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Teyra J, Singer AU, Schmitges FW, Jaynes P, Kit Leng Lui S, Polyak MJ, Fodil N, Krieger JR, Tong J, Schwerdtfeger C, Brasher BB, Ceccarelli DFJ, Moffat J, Sicheri F, Moran MF, Gros P, Eichhorn PJA, Lenter M, Boehmelt G, Sidhu SS. Structural and Functional Characterization of Ubiquitin Variant Inhibitors of USP15. Structure 2019; 27:590-605.e5. [PMID: 30713027 DOI: 10.1016/j.str.2019.01.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/23/2018] [Accepted: 12/31/2018] [Indexed: 12/12/2022]
Abstract
The multi-domain deubiquitinase USP15 regulates diverse eukaryotic processes and has been implicated in numerous diseases. We developed ubiquitin variants (UbVs) that targeted either the catalytic domain or each of three adaptor domains in USP15, including the N-terminal DUSP domain. We also designed a linear dimer (diUbV), which targeted the DUSP and catalytic domains, and exhibited enhanced specificity and more potent inhibition of catalytic activity than either UbV alone. In cells, the UbVs inhibited the deubiquitination of two USP15 substrates, SMURF2 and TRIM25, and the diUbV inhibited the effects of USP15 on the transforming growth factor β pathway. Structural analyses revealed that three distinct UbVs bound to the catalytic domain and locked the active site in a closed, inactive conformation, and one UbV formed an unusual strand-swapped dimer and bound two DUSP domains simultaneously. These inhibitors will enable the study of USP15 function in oncology, neurology, immunology, and inflammation.
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Affiliation(s)
- Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Alex U Singer
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Frank W Schmitges
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Sarah Kit Leng Lui
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Maria J Polyak
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Nassima Fodil
- Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada
| | - Jonathan R Krieger
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jiefei Tong
- Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | | | - Bradley B Brasher
- Boston Biochem, a Bio-Techne Brand, 840 Memorial Drive, Cambridge, MA 02139, USA
| | - Derek F J Ceccarelli
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Jason Moffat
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Frank Sicheri
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Michael F Moran
- SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Philippe Gros
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Pieter J A Eichhorn
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Martin Lenter
- Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany
| | | | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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35
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Abstract
Proteases drive the life cycle of all proteins, ensuring the transportation and activation of newly minted, would-be proteins into their functional form while recycling spent or unneeded proteins. Far from their image as engines of protein digestion, proteases play fundamental roles in basic physiology and regulation at multiple levels of systems biology. Proteases are intimately associated with disease and modulation of proteolytic activity is the presumed target for successful therapeutics. "Proteases: Pivot Points in Functional Proteomics" examines the crucial roles of proteolysis across a wide range of physiological processes and diseases. The existing and potential impacts of proteolysis-related activity on drug and biomarker development are presented in detail. All told the decisive roles of proteases in four major categories comprising 23 separate subcategories are addressed. Within this construct, 15 sets of subject-specific, tabulated data are presented that include identification of proteases, protease inhibitors, substrates, and their actions. Said data are derived from and confirmed by over 300 references. Cross comparison of datasets indicates that proteases, their inhibitors/promoters and substrates intersect over a range of physiological processes and diseases, both chronic and pathogenic. Indeed, "Proteases: Pivot Points …" closes by dramatizing this very point through association of (pro)Thrombin and Fibrin(ogen) with: hemostasis, innate immunity, cardiovascular and metabolic disease, cancer, neurodegeneration, and bacterial self-defense.
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Affiliation(s)
- Ingrid M Verhamme
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Sarah E Leonard
- Chemical and Biomolecular Engineering, University of Illinois Champaign-Urbana School of Chemical Sciences, Champaign, IL, USA
| | - Ray C Perkins
- New Liberty Proteomics Corporation, New Liberty, KY, USA.
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36
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Unsworth AJ, Bombik I, Pinto-Fernandez A, McGouran JF, Konietzny R, Zahedi RP, Watson SP, Kessler BM, Pears CJ. Human Platelet Protein Ubiquitylation and Changes following GPVI Activation. Thromb Haemost 2018; 119:104-116. [PMID: 30597505 PMCID: PMC6327716 DOI: 10.1055/s-0038-1676344] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Platelet activators stimulate post-translational modification of signalling proteins to change their activity or their molecular interactions leading to signal propagation. One covalent modification is attachment of the small protein ubiquitin to lysine residues in target proteins. Modification by ubiquitin can either target proteins for degradation by the proteasome or act as a scaffold for other proteins. Pharmacological inhibition of deubiquitylases or the proteasome inhibition of platelet activation by collagen, demonstrating a role for ubiquitylation, but relatively few substrates for ubiquitin have been identified and the molecular basis of inhibition is not established. Here, we report the ubiquitome of human platelets and changes in ubiquitylated proteins following stimulation by collagen-related peptide (CRP-XL). Using platelets from six individuals over three independent experiments, we identified 1,634 ubiquitylated peptides derived from 691 proteins, revealing extensive ubiquitylation in resting platelets. Note that 925 of these peptides show an increase of more than twofold following stimulation with CRP-XL. Multiple sites of ubiquitylation were identified on several proteins including Syk, filamin and integrin heterodimer sub-units. This work reveals extensive protein ubiquitylation during activation of human platelets and opens the possibility of novel therapeutic interventions targeting the ubiquitin machinery.
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Affiliation(s)
- Amanda J Unsworth
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom.,Institute for Cardiovascular and Metabolic Research, University of Reading, Reading, United Kingdom
| | - Izabela Bombik
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Adan Pinto-Fernandez
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Joanna F McGouran
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Rebecca Konietzny
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - René P Zahedi
- JGH Proteomics Centre, Lady Davis Institute, Jewish General Hospital, Montreal, Quebec, Canada
| | - Steve P Watson
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.,Centre of Membrane Proteins and Receptors, Universities of Birmingham and Nottingham, The Midlands, United Kingdom
| | - Benedikt M Kessler
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom
| | - Catherine J Pears
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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37
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Gong P, Davidson GA, Gui W, Yang K, Bozza WP, Zhuang Z. Activity-based ubiquitin-protein probes reveal target protein specificity of deubiquitinating enzymes. Chem Sci 2018; 9:7859-7865. [PMID: 30429995 PMCID: PMC6194582 DOI: 10.1039/c8sc01573b] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 08/08/2018] [Indexed: 12/26/2022] Open
Abstract
Ubiquitination is an essential eukaryotic post-translational modification that regulates various cellular processes. The removal of ubiquitin from its target protein is catalyzed by deubiquitinating enzymes (DUBs). Although it was proposed that many DUBs specifically interact and recognize ubiquitinated proteins as substrates, more direct evidence is needed to support this notion. Here we report protein-targeting activity-based DUB probes that allowed the identification of DUBs recognizing monoubiquitinated proliferating cell nuclear antigen (PCNA) in Saccharomyces cerevisiae. This new class of DUB probes contain a Michael acceptor as a warhead between ubiquitin and the target protein PCNA through a linkage that mimics the native isopeptide bond. We selected two known and biologically relevant ubiquitination sites on PCNA to generate the DUB probes. This allowed us to interrogate the site-specific deubiquitination of a target protein by DUBs. DUBs were profiled in yeast cell lysates using the two Ub-PCNA DUB probes in conjunction with two control probes that contain a noncleavable linkage but no warhead. We identified yeast DUBs through pulldown coupled with quantitative mass spectrometry analysis of the pulled down proteins. Our results showed that specific yeast DUBs recognize monoubiquitinated PCNA and corroborated previous genetic study. We also identified DUBs as potential new deubiquitinase of PCNA. Remarkably, identified DUBs clearly distinguish the different modification sites on PCNA, thus supporting a high level of DUB specificity beyond the target protein identity.
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Affiliation(s)
- Ping Gong
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , DE , USA 19716 .
| | - Gregory A Davidson
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , DE , USA 19716 .
| | - Weijun Gui
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , DE , USA 19716 .
| | - Kun Yang
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , DE , USA 19716 .
| | - William P Bozza
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , DE , USA 19716 .
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry , University of Delaware , 214A Drake Hall , Newark , DE , USA 19716 .
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38
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Chen XX, Yin Y, Cheng JW, Huang A, Hu B, Zhang X, Sun YF, Wang J, Wang YP, Ji Y, Qiu SJ, Fan J, Zhou J, Yang XR. BAP1 acts as a tumor suppressor in intrahepatic cholangiocarcinoma by modulating the ERK1/2 and JNK/c-Jun pathways. Cell Death Dis 2018; 9:1036. [PMID: 30305612 PMCID: PMC6179995 DOI: 10.1038/s41419-018-1087-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 12/15/2022]
Abstract
Current therapeutic options for intrahepatic cholangiocarcinoma (ICC) are very limited, which is largely attributed to poor understanding of molecular pathogenesis of ICC. Breast cancer type 1 susceptibility protein-associated protein-1 (BAP1) has been reported to be a broad-spectrum tumor suppressor in many tumor types, yet its role in ICC remains unknown. The aim of this study was to investigate the clinical implications and biological function of BAP1 in ICC. Our results showed that the messenger RNA and protein levels of BAP1 were significantly downregulated in ICC versus paired non-tumor tissues. Overexpression of wild-type but not mutant BAP1 significantly suppressed ICC cell proliferation, cell cycle progression, and invasion in vitro, as well as tumor progression in vivo. Conversely, knockdown of BAP1 yielded opposing effects. Mechanistically, BAP1 functioned as a tumor suppressor in ICC by inhibiting the extracellular signal-regulated kinase 1/2 and c-Jun N-terminal kinase/c-Jun pathways, and this function was abolished by inactivating mutations. Clinically, low BAP1 expression was positively correlated with aggressive tumor characteristics, such as larger tumor size, presence of lymphatic metastasis, and advanced tumor node metastasis stage. Survival analysis revealed that low BAP1 expression was significantly and independently associated with poor overall survival and relapse-free survival after curative surgery. In conclusion, BAP1 is a putative tumor suppressor of ICC, and may serve as a valuable prognostic biomarker as well as potential therapeutic target for ICC.
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Affiliation(s)
- Xu-Xiao Chen
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Yue Yin
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Jian-Wen Cheng
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Ao Huang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Bo Hu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Xin Zhang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Yun-Fan Sun
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Jian Wang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Yu-Peng Wang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Yuan Ji
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Department of Pathology, Zhongshan Hospital, Fudan University, 200032, Shanghai, China
| | - Shuang-Jian Qiu
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Jia Fan
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Jian Zhou
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China
| | - Xin-Rong Yang
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 200032, Shanghai, China.
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Kocaturk NM, Gozuacik D. Crosstalk Between Mammalian Autophagy and the Ubiquitin-Proteasome System. Front Cell Dev Biol 2018; 6:128. [PMID: 30333975 PMCID: PMC6175981 DOI: 10.3389/fcell.2018.00128] [Citation(s) in RCA: 270] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 09/13/2018] [Indexed: 12/16/2022] Open
Abstract
Autophagy and the ubiquitin-proteasome system (UPS) are the two major intracellular quality control and recycling mechanisms that are responsible for cellular homeostasis in eukaryotes. Ubiquitylation is utilized as a degradation signal by both systems, yet, different mechanisms are in play. The UPS is responsible for the degradation of short-lived proteins and soluble misfolded proteins whereas autophagy eliminates long-lived proteins, insoluble protein aggregates and even whole organelles (e.g., mitochondria, peroxisomes) and intracellular parasites (e.g., bacteria). Both the UPS and selective autophagy recognize their targets through their ubiquitin tags. In addition to an indirect connection between the two systems through ubiquitylated proteins, recent data indicate the presence of connections and reciprocal regulation mechanisms between these degradation pathways. In this review, we summarize these direct and indirect interactions and crosstalks between autophagy and the UPS, and their implications for cellular stress responses and homeostasis.
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Affiliation(s)
- Nur Mehpare Kocaturk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Devrim Gozuacik
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
- Center of Excellence for Functional Surfaces and Interfaces for Nano Diagnostics (EFSUN), Sabanci University, Istanbul, Turkey
- Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
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40
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Gillespie JJ, Driscoll TP, Verhoeve VI, Rahman MS, Macaluso KR, Azad AF. A Tangled Web: Origins of Reproductive Parasitism. Genome Biol Evol 2018; 10:2292-2309. [PMID: 30060072 PMCID: PMC6133264 DOI: 10.1093/gbe/evy159] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2018] [Indexed: 12/13/2022] Open
Abstract
While typically a flea parasite and opportunistic human pathogen, the presence of Rickettsia felis (strain LSU-Lb) in the non-blood-feeding, parthenogenetically reproducing booklouse, Liposcelis bostrychophila, provides a system to ascertain factors governing not only host transitions but also obligate reproductive parasitism (RP). Analysis of plasmid pLbAR, unique to R. felis str. LSU-Lb, revealed a toxin–antitoxin module with similar features to prophage-encoded toxin–antitoxin modules utilized by parasitic Wolbachia strains to induce another form of RP, cytoplasmic incompatibility, in their arthropod hosts. Curiously, multiple deubiquitinase and nuclease domains of the large (3,841 aa) pLbAR toxin, as well the entire antitoxin, facilitated the detection of an assortment of related proteins from diverse intracellular bacteria, including other reproductive parasites. Our description of these remarkable components of the intracellular mobilome, including their presence in certain arthropod genomes, lends insight on the evolution of RP, while invigorating research on parasite-mediated biocontrol of arthropod-borne viral and bacterial pathogens.
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Affiliation(s)
- Joseph J Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine
| | | | | | | | - Kevin R Macaluso
- Vector-borne Disease Laboratories, Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University
| | - Abdu F Azad
- Department of Microbiology and Immunology, University of Maryland School of Medicine
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41
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Emerging insights into HAUSP (USP7) in physiology, cancer and other diseases. Signal Transduct Target Ther 2018; 3:17. [PMID: 29967688 PMCID: PMC6023882 DOI: 10.1038/s41392-018-0012-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/13/2018] [Accepted: 02/23/2018] [Indexed: 12/13/2022] Open
Abstract
Herpesvirus-associated ubiquitin-specific protease (HAUSP) is a USP family deubiquitinase. HAUSP is a protein of immense biological importance as it is involved in several cellular processes, including host-virus interactions, oncogenesis and tumor suppression, DNA damage and repair processes, DNA dynamics and epigenetic modulations, regulation of gene expression and protein function, spatio-temporal distribution, and immune functions. Since its discovery in the late 1990s as a protein interacting with a herpes virus regulatory protein, extensive studies have assessed its complex roles in p53-MDM2-related networks, identified numerous additional interacting partners, and elucidated the different roles of HAUSP in the context of cancer, development, and metabolic and neurological pathologies. Recent analyses have provided new insights into its biochemical and functional dynamics. In this review, we provide a comprehensive account of our current knowledge about emerging insights into HAUSP in physiology and diseases, which shed light on fundamental biological questions and promise to provide a potential target for therapeutic intervention. Improved understandings of a molecular-tag-removing enzyme could lead to the development of therapies for many diseases. Dr. Mrinal K Ghosh of the Council of Scientific and Industrial Research-Indian Institute of Chemical Biology (CSIR-IICB) and colleagues reviewed 20 years of research on herpesvirus-associated ubiquitin-specific protease (HAUSP), involved in a wide range of cellular processes through its role in removing the ubiquitin from molecules, thus signaling their fate. It was first discovered in/as a herpes virus infected cells, ultimately enhancing infection. It was later found to have a wide range of functions depending on the molecules it interacts with under normal physiological and disease conditions. Targeting HAUSP with drugs shows promise for suppressing prostate, lung, colon, breast, blood, and other cancers. It could also impact treatment of neurological conditions such as Huntington’s disease, and metabolic disorders, such as diabetes.
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42
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Kwasna D, Abdul Rehman SA, Natarajan J, Matthews S, Madden R, De Cesare V, Weidlich S, Virdee S, Ahel I, Gibbs-Seymour I, Kulathu Y. Discovery and Characterization of ZUFSP/ZUP1, a Distinct Deubiquitinase Class Important for Genome Stability. Mol Cell 2018; 70:150-164.e6. [PMID: 29576527 PMCID: PMC5896202 DOI: 10.1016/j.molcel.2018.02.023] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/17/2018] [Accepted: 02/15/2018] [Indexed: 01/17/2023]
Abstract
Deubiquitinating enzymes (DUBs) are important regulators of ubiquitin signaling. Here, we report the discovery of deubiquitinating activity in ZUFSP/C6orf113. High-resolution crystal structures of ZUFSP in complex with ubiquitin reveal several distinctive features of ubiquitin recognition and catalysis. Our analyses reveal that ZUFSP is a novel DUB with no homology to any known DUBs, leading us to classify ZUFSP as the seventh DUB family. Intriguingly, the minimal catalytic domain does not cleave polyubiquitin. We identify two ubiquitin binding domains in ZUFSP: a ZHA (ZUFSP helical arm) that binds to the distal ubiquitin and an atypical UBZ domain in ZUFSP that binds to polyubiquitin. Importantly, both domains are essential for ZUFSP to selectively cleave K63-linked polyubiquitin. We show that ZUFSP localizes to DNA lesions, where it plays an important role in genome stability pathways, functioning to prevent spontaneous DNA damage and also promote cellular survival in response to exogenous DNA damage.
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Affiliation(s)
- Dominika Kwasna
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Syed Arif Abdul Rehman
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jayaprakash Natarajan
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Stephen Matthews
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ross Madden
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Virginia De Cesare
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Simone Weidlich
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Ivan Ahel
- DNA Damage Response Laboratory, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Ian Gibbs-Seymour
- DNA Damage Response Laboratory, Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, 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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43
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Wu Y, Kang J, Zhang L, Liang Z, Tang X, Yan Y, Qian H, Zhang X, Xu W, Mao F. Ubiquitination regulation of inflammatory responses through NF-κB pathway. Am J Transl Res 2018; 10:881-891. [PMID: 29636878 PMCID: PMC5883129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/01/2018] [Indexed: 06/08/2023]
Abstract
The development of inflammation is mutually affected with damaged DNA and the abnormal expression of protein modification. Ubiquitination, a way of protein modification, plays a key role in regulating various biological functions including inflammation responses. The ubiquitin enzymes and deubiquitinating enzymes (DUBs) jointly control the ubiquitination. The fact that various ubiquitin linkage chains control the fate of the substrate suggests that the regulatory mechanisms of ubiquitin enzymes are central for ubiquitination. In inflammation diseases, the pro-inflammatory transcription factor NF-κB regulates transcription of pro-labour mediators in response to inflammatory stimuli and expression of numerous genes that control inflammation which is associated with ubiquitination. The ubiquitination regulates NF-κB signaling pathway with many receptor families, including NOD-like receptors (NLR), Toll-like receptors (TLR) and RIG-I-like receptors (RLR), mainly by K63-linked polyubiquitin chains. In this review, we highlight the study of ubiquitination in the inflammatory signaling pathway including NF-κB signaling regulated by ubiquitin enzymes and DUBs. Furthermore, it is emphasized that the interaction of ubiquitin-mediated inflammatory signaling system accurately regulates the inflammatory responses.
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Affiliation(s)
- Yunbing Wu
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Jingjing Kang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Lu Zhang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Zhaofeng Liang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Xudong Tang
- Jiangsu University of Science and TechnologyZhenjiang 212018, Jiangsu, China
| | - Yongmin Yan
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Hui Qian
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Xu Zhang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Wenrong Xu
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine, Jiangsu UniversityZhenjiang 212013, Jiangsu, China
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44
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The deubiquitylase USP15 regulates topoisomerase II alpha to maintain genome integrity. Oncogene 2018; 37:2326-2342. [PMID: 29429988 PMCID: PMC5916918 DOI: 10.1038/s41388-017-0092-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/25/2017] [Accepted: 11/24/2017] [Indexed: 02/04/2023]
Abstract
Ubiquitin-specific protease 15 (USP15) is a widely expressed deubiquitylase that has been implicated in diverse cellular processes in cancer. Here we identify topoisomerase II (TOP2A) as a novel protein that is regulated by USP15. TOP2A accumulates during G2 and functions to decatenate intertwined sister chromatids at prophase, ensuring the replicated genome can be accurately divided into daughter cells at anaphase. We show that USP15 is required for TOP2A accumulation, and that USP15 depletion leads to the formation of anaphase chromosome bridges. These bridges fail to decatenate, and at mitotic exit form micronuclei that are indicative of genome instability. We also describe the cell cycle-dependent behaviour for two major isoforms of USP15, which differ by a short serine-rich insertion that is retained in isoform-1 but not in isoform-2. Although USP15 is predominantly cytoplasmic in interphase, we show that both isoforms move into the nucleus at prophase, but that isoform-1 is phosphorylated on its unique S229 residue at mitotic entry. The micronuclei phenotype we observe on USP15 depletion can be rescued by either USP15 isoform and requires USP15 catalytic activity. Importantly, however, an S229D phospho-mimetic mutant of USP15 isoform-1 cannot rescue either the micronuclei phenotype, or accumulation of TOP2A. Thus, S229 phosphorylation selectively abrogates this role of USP15 in maintaining genome integrity in an isoform-specific manner. Finally, we show that USP15 isoform-1 is preferentially upregulated in a panel of non-small cell lung cancer cell lines, and propose that isoform imbalance may contribute to genome instability in cancer. Our data provide the first example of isoform-specific deubiquitylase phospho-regulation and reveal a novel role for USP15 in guarding genome integrity.
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45
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Lamberto I, Liu X, Seo HS, Schauer NJ, Iacob RE, Hu W, Das D, Mikhailova T, Weisberg EL, Engen JR, Anderson KC, Chauhan D, Dhe-Paganon S, Buhrlage SJ. Structure-Guided Development of a Potent and Selective Non-covalent Active-Site Inhibitor of USP7. Cell Chem Biol 2017; 24:1490-1500.e11. [PMID: 29056421 DOI: 10.1016/j.chembiol.2017.09.003] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 08/09/2017] [Accepted: 09/05/2017] [Indexed: 01/30/2023]
Abstract
Deubiquitinating enzymes (DUBs) have garnered significant attention as drug targets in the last 5-10 years. The excitement stems in large part from the powerful ability of DUB inhibitors to promote degradation of oncogenic proteins, especially proteins that are challenging to directly target but which are stabilized by DUB family members. Highly optimized and well-characterized DUB inhibitors have thus become highly sought after tools. Most reported DUB inhibitors, however, are polypharmacological agents possessing weak (micromolar) potency toward their primary target, limiting their utility in target validation and mechanism studies. Due to a lack of high-resolution DUB⋅small-molecule ligand complex structures, no structure-guided optimization efforts have been reported for a mammalian DUB. Here, we report a small-molecule⋅ubiquitin-specific protease (USP) family DUB co-structure and rapid design of potent and selective inhibitors of USP7 guided by the structure. Interestingly, the compounds are non-covalent active-site inhibitors.
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Affiliation(s)
- Ilaria Lamberto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Xiaoxi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan J Schauer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Wanyi Hu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Deepika Das
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tatiana Mikhailova
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen L Weisberg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Dharminder Chauhan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Sara J Buhrlage
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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46
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Darling S, Fielding AB, Sabat-Pośpiech D, Prior IA, Coulson JM. Regulation of the cell cycle and centrosome biology by deubiquitylases. Biochem Soc Trans 2017; 45:1125-1136. [PMID: 28900014 PMCID: PMC5652225 DOI: 10.1042/bst20170087] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022]
Abstract
Post-translational modification of proteins by ubiquitylation is increasingly recognised as a highly complex code that contributes to the regulation of diverse cellular processes. In humans, a family of almost 100 deubiquitylase enzymes (DUBs) are assigned to six subfamilies and many of these DUBs can remove ubiquitin from proteins to reverse signals. Roles for individual DUBs have been delineated within specific cellular processes, including many that are dysregulated in diseases, particularly cancer. As potentially druggable enzymes, disease-associated DUBs are of increasing interest as pharmaceutical targets. The biology, structure and regulation of DUBs have been extensively reviewed elsewhere, so here we focus specifically on roles of DUBs in regulating cell cycle processes in mammalian cells. Over a quarter of all DUBs, representing four different families, have been shown to play roles either in the unidirectional progression of the cell cycle through specific checkpoints, or in the DNA damage response and repair pathways. We catalogue these roles and discuss specific examples. Centrosomes are the major microtubule nucleating centres within a cell and play a key role in forming the bipolar mitotic spindle required to accurately divide genetic material between daughter cells during cell division. To enable this mitotic role, centrosomes undergo a complex replication cycle that is intimately linked to the cell division cycle. Here, we also catalogue and discuss DUBs that have been linked to centrosome replication or function, including centrosome clustering, a mitotic survival strategy unique to cancer cells with supernumerary centrosomes.
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Affiliation(s)
- Sarah Darling
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Andrew B Fielding
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Dorota Sabat-Pośpiech
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Ian A Prior
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K
| | - Judy M Coulson
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool L69 3BX, U.K.
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47
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Kaistha BP, Krattenmacher A, Fredebohm J, Schmidt H, Behrens D, Widder M, Hackert T, Strobel O, Hoheisel JD, Gress TM, Buchholz M. The deubiquitinating enzyme USP5 promotes pancreatic cancer via modulating cell cycle regulators. Oncotarget 2017; 8:66215-66225. [PMID: 29029505 PMCID: PMC5630405 DOI: 10.18632/oncotarget.19882] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/11/2017] [Indexed: 11/25/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid tumors. With an overall five-year survival rate remaining below 6%, there is an explicit need to search for new molecular targets for therapeutic interventions. We undertook a barcode labelled short-hairpin (shRNA) library screen in pancreatic cancer cells in order to identify novel genes promoting cancer survival and progression. Among the candidate genes identified in this screen was the deubiquitinase USP5, which subsequent gene expression analyses demonstrated to be significantly upregulated in primary human pancreatic cancer tissues. Using different knockdown approaches, we show that expression of USP5 is essential for the proliferation and survival of pancreatic cancer cells, tested under different 2D and 3D cell culture conditions as well as in in vivo experiments. These growth inhibition effects upon knockdown of USP5 are mediated primarily by the attenuation of G1/S phase transition in the cells, which is accompanied by accumulation of DNA damage, upregulation of p27, and increased apoptosis rates. Since USP5 is overexpressed in cancer tissues, it can thus potentially serve as a new target for therapeutic interventions, especially given the fact that deubiquitinases are currently emerging as new class of attractive drug targets in cancer.
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Affiliation(s)
- Brajesh P Kaistha
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
| | - Anja Krattenmacher
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
| | - Johannes Fredebohm
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Harald Schmidt
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
| | - Diana Behrens
- Experimantal Pharmacology and Oncology (EPO Berlin-Buch), Berlin, Germany
| | - Miriam Widder
- Institute for Bioprocessing and Analytical Measurement Techniques (IBA-Heiligenstadt), Heilbad Heiligenstadt, Germany
| | - Thilo Hackert
- Department of Surgery, University Clinic Heidelberg, Heidelberg, Germany
| | - Oliver Strobel
- Department of Surgery, University Clinic Heidelberg, Heidelberg, Germany
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas M Gress
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
| | - Malte Buchholz
- Department of Medicine, Division of Gastroenterology, Endocrinology and Metabolism, Philipps-University Marburg, Marburg, Germany
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48
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Affiliation(s)
- Tycho E.T. Mevissen
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - David Komander
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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49
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The functional interplay between the HIF pathway and the ubiquitin system - more than a one-way road. Exp Cell Res 2017; 356:152-159. [PMID: 28315321 DOI: 10.1016/j.yexcr.2017.03.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/13/2017] [Indexed: 12/30/2022]
Abstract
The hypoxia inducible factor (HIF) pathway and the ubiquitin system represent major cellular processes that are involved in the regulation of a plethora of cellular signaling pathways and tissue functions. The ubiquitin system controls the ubiquitination of proteins, which is the covalent linkage of one or several ubiquitin molecules to specific targets. This ubiquitination is catalyzed by approximately 1000 different E3 ubiquitin ligases and can lead to different effects, depending on the type of internal ubiquitin chain linkage. The best-studied function is the targeting of proteins for proteasomal degradation. The activity of E3 ligases is antagonized by proteins called deubiquitinases (or deubiquitinating enzymes), which negatively regulate ubiquitin chains. This is performed in most cases by the catalytic removal of these chains from the targeted protein. The HIF pathway is regulated in an oxygen-dependent manner by oxygen-sensing hydroxylases. Covalent modification of HIFα subunits leads to the recruitment of an E3 ligase complex via the von Hippel-Lindau (VHL) protein and the subsequent polyubiquitination and proteasomal degradation of HIFα subunits, demonstrating the regulation of the HIF pathway by the ubiquitin system. This unidirectional effect of an E3 ligase on the HIF pathway is the best-studied example for the interplay between these two important cellular processes. However, additional regulatory mechanisms of the HIF pathway through the ubiquitin system are emerging and, more recently, also the reciprocal regulation of the ubiquitin system through components of the HIF pathway. Understanding these mechanisms and their relevance for the activity of each other is of major importance for the comprehensive elucidation of the oxygen-dependent regulation of cellular processes. This review describes the current knowledge of the functional bidirectional interplay between the HIF pathway and the ubiquitin system on the protein level.
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50
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He M, Zhou Z, Shah AA, Zou H, Tao J, Chen Q, Wan Y. The emerging role of deubiquitinating enzymes in genomic integrity, diseases, and therapeutics. Cell Biosci 2016; 6:62. [PMID: 28031783 PMCID: PMC5168870 DOI: 10.1186/s13578-016-0127-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/05/2016] [Indexed: 02/05/2023] Open
Abstract
The addition of mono-ubiquitin or poly-ubiquitin chain to signaling proteins in response to DNA damage signal is thought to be a critical event that facilitates the recognition of DNA damage lesion site, the activation of checkpoint function, termination and checkpoint response and the recruitment of DNA repair proteins. Despite the ubiquitin modifiers, removal of ubiquitin from the functional proteins by the deubiquitinating enzymes (DUBs) plays an important role in orchestrating DNA damage response as well as DNA repair processes. Deregulated ubiquitination and deubiquitination could lead to genome instability that in turn causes tumorigenesis. Recent TCGA study has further revealed the connection between mutations in alteration of DUBs and various types of tumors. In addition, emerging drug design based on DUBs provides a new avenue for anti-cancer therapy. In this review, we will summarize the role of deubiquitination and specificity of DUBs, and highlight the recent discoveries of DUBs in the modulation of ubiquitin-mediated DNA damage response and DNA damage repair. We will furthermore discuss the DUBs involved in the tumorigenesis as well as interception of deubiquitination as a novel strategy for anti-cancer therapy.
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Affiliation(s)
- Mingjing He
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA ; State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041 Sichuan People's Republic of China
| | - Zhuan Zhou
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Anil A Shah
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Haojing Zou
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Jin Tao
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041 Sichuan People's Republic of China
| | - Yong Wan
- Department of Cell Biology, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Hillman Cancer Center, HCC2.6c, Pittsburgh, PA 15213 USA
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