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Schmidt M, Grethe C, Recknagel S, Kipka GM, Klink N, Gersch M. N-Cyanopiperazines as Specific Covalent Inhibitors of the Deubiquitinating Enzyme UCHL1. Angew Chem Int Ed Engl 2024; 63:e202318849. [PMID: 38239128 DOI: 10.1002/anie.202318849] [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: 12/07/2023] [Indexed: 02/10/2024]
Abstract
Cyanamides have emerged as privileged scaffolds in covalent inhibitors of deubiquitinating enzymes (DUBs). However, many compounds with a cyanopyrrolidine warhead show cross-reactivity toward small subsets of DUBs or toward the protein deglycase PARK7/DJ-1, hampering their use for the selective perturbation of a single DUB in living cells. Here, we disclose N'-alkyl,N-cyanopiperazines as structures for covalent enzyme inhibition with exceptional specificity for the DUB UCHL1 among 55 human deubiquitinases and with effective target engagement in cells. Notably, transitioning from 5-membered pyrrolidines to 6-membered heterocycles eliminated PARK7 binding and introduced context-dependent reversibility of the isothiourea linkage to the catalytic cysteine of UCHL1. Compound potency and specificity were analysed by a range of biochemical assays and with a crystal structure of a cyanopiperazine in covalent complex with UCHL1. The structure revealed a compound-induced conformational restriction of the cross-over loop, which underlies the observed inhibitory potencies. Through the rationalization of specificities of different cyanamides, we introduce a framework for the investigation of protein reactivity of bioactive nitriles of this compound class. Our results represent an encouraging case study for the refining of electrophilic compounds into chemical probes, emphasizing the potential to engineer specificity through subtle chemical modifications around the warhead.
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Affiliation(s)
- Mirko Schmidt
- Chemical Genomics Centre, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
| | - Christian Grethe
- Chemical Genomics Centre, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
| | - Sarah Recknagel
- Chemical Genomics Centre, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
| | - Gian-Marvin Kipka
- Chemical Genomics Centre, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
| | - Nikolas Klink
- Chemical Genomics Centre, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
| | - Malte Gersch
- Chemical Genomics Centre, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 15, D-44227, Dortmund, Germany
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2
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Ren W, Xu Z, Chang Y, Ju F, Wu H, Liang Z, Zhao M, Wang N, Lin Y, Xu C, Chen S, Rao Y, Lin C, Yang J, Liu P, Zhang J, Huang C, Xia N. Pharmaceutical targeting of OTUB2 sensitizes tumors to cytotoxic T cells via degradation of PD-L1. Nat Commun 2024; 15:9. [PMID: 38167274 PMCID: PMC10761827 DOI: 10.1038/s41467-023-44466-7] [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: 01/25/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
PD-1 is a co-inhibitory receptor expressed by CD8+ T cells which limits their cytotoxicity. PD-L1 expression on cancer cells contributes to immune evasion by cancers, thus, understanding the mechanisms that regulate PD-L1 protein levels in cancers is important. Here we identify tumor-cell-expressed otubain-2 (OTUB2) as a negative regulator of antitumor immunity, acting through the PD-1/PD-L1 axis in various human cancers. Mechanistically, OTUB2 directly interacts with PD-L1 to disrupt the ubiquitination and degradation of PD-L1 in the endoplasmic reticulum. Genetic deletion of OTUB2 markedly decreases the expression of PD-L1 proteins on the tumor cell surface, resulting in increased tumor cell sensitivity to CD8+ T-cell-mediated cytotoxicity. To underscore relevance in human patients, we observe a significant correlation between OTUB2 expression and PD-L1 abundance in human non-small cell lung cancer. An inhibitor of OTUB2, interfering with its deubiquitinase activity without disrupting the OTUB2-PD-L1 interaction, successfully reduces PD-L1 expression in tumor cells and suppressed tumor growth. Together, these results reveal the roles of OTUB2 in PD-L1 regulation and tumor evasion and lays down the proof of principle for OTUB2 targeting as therapeutic strategy for cancer treatment.
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Affiliation(s)
- Wenfeng Ren
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Zilong Xu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yating Chang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Fei Ju
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Hongning Wu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Zhiqi Liang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Min Zhao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Naizhen Wang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yanhua Lin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chenhang Xu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Shengming Chen
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yipeng Rao
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chaolong Lin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jianxin Yang
- Department of Hepatobiliary & Pancreatic Surgery, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361004, China
- Fujian Provincial Key Laboratory and Chronic Liver Disease and Hepatocellular Carcinoma, Xiamen, Fujian, 361004, China
| | - Pingguo Liu
- Department of Hepatobiliary & Pancreatic Surgery, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, 361004, China.
- Fujian Provincial Key Laboratory and Chronic Liver Disease and Hepatocellular Carcinoma, Xiamen, Fujian, 361004, China.
| | - Jun Zhang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Chenghao Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China.
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, Fujian, 361102, China.
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, Fujian, 361102, China.
- School of Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China.
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3
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Klonisch T, Logue SE, Hombach-Klonisch S, Vriend J. DUBing Primary Tumors of the Central Nervous System: Regulatory Roles of Deubiquitinases. Biomolecules 2023; 13:1503. [PMID: 37892185 PMCID: PMC10605193 DOI: 10.3390/biom13101503] [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: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023] Open
Abstract
The ubiquitin proteasome system (UPS) utilizes an orchestrated enzymatic cascade of E1, E2, and E3 ligases to add single or multiple ubiquitin-like molecules as post-translational modification (PTM) to proteins. Ubiquitination can alter protein functions and/or mark ubiquitinated proteins for proteasomal degradation but deubiquitinases (DUBs) can reverse protein ubiquitination. While the importance of DUBs as regulatory factors in the UPS is undisputed, many questions remain on DUB selectivity for protein targeting, their mechanism of action, and the impact of DUBs on the regulation of diverse biological processes. Furthermore, little is known about the expression and role of DUBs in tumors of the human central nervous system (CNS). In this comprehensive review, we have used publicly available transcriptional datasets to determine the gene expression profiles of 99 deubiquitinases (DUBs) from five major DUB families in seven primary pediatric and adult CNS tumor entities. Our analysis identified selected DUBs as potential new functional players and biomarkers with prognostic value in specific subtypes of primary CNS tumors. Collectively, our analysis highlights an emerging role for DUBs in regulating CNS tumor cell biology and offers a rationale for future therapeutic targeting of DUBs in CNS tumors.
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Affiliation(s)
- Thomas Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Medical Microbiology & Infectious Diseases, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Susan E. Logue
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- CancerCare Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Sabine Hombach-Klonisch
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Department of Pathology, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Jerry Vriend
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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4
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De Cesare V. MALDI-TOF Mass Spectrometry for interrogating ubiquitin enzymes. Front Mol Biosci 2023; 10:1184934. [PMID: 37234921 PMCID: PMC10206504 DOI: 10.3389/fmolb.2023.1184934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023] Open
Abstract
The attachment of ubiquitin to a substrate (ubiquitination or ubiquitylation) impacts its lifetime and regulates its function within the cell. Several classes of enzymes oversee the attachment of ubiquitin to the substrate: an E1 activating enzyme that makes ubiquitin chemically susceptible prior to the following stages of conjugation and ligation, respectively mediated by E2 conjugating enzymes (E2s) and E3 ligases (E3s). Around 40 E2s and more than 600 E3s are encoded in the human genome, and their combinatorial and cooperative behaviour dictate the tight specificity necessary for the regulation of thousands of substrates. The removal of ubiquitin is orchestrated by a network of about 100 deubiquitylating enzymes (DUBs). Many cellular processes are tightly controlled by ubiquitylation, which is essential in maintaining cellular homeostasis. Because of the fundamental role(s) of ubiquitylation, there is an interest in better understanding the function and specificity of the ubiquitin machinery. Since 2014, an expanding array of Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) Mass Spectrometry (MS) assays have been developed to systematically characterise the activity of a variety of ubiquitin enzymes in vitro. Here we recapitulate how MALDI-TOF MS aided the in vitro characterization of ubiquitin enzymes and the discovery of new and unexpected of E2s and DUBs functions. Given the versatility of the MALDI-TOF MS approach, we foreseen the use of this technology to further expand our understanding of ubiquitin and ubiquitin-like enzymes.
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Affiliation(s)
- Virginia De Cesare
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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5
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Li F, Lu ZY, Xue YT, Liu Y, Cao J, Sun ZT, Zhang Q, Xu MD, Wang XY, Xu KL, Wu QY. Molecular basis of JAK2 H608Y and H608N mutations in the pathology of acute myeloid leukemia. Int J Biol Macromol 2023; 229:247-259. [PMID: 36529225 DOI: 10.1016/j.ijbiomac.2022.12.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/11/2022] [Accepted: 12/12/2022] [Indexed: 12/16/2022]
Abstract
Risk-stratification of acute myeloid leukemia (AML) based on (cyto)genetic aberrations, including hotspot mutations, deletions and point mutations have evolved substantially in recent years. With the development of next-generation sequence technology, more and more novel mutations in the AML were identified. Thus, to unravel roles and mechanism of novel mutations would improve prognostic and predictive abilities. In this study, two novel germline JAK2 His608Tyr (H608Y) and His608Asn (H608N) mutations were identified and the molecular basis of these mutations in the leukemiagenesis of AML was elucidated. Our results indicated that JAK2 H608Y and H608N mutations disrupted the hydrogen bond between Q656 and H608 which reduced the JH2 domain's activity and abolished interactions between JH1 and JH2 domains, forced JAK2 into the active conformation, facilitated the entrance of substrates and thus caused JAK2 hyperactivation. Further studies suggested that JAK2 H608Y and H608N mutations enhanced the cell proliferation and inhibited the differentiation of Ba/F3 and MV4-11 cells via activating the JAK2-STAT5 signaling pathway. Moreover, rescue experiments demonstrated that mutations repaired the hydrogen bond between Q656 and H608 displayed opposite results. Thus, this study revealed the molecular basis of JAK2 H608Y and H608N mutations in the pathology of AML.
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Affiliation(s)
- Feng Li
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Cell Biology and Neurobiology, Xuzhou Medical University, Xuzhou 221002, China
| | - Zi-Yi Lu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yu-Tong Xue
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yang Liu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Jiang Cao
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zeng-Tian Sun
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Qi Zhang
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Meng-Di Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiao-Yun Wang
- College of Life Sciences, Shandong Agricultural University, Shandong 271018, China.
| | - Kai-Lin Xu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Qing-Yun Wu
- Blood Diseases Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China; Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.
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6
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Grethe C, Schmidt M, Kipka GM, O'Dea R, Gallant K, Janning P, Gersch M. Structural basis for specific inhibition of the deubiquitinase UCHL1. Nat Commun 2022; 13:5950. [PMID: 36216817 PMCID: PMC9549030 DOI: 10.1038/s41467-022-33559-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 09/15/2022] [Indexed: 11/11/2022] Open
Abstract
Ubiquitination regulates protein homeostasis and is tightly controlled by deubiquitinases (DUBs). Loss of the DUB UCHL1 leads to neurodegeneration, and its dysregulation promotes cancer metastasis and invasiveness. Small molecule probes for UCHL1 and DUBs in general could help investigate their function, yet specific inhibitors and structural information are rare. Here we report the potent and non-toxic chemogenomic pair of activity-based probes GK13S and GK16S for UCHL1. Biochemical characterization of GK13S demonstrates its stereoselective inhibition of cellular UCHL1. The crystal structure of UCHL1 in complex with GK13S shows the enzyme locked in a hybrid conformation of apo and Ubiquitin-bound states, which underlies its UCHL1-specificity within the UCH DUB family. Phenocopying a reported inactivating mutation of UCHL1 in mice, GK13S, but not GK16S, leads to reduced levels of monoubiquitin in a human glioblastoma cell line. Collectively, we introduce a set of structurally characterized, chemogenomic probes suitable for the cellular investigation of UCHL1. The deubiquitinase UCHL1 has been linked to cancer invasiveness and neurodegeneration yet its molecular roles have remained poorly defined. Here the authors reveal the structural basis for how UCHL1 can be specifically inhibited and how chemogenomic probes can be used to dissect its functions in living cells.
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Affiliation(s)
- Christian Grethe
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Mirko Schmidt
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Gian-Marvin Kipka
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Rachel O'Dea
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Kai Gallant
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany.,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany
| | - Petra Janning
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Str. 11, Dortmund, Germany
| | - Malte Gersch
- Max Planck Institute of Molecular Physiology, Chemical Genomics Centre, Otto-Hahn-Str. 15, Dortmund, Germany. .,TU Dortmund University, Department of Chemistry and Chemical Biology, Otto-Hahn-Str. 15, Dortmund, Germany.
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7
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Zhou L, Chen G, Liu T, Liu X, Yang C, Jiang J. MJDs family members: Potential prognostic targets and immune-associated biomarkers in hepatocellular carcinoma. Front Genet 2022; 13:965805. [PMID: 36159990 PMCID: PMC9500549 DOI: 10.3389/fgene.2022.965805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 11/21/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common gastrointestinal malignancies. It is not easy to be diagnosed in the early stage and is prone to relapse, with a very poor prognosis. And immune cell infiltration and tumor microenvironment play important roles in predicting therapeutic response and prognosis of HCC. Machado-Joseph domain-containing proteases (MJDs), as a gene family extensively involved in tumor progression, has pro-cancer and anti-cancer effects. However, the relationship between MJDs family members and immune cell infiltration and tumor microenvironment in HCC remains unclear. Therefore, cBio Cancer Genomics Portal (cBioPortal), The Cancer Genome Atlas (TCGA), UALCAN, Human Protein Atlas (HPA), MethSurv, and Tumor Immune Estimation Resource (TIMER) databases were performed to investigate the mRNA expression, DNA methylation, clinicopathologic features, immune cell infiltration and other related functions of MJDs family members in HCC. The results indicated that the expression of ATXN3, JOSD1, and JOSD2 was dramatically increased in HCC tissues and cell lines, and was correlated with histological grade, specimen type, TP53 mutation, lymph node metastatic, gender, and age of patients with HCC. Meanwhile, these genes also showed clinical value in improving the overall survival (OS), disease-specific survival (DSS), progression free survival (PFS), and relapse-free survival (RFS) in patients with HCC. The prognostic model indicated that the worse survival was associated with overall high expression of MJDs members. Next, the results suggested that promotor methylation levels of the MJDs family were closely related to these family mRNA expression levels, clinicopathologic features, and prognostic values in HCC. Moreover, the MJDs family were significantly correlated with CD4+ T cells, CD8+ T cells, B cells, neutrophils, macrophages, and DCs. And MJDs family members’ expression were substantially associated with the levels of several lymphocytes, immunomoinhibitors, immunomostimulators, chemokine ligands, and chemokine receptors. In addition, the expression levels of MJDs family were significantly correlated with cancer-related signaling pathways. Taken together, our results indicated that the aberrant expression of MJDs family in HCC played a critical role in clinical feature, prognosis, tumor microenvironment, immune-related molecules, mutation, gene copy number, and promoter methylation level. And MJDs family may be effective immunotherapeutic targets for patients with HCC and have the potential to be prognostic biomarkers.
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Affiliation(s)
- Lei Zhou
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Guojie Chen
- Hunan YoBon Biotechnology Limited Company, Changsha, China
| | - Tao Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Xinyuan Liu
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Chengxiao Yang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
| | - Jianxin Jiang
- Department of Hepatobiliary Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- School of Clinical Medicine, Guizhou Medical University, Guiyang, China
- Department of Hepatobiliary Surgery, Renmin Hospital of Wuhan University, Wuhan, China
- *Correspondence: Jianxin Jiang,
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8
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Ran Y, He J, Peng W, Liu Z, Mei Y, Zhou Y, Yin N, Qi H. Development and validation of a transcriptomic signature-based model as the predictive, preventive, and personalized medical strategy for preterm birth within 7 days in threatened preterm labor women. EPMA J 2022; 13:87-106. [PMID: 35273661 PMCID: PMC8897543 DOI: 10.1007/s13167-021-00268-9] [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: 11/09/2021] [Accepted: 12/24/2021] [Indexed: 12/08/2022]
Abstract
Preterm birth (PTB) is the leading cause of neonatal death. The essential strategy to prevent PTB is the accurate identification of threatened preterm labor (TPTL) women who will have PTB in a short time (< 7 days). Here, we aim to propose a clinical model to contribute to the effective prediction, precise prevention, and personalized medical treatment for PTB < 7 days in TPTL women through bioinformatics analysis and prospective cohort studies. In this study, the 1090 key genes involved in PTB < 7 days in the peripheral blood of TPTL women were ascertained using WGCNA. Based on this, the biological basis of immune-inflammatory activation (e.g., IFNγ and TNFα signaling) as well as immune cell disorders (e.g., monocytes and Th17 cells) in PTB < 7 days were revealed. Then, four core genes (JOSD1, IDNK, ZMYM3, and IL1B) that best represent their transcriptomic characteristics were screened by SVM and LASSO algorithm. Therefore, a prediction model with an AUC of 0.907 was constructed, which was validated in a larger population (AUC = 0.783). Moreover, the predictive value (AUC = 0.957) and clinical feasibility of this model were verified through the clinical prospective cohort we established. In conclusion, in the context of Predictive, Preventive, and Personalized Medicine (3PM), we have developed and validated a model to predict PTB < 7 days in TPTL women. This is promising to greatly improve the accuracy of clinical prediction, which would facilitate the personalized management of TPTL women to precisely prevent PTB < 7 days and improve maternal-fetal outcomes.
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Affiliation(s)
- Yuxin Ran
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Rd, Yuzhong District, Chongqing, 400016 China
- Chongqing Health Center for Women and Children, No. 120 Longshan Road, Yubei District, Chongqing, 401120 China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
- Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
| | - Jie He
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Rd, Yuzhong District, Chongqing, 400016 China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
- Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
| | - Wei Peng
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Rd, Yuzhong District, Chongqing, 400016 China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
- Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
| | - Zheng Liu
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Rd, Yuzhong District, Chongqing, 400016 China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
- Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
| | - Youwen Mei
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Rd, Yuzhong District, Chongqing, 400016 China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
- Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
| | - Yunqian Zhou
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Rd, Yuzhong District, Chongqing, 400016 China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
- Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
| | - Nanlin Yin
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Rd, Yuzhong District, Chongqing, 400016 China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
- Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
- Center for Reproductive Medicine, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Rd, Yuzhong District, Chongqing, 400016 China
| | - Hongbo Qi
- Chongqing Health Center for Women and Children, No. 120 Longshan Road, Yubei District, Chongqing, 401120 China
- Chongqing Key Laboratory of Maternal and Fetal Medicine, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
- Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, No. 1 Yixueyuan Rd, Yuzhong District, Chongqing, 400016 China
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Inhibition of the deubiquitinating enzyme USP47 as a novel targeted therapy for hematologic malignancies expressing mutant EZH2. Leukemia 2022; 36:1048-1057. [PMID: 35034955 DOI: 10.1038/s41375-021-01494-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 11/08/2022]
Abstract
Activating mutations in EZH2, the catalytic component of PRC2, promote cell proliferation, tumorigenesis, and metastasis through enzymatic or non-enzymatic activity. The EZH2-Y641 gain-of-function mutation is one of the most significant in diffuse large B-cell lymphoma (DLBCL). Although EZH2 kinase inhibitors, such as EPZ-6438, provide clinical benefit, certain cancer cells are resistant to the enzymatic inhibition of EZH2 because of the inability to functionally target mutant EZH2, or because of cells' dependence on the non-histone methyltransferase activity of EZH2. Consequently, destroying mutant EZH2 protein may be more effective in targeting EZH2 mutant cancers that are dependent on the non-catalytic activity of EZH2. Here, using extensive selectivity profiling, combined with genetic and animal model studies, we identified USP47 as a novel regulator of mutant EZH2. Inhibition of USP47 would be anticipated to block the function of mutated EZH2 through induction of EZH2 degradation by promoting its ubiquitination. Moreover, targeting of USP47 leads to death of mutant EZH2-positive cells in vitro and in vivo. Taken together, we propose targeting USP47 with a small molecule inhibitor as a novel potential therapy for DLBCL and other hematologic malignancies characterized by mutant EZH2 expression.
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