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Lecoquierre F, Punt AM, Ebstein F, Wallaard I, Verhagen R, Studencka-Turski M, Duffourd Y, Moutton S, Tran Mau-Them F, Philippe C, Dean J, Tennant S, Brooks AS, van Slegtenhorst MA, Jurgens JA, Barry BJ, Chan WM, England EM, Martinez Ojeda M, Engle EC, Robson CD, Morrow M, Innes AM, Lamont R, Sanderson M, Krüger E, Thauvin C, Distel B, Faivre L, Elgersma Y, Vitobello A. A recurrent missense variant in the E3 ubiquitin ligase substrate recognition subunit FEM1B causes a rare syndromic neurodevelopmental disorder. Genet Med 2024; 26:101119. [PMID: 38465576 DOI: 10.1016/j.gim.2024.101119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024] Open
Abstract
PURPOSE Fem1 homolog B (FEM1B) acts as a substrate recognition subunit for ubiquitin ligase complexes belonging to the CULLIN 2-based E3 family. Several biological functions have been proposed for FEM1B, including a structurally resolved function as a sensor for redox cell status by controlling mitochondrial activity, but its implication in human disease remains elusive. METHODS To understand the involvement of FEM1B in human disease, we made use of Matchmaker exchange platforms to identify individuals with de novo variants in FEM1B and performed their clinical evaluation. We performed functional validation using primary neuronal cultures and in utero electroporation assays, as well as experiments on patient's cells. RESULTS Five individuals with a recurrent de novo missense variant in FEM1B were identified: NM_015322.5:c.377G>A NP_056137.1:p.(Arg126Gln) (FEM1BR126Q). Affected individuals shared a severe neurodevelopmental disorder with behavioral phenotypes and a variable set of malformations, including brain anomalies, clubfeet, skeletal abnormalities, and facial dysmorphism. Overexpression of the FEM1BR126Q variant but not FEM1B wild-type protein, during mouse brain development, resulted in delayed neuronal migration of the target cells. In addition, the individuals' cells exhibited signs of oxidative stress and induction of type I interferon signaling. CONCLUSION Overall, our data indicate that p.(Arg126Gln) induces aberrant FEM1B activation, resulting in a gain-of-function mechanism associated with a severe syndromic developmental disorder in humans.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, Rouen, France; UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France.
| | - A Mattijs Punt
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Frédéric Ebstein
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany; Nantes Université, INSERM, CNRS, l'institut du thorax, Nantes Cedex 1, France
| | - Ilse Wallaard
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Rob Verhagen
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Maja Studencka-Turski
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Yannis Duffourd
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Sébastien Moutton
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Frédédic Tran Mau-Them
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Laboratoire de Génétique, CHR Metz-Thionville, Hôpital Mercy, Metz, France
| | - John Dean
- Department of Medical Genetics, NHS Grampian, Aberdeen, United Kingdom
| | - Stephen Tennant
- NHS Grampian, Genetics & Molecular Pathology Laboratory Services, Aberdeen, United Kingdom
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Julie A Jurgens
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA
| | - Brenda J Barry
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Department of Neurology, Boston Children's Hospital, Boston, MA; Howard Hughes Medical Institute, Chevy Chase, MD
| | - Wai-Man Chan
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Howard Hughes Medical Institute, Chevy Chase, MD
| | - Eleina M England
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | | | - Elizabeth C Engle
- F.M. Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA; Department of Neurology, Boston Children's Hospital, Boston, MA; Department of Neurology, Harvard Medical School, Boston, MA; Broad Institute of MIT and Harvard, Cambridge, MA; Howard Hughes Medical Institute, Chevy Chase, MD; Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Caroline D Robson
- Division of Neuroradiology, Department of Radiology, Boston Children's Hospital, Boston, MA; Department of Radiology, Harvard Medical School, Boston, MA
| | | | - A Micheil Innes
- Alberta Children's Hospital Research Institute for Child and Maternal Health and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ryan Lamont
- Alberta Children's Hospital Research Institute for Child and Maternal Health and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Matthea Sanderson
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | - Elke Krüger
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Greifswald, Germany
| | - Christel Thauvin
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France; Centre de référence maladies rares « Déficiences Intellectuelles de Causes Rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Ben Distel
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Laurence Faivre
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Centre de Référence maladies rares « Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Ype Elgersma
- Department of Clinical Genetics, Erasmus MC, Rotterdam, The Netherlands; ENCORE Expertise Center for Neurodevelopmental Disorders, Erasmus MC, Rotterdam, The Netherlands
| | - Antonio Vitobello
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, Fédération Hospitalo-Universitaire-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
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2
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Dai Z, Liang L, Wang W, Zuo P, Yu S, Liu Y, Zhao X, Lu Y, Jin Y, Zhang F, Ding D, Deng W, Yin Y. Structural insights into the ubiquitylation strategy of the oligomeric CRL2 FEM1B E3 ubiquitin ligase. EMBO J 2024; 43:1089-1109. [PMID: 38360992 PMCID: PMC10943247 DOI: 10.1038/s44318-024-00047-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: 08/22/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Cullin-RING E3 ubiquitin ligase (CRL) family members play critical roles in numerous biological processes and diseases including cancer and Alzheimer's disease. Oligomerization of CRLs has been reported to be crucial for the regulation of their activities. However, the structural basis for its regulation and mechanism of its oligomerization are not fully known. Here, we present cryo-EM structures of oligomeric CRL2FEM1B in its unneddylated state, neddylated state in complex with BEX2 as well as neddylated state in complex with FNIP1/FLCN. These structures reveal that asymmetric dimerization of N8-CRL2FEM1B is critical for the ubiquitylation of BEX2 while FNIP1/FLCN is ubiquitylated by monomeric CRL2FEM1B. Our data present an example of the asymmetric homo-dimerization of CRL. Taken together, this study sheds light on the ubiquitylation strategy of oligomeric CRL2FEM1B according to substrates with different scales.
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Affiliation(s)
- Zonglin Dai
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ling Liang
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weize Wang
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Zuo
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Shang Yu
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yaqi Liu
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Xuyang Zhao
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yishuo Lu
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Jin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Fangting Zhang
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Dian Ding
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weiwei Deng
- Department of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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Hedrich V, Breitenecker K, Ortmayr G, Pupp F, Huber H, Chen D, Sahoo S, Jolly MK, Mikulits W. PRAME Is a Novel Target of Tumor-Intrinsic Gas6/Axl Activation and Promotes Cancer Cell Invasion in Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:2415. [PMID: 37173882 PMCID: PMC10177160 DOI: 10.3390/cancers15092415] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
(1) Background: Activation of the receptor tyrosine kinase Axl by Gas6 fosters oncogenic effects in hepatocellular carcinoma (HCC), associating with increased mortality of patients. The impact of Gas6/Axl signaling on the induction of individual target genes in HCC and its consequences is an open issue. (2) Methods: RNA-seq analysis of Gas6-stimulated Axl-proficient or Axl-deficient HCC cells was used to identify Gas6/Axl targets. Gain- and loss-of-function studies as well as proteomics were employed to characterize the role of PRAME (preferentially expressed antigen in melanoma). Expression of Axl/PRAME was assessed in publicly available HCC patient datasets and in 133 HCC cases. (3) Results: Exploitation of well-characterized HCC models expressing Axl or devoid of Axl allowed the identification of target genes including PRAME. Intervention with Axl signaling or MAPK/ERK1/2 resulted in reduced PRAME expression. PRAME levels were associated with a mesenchymal-like phenotype augmenting 2D cell migration and 3D cell invasion. Interactions with pro-oncogenic proteins such as CCAR1 suggested further tumor-promoting functions of PRAME in HCC. Moreover, PRAME showed elevated expression in Axl-stratified HCC patients, which correlates with vascular invasion and lowered patient survival. (4) Conclusions: PRAME is a bona fide target of Gas6/Axl/ERK signaling linked to EMT and cancer cell invasion in HCC.
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Affiliation(s)
- Viola Hedrich
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (V.H.)
| | - Kristina Breitenecker
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (V.H.)
| | - Gregor Ortmayr
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (V.H.)
| | - Franziska Pupp
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (V.H.)
| | - Heidemarie Huber
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (V.H.)
| | - Doris Chen
- Department of Chromosome Biology, Max Perutz Labs Vienna, University of Vienna, 1030 Vienna, Austria
| | - Sarthak Sahoo
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Mohit Kumar Jolly
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Wolfgang Mikulits
- Center for Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; (V.H.)
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4
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Minatel BC, Cohn DE, Pewarchuk ME, Barros-Filho MC, Sage AP, Stewart GL, Marshall EA, Telkar N, Martinez VD, Reis PP, Robinson WP, Lam WL. Genetic and Epigenetic Mechanisms Deregulate the CRL2pVHL Complex in Hepatocellular Carcinoma. Front Genet 2022; 13:910221. [PMID: 35664333 PMCID: PMC9159809 DOI: 10.3389/fgene.2022.910221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/02/2022] [Indexed: 12/02/2022] Open
Abstract
Dysregulation of ubiquitin-proteasome pathway genes through copy number alteration, promoter hypomethylation, and miRNA deregulation is involved in cancer development and progression. Further characterizing alterations in these genes may uncover novel drug targets across a range of diseases in which druggable alterations are uncommon, including hepatocellular carcinoma (HCC). We analyzed 377 HCC and 59 adjacent non-malignant liver tissue samples, focusing on alterations to component genes of the widely studied CRL2pVHL E3 ubiquitin ligase complex. mRNA upregulation of the component genes was common, and was correlated with DNA hypomethylation and copy number increase, but many tumours displayed overexpression that was not explained by either mechanism. Interestingly, we found 66 miRNAs, including 39 previously unannotated miRNAs, that were downregulated in HCC and predicted to target one or more CRL2pVHL components. Several miRNAs, including hsa-miR-101-3p and hsa-miR-139-5p, were negatively correlated with multiple component genes, suggesting that miRNA deregulation may contribute to CRL2pVHL overexpression. Combining miRNA and mRNA expression, DNA copy number, and methylation status into one multidimensional survival analysis, we found a significant association between greater numbers of alterations and poorer overall survival for multiple component genes. While the intricacies of CRL2pVHL complex gene regulation require additional research, it is evident that multiple causes for the deregulation of these genes must be considered in HCC, including non-traditional mechanisms.
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Affiliation(s)
- Brenda C. Minatel
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - David E. Cohn
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- *Correspondence: David E. Cohn,
| | - Michelle E. Pewarchuk
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Mateus C. Barros-Filho
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Oncology, Hospital Sírio-Libanes, São Paulo, Brazil
| | - Adam P. Sage
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Greg L. Stewart
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Erin A. Marshall
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
| | - Nikita Telkar
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Victor D. Martinez
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada
| | - Patricia P. Reis
- Department of Surgery and Orthopedics and Experimental Research Unity (UNIPEX), Faculty of Medicine, São Paulo State University (UNESP), Botucatu, Brazil
| | - Wendy P. Robinson
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Wan L. Lam
- Department of Integrative Oncology, British Columbia Cancer Research Institute, Vancouver, BC, Canada
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Huang R, Li J, Fu Y, Deng Y. Downregulation of FEM1C enhances metastasis and proliferation in colorectal cancer. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1391. [PMID: 34733943 PMCID: PMC8506547 DOI: 10.21037/atm-21-4244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/30/2021] [Indexed: 11/25/2022]
Abstract
Background Feminization-1 (FEM-1) is considered a substrate recognition subunit of CUL2-RING E3 ubiquitin ligase complexes, which refers to sex determination by modulating TRA-1 stability in C. elegans. The function of mammalian orthologous gene of FEM-1 remains to be elucidated. Methods The expression of FEM1C in colorectal cancer (CRC) cells was interfered by small interference RNA (siRNA) transfection, and Cell counting kit-8 (CCK-8) assay, colony formation assay and transwell assay were performed. In order to estimate the function on metastasis, stable knockdown FEM1C cells were used to established liver and lung metastasis models. In addition, the expression of FEM1C in normal tissues, adenomas and tumor tissues were analyzed, and the relationship between FEM1C expression level and prognosis was analyzed by Kaplan-Meier method. Results Here, we report that the elimination of FEM1C, one of the members of FEM-1, significantly promoted the migration and invasion of colorectal cancer (CRC) cells in vitro and promoted liver and lung metastases in vivo. It also showed that the removal of FEM1C improved the proliferation ability of CRC cells. In particular, the cell shape changed from epithelial to fibroblast-like morphology. The tight cell monolayer was transformed into a dispersed distribution. Furthermore, it was demonstrated that FEM1C is down-regulated in tissues of CRC compared to normal tissues, and the high expression of FEM1C positively correlates with a good prognosis in patients with CRC. GSEA analysis showed that EMT signatures was enriched in FEM1C knockdown groups. Conclusions Down-regulation of FEM1C promotes proliferation and metastasis, and FEM1C may be a tumor suppressor in the development of CRC.
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Affiliation(s)
- Runqing Huang
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Research Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianxia Li
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Research Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yang Fu
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Research Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanhong Deng
- Department of Medical Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Research Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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6
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Márquez-Cantudo L, Ramos A, Coderch C, de Pascual-Teresa B. Proteasomal Degradation of Zn-Dependent Hdacs: The E3-Ligases Implicated and the Designed Protacs That Enable Degradation. Molecules 2021; 26:molecules26185606. [PMID: 34577077 PMCID: PMC8467390 DOI: 10.3390/molecules26185606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/21/2022] Open
Abstract
Protein degradation by the Ubiquitin-Proteasome System is one of the main mechanisms of the regulation of cellular proteostasis, and the E3 ligases are the key effectors for the protein recognition and degradation. Many E3 ligases have key roles in cell cycle regulation, acting as checkpoints and checkpoint regulators. One of the many important proteins involved in the regulation of the cell cycle are the members of the Histone Deacetylase (HDAC) family. The importance of zinc dependent HDACs in the regulation of chromatin packing and, therefore, gene expression, has made them targets for the design and synthesis of HDAC inhibitors. However, achieving potency and selectivity has proven to be a challenge due to the homology between the zinc dependent HDACs. PROteolysis TArgeting Chimaera (PROTAC) design has been demonstrated to be a useful strategy to inhibit and selectively degrade protein targets. In this review, we attempt to summarize the E3 ligases that naturally ubiquitinate HDACs, analyze their structure, and list the known ligands that can bind to these E3 ligases and be used for PROTAC design, as well as the already described HDAC-targeted PROTACs.
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7
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Xu D, Wu J, Chen J, Jiang L, Chen J, Bao W, Chen X, Yang Q, Zhang X, Yao L, Su H, Liu J. Cullin 2-RBX1 E3 ligase and USP2 regulate antithrombin ubiquitination and stability. FASEB J 2021; 35:e21800. [PMID: 34324733 DOI: 10.1096/fj.202001146rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/20/2021] [Accepted: 07/01/2021] [Indexed: 11/11/2022]
Abstract
Hemophilia A and B are congenital bleeding disorders caused by a deficiency in pro-coagulant factor VIII or IX that is treated by downregulation of antithrombin. However, the molecular mechanisms that regulate antithrombin expression remain poorly understood. Here, we identified Cullin 2 and USP2 (ubiquitin-specific peptidase-2) as novel regulators of antithrombin expression that act by modulating antithrombin ubiquitination. Inhibition of the proteasome caused accumulation of antithrombin and its ubiquitinated forms in HepG2 and SMMC7721 cells. Notably, inhibition of neddylation with MLN4924 suppressed both ubiquitination and degradation of antithrombin, which is recapitulated by silencing of the neddylation enzymes, NAE1, UBA3, and UBE2M, with small interfering RNA (siRNA). We identified Cullin 2 as the interaction partner of antithrombin, and siRNA-mediated Cullin 2 knockdown reduced antithrombin ubiquitination and increased antithrombin protein. We further found that USP2 interacted with antithrombin and regulated antithrombin expression, showing that overexpression of USP2 inhibits the ubiquitination and proteasomal clearance of antithrombin, whereas pharmacological inhibition or siRNA-mediated knockdown of USP2 downregulates antithrombin. Collectively, these results suggest that Cullin 2 E3 ubiquitin ligase and USP2 coordinately regulate antithrombin ubiquitination and degradation. Thus, targeting Cullin 2 and USP2 could be a potential strategy for treatment of hemophilia.
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Affiliation(s)
- Dacai Xu
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiawen Wu
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jinghong Chen
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liling Jiang
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Juan Chen
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wenhao Bao
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Chen
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qianqian Yang
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaolan Zhang
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Leyi Yao
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huabo Su
- Vascular Biology Center, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Jinbao Liu
- Guangzhou Municipal and Guangdong Provincial Key Lab of Protein Modification and Degradation Lab, State Key Lab of Respiratory Disease, School of Basic Medical Sciences, Affiliated Cancer Hospital of Guangzhou Medical University, Guangzhou, China
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8
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Molecular basis for ubiquitin ligase CRL2 FEM1C-mediated recognition of C-degron. Nat Chem Biol 2021; 17:263-271. [PMID: 33398170 DOI: 10.1038/s41589-020-00703-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/30/2020] [Indexed: 01/28/2023]
Abstract
Proteome integrity depends on the ubiquitin-proteasome system to degrade unwanted or abnormal proteins. In addition to the N-degrons, C-terminal residues of proteins can also serve as degradation signals (C-degrons) that are recognized by specific cullin-RING ubiquitin ligases (CRLs) for proteasomal degradation. FEM1C is a CRL2 substrate receptor that targets the C-terminal arginine degron (Arg/C-degron), but the molecular mechanism of substrate recognition remains largely elusive. Here, we present crystal structures of FEM1C in complex with Arg/C-degron and show that FEM1C utilizes a semi-open binding pocket to capture the C-terminal arginine and that the extreme C-terminal arginine is the major structural determinant in recognition by FEM1C. Together with biochemical and mutagenesis studies, we provide a framework for understanding molecular recognition of the Arg/C-degron by the FEM family of proteins.
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9
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Charoensuk C, Thamtarana PJ, Chanprasert C, Tangjittipokin W, Shirakawa J, Togashi Y, Orime K, Songprakhon P, Chaichana C, Abubakar Z, Ouying P, Sujjitjoon J, Doria A, Plengvidhya N, Yenchitsomanus PT. Autosomal dominant diabetes associated with a novel ZYG11A mutation resulting in cell cycle arrest in beta-cells. Mol Cell Endocrinol 2021; 522:111126. [PMID: 33321115 DOI: 10.1016/j.mce.2020.111126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 01/20/2023]
Abstract
Diabetes is a genetically heterogeneous disease, for which we are aiming to identify causative genes. Here, we report a missense mutation (c.T1424C:p.L475P) in ZYG11A identified by exome sequencing as segregating with hyperglycemia in a Thai family with autosomal dominant diabetes. ZYG11A functions as a target recruitment subunit of an E3 ubiquitin ligase complex that plays an important role in the regulation of cell cycle. We demonstrate an increase in cells arrested at G2/mitotic phase among beta-cells deficient for ZYG11A or overexpressing L475P-ZYG11A, which is associated with a decreased growth rate. This is the first evidence linking a ZYG11A mutation to hyperglycemia, and suggesting ZYG11A as a cell cycle regulator required for beta-cell growth. Since most family members were either overweight or obese, but only mutation carriers developed hyperglycemia, our data also suggests the ZYG11A mutation as a genetic factor predisposing obese individuals to beta-cell failure in maintenance of glucose homeostasis.
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Affiliation(s)
- Chutima Charoensuk
- Graduate Program in Immunology, Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Prapaporn Jungtrakoon Thamtarana
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
| | - Chutima Chanprasert
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Watip Tangjittipokin
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Jun Shirakawa
- Laboratory of Diabetes and Metabolic Disorders, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, 371-8512, Japan; Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Yu Togashi
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Kazuki Orime
- Department of Endocrinology and Metabolism, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Pucharee Songprakhon
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Chartchai Chaichana
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Zuroida Abubakar
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Paweena Ouying
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Jatuporn Sujjitjoon
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Alessandro Doria
- Section on Genetics and Epidemiology, Joslin Diabetes Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Nattachet Plengvidhya
- Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Division of Endocrinology and Metabolism, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Cellular and Molecular Biology of Diabetes Research Group, Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand; Siriraj Center of Research Excellence for Diabetes and Obesity, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, 10700, Thailand.
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10
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Kulaga AY, Ursu E, Toren D, Tyshchenko V, Guinea R, Pushkova M, Fraifeld VE, Tacutu R. Machine Learning Analysis of Longevity-Associated Gene Expression Landscapes in Mammals. Int J Mol Sci 2021; 22:1073. [PMID: 33499037 PMCID: PMC7865694 DOI: 10.3390/ijms22031073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/16/2021] [Accepted: 01/20/2021] [Indexed: 12/28/2022] Open
Abstract
One of the important questions in aging research is how differences in transcriptomics are associated with the longevity of various species. Unfortunately, at the level of individual genes, the links between expression in different organs and maximum lifespan (MLS) are yet to be fully understood. Analyses are complicated further by the fact that MLS is highly associated with other confounding factors (metabolic rate, gestation period, body mass, etc.) and that linear models may be limiting. Using gene expression from 41 mammalian species, across five organs, we constructed gene-centric regression models associating gene expression with MLS and other species traits. Additionally, we used SHapley Additive exPlanations and Bayesian networks to investigate the non-linear nature of the interrelations between the genes predicted to be determinants of species MLS. Our results revealed that expression patterns correlate with MLS, some across organs, and others in an organ-specific manner. The combination of methods employed revealed gene signatures formed by only a few genes that are highly predictive towards MLS, which could be used to identify novel longevity regulator candidates in mammals.
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Affiliation(s)
- Anton Y. Kulaga
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
- International Longevity Alliance, 92330 Sceaux, France
- CellFabrik SRL, 060512 Bucharest, Romania
| | - Eugen Ursu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
| | - Dmitri Toren
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel;
| | | | - Rodrigo Guinea
- Escuela de Postgrado, Pontificia Universidad Católica del Perú, 15023 San Miguel, Peru;
| | - Malvina Pushkova
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
| | - Vadim E. Fraifeld
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Center for Multidisciplinary Research on Aging, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel;
| | - Robi Tacutu
- Systems Biology of Aging Group, Institute of Biochemistry of the Romanian Academy, 060031 Bucharest, Romania; (A.Y.K.); (E.U.); (D.T.); (M.P.)
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11
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Zheng S, Wu Y, Li Z. Integrating cullin2-RING E3 ligase as a potential biomarker for glioblastoma multiforme prognosis and radiosensitivity profiling. Radiother Oncol 2021; 154:36-44. [DOI: 10.1016/j.radonc.2020.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/25/2022]
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12
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Zhao W, Liu Y, Zhang L, Ding L, Li Y, Zhang H, Wang T, Hao M. MicroRNA-154-5p regulates the HPV16 E7-pRb pathway in Cervical Carcinogenesis by targeting CUL2. J Cancer 2020; 11:5379-5389. [PMID: 32742484 PMCID: PMC7391205 DOI: 10.7150/jca.45871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023] Open
Abstract
Cervical cancer, induced by persistent HPV infection, has a high mortality rate. The E3 ubiquitin ligase Cullin 2 (CUL2) is critical for HPV16 E7-mediated degradation of retinoblastoma protein (pRb). Dysregulation of microRNAs (miRNAs) is induced during tumorigenesis; however, the association between miRNA networks and CUL2, specific to cervical cancer, remains unknown. Herein, we determined miRNA profiles in cervical cancer tissues using an Affymetrix miRNA array. We found that miR-154-5p was downregulated during cancer progression using real-time quantitative reverse transcription PCR in 130 biopsy specimens. Bioinformatics analysis and dual-luciferase reporter assays indicated that miR-154-5p directly targets the CUL2 3'UTR. To determine the functional consequences of modulating miR-154-5p and CUL2 levels, HPV16-positive cervical cancer cell line (SiHa) was transfected with miR-154-5p mimic, miR-154-5p inhibitor, or CUL2 siRNA. The proliferation, migration, and invasion of transfected cells were evaluated using CCK8 cell counting kit, wound-healing assay, and Transwell invasion assay. Increased miR-154-5p expression promoted significantly reduced SiHa cell proliferation, migration, and invasion, whereas the miR-154-5p inhibitor had the opposite effect. CUL2 silencing had similar effects to those of the miR-154-5p mimic. Consistent with the inverse correlation between miR-154-5p and CUL2 levels, CUL2 silencing also increased pRb expression. To our knowledge, this is the first study to demonstrate that miR-154-5p regulates pRb expression by targeting CUL2 3'UTR, thereby playing a tumor-suppressive role in HPV16 E7-induced cervical carcinogenesis.
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Affiliation(s)
- Weihong Zhao
- Department of Obstetrics and Gynecology, the Second Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Yatao Liu
- Department of Obstetrics and Gynecology, the Second Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Lili Zhang
- Department of Obstetrics and Gynecology, the Second Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Ling Ding
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Yaqin Li
- Department of Obstetrics and Gynecology, the Second Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Honglei Zhang
- Department of Obstetrics and Gynecology, the Second Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Tong Wang
- Department of Health Statistics, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Min Hao
- Department of Obstetrics and Gynecology, the Second Hospital of Shanxi Medical University, Taiyuan 030001, China
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13
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Wang Y, Jiang X, Feng F, Liu W, Sun H. Degradation of proteins by PROTACs and other strategies. Acta Pharm Sin B 2020; 10:207-238. [PMID: 32082969 PMCID: PMC7016280 DOI: 10.1016/j.apsb.2019.08.001] [Citation(s) in RCA: 175] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022] Open
Abstract
Blocking the biological functions of scaffold proteins and aggregated proteins is a challenging goal. PROTAC proteolysis-targeting chimaera (PROTAC) technology may be the solution, considering its ability to selectively degrade target proteins. Recent progress in the PROTAC strategy include identification of the structure of the first ternary eutectic complex, extra-terminal domain-4-PROTAC-Von-Hippel-Lindau (BRD4-PROTAC-VHL), and PROTAC ARV-110 has entered clinical trials for the treatment of prostate cancer in 2019. These discoveries strongly proved the value of the PROTAC strategy. In this perspective, we summarized recent meaningful research of PROTAC, including the types of degradation proteins, preliminary biological data in vitro and in vivo, and new E3 ubiquitin ligases. Importantly, the molecular design, optimization strategy and clinical application of candidate molecules are highlighted in detail. Future perspectives for development of advanced PROTAC in medical fields have also been discussed systematically.
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Affiliation(s)
- Yang Wang
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Xueyang Jiang
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Feng
- Jiangsu Food and Pharmaceutical Science College, Huaian 223003, China
- Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing 210009, China
| | - Haopeng Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, China
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14
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Liu X, Zurlo G, Zhang Q. The Roles of Cullin-2 E3 Ubiquitin Ligase Complex in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:173-186. [PMID: 31898228 DOI: 10.1007/978-981-15-1025-0_11] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Posttranslational protein modifications play an important role in regulating protein stability and cellular function. There are at least eight Cullin family members. Among them, Cullin-2 forms a functional E3 ligase complex with elongin B, elongin C, RING-box protein 1 (RBX1, also called ROC1), as well as the substrate recognition subunit (SRS) to promote the substrate ubiquitination and degradation. In this book chapter, we will review Cullin-2 E3 ligase complexes that include various SRS proteins, including von Hippel Lindau (pVHL), leucine-rich repeat protein-1 (LRR-1), preferentially expressed antigen of melanoma (PRAME), sex-determining protein FEM-1 and early embryogenesis protein ZYG-11. We will focus on the VHL signaling pathway in clear cell renal cell carcinoma (ccRCC), which may reveal various therapeutic avenues in treating this lethal cancer.
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Affiliation(s)
- Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Giada Zurlo
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA.,Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA. .,Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA. .,Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA. .,Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA.
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15
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Wang X, Rusin A, Walkey CJ, Lin JJ, Johnson DL. The RNA polymerase III repressor MAF1 is regulated by ubiquitin-dependent proteasome degradation and modulates cancer drug resistance and apoptosis. J Biol Chem 2019; 294:19255-19268. [PMID: 31645432 DOI: 10.1074/jbc.ra119.008849] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/01/2019] [Indexed: 01/03/2023] Open
Abstract
MAF1 homolog, negative regulator of RNA polymerase III (MAF1) is a key repressor of RNA polymerase (pol) III-dependent transcription and functions as a tumor suppressor. Its expression is frequently down-regulated in primary human hepatocellular carcinomas (HCCs). However, this reduction in MAF1 protein levels does not correlate with its transcript levels, indicating that MAF1 is regulated post-transcriptionally. Here, we demonstrate that MAF1 is a labile protein whose levels are regulated through the ubiquitin-dependent proteasome pathway. We found that MAF1 ubiquitination is enhanced upon mTOR complex 1 (TORC1)-mediated phosphorylation at Ser-75. Moreover, we observed that the E3 ubiquitin ligase cullin 2 (CUL2) critically regulates MAF1 ubiquitination and controls its stability and subsequent RNA pol III-dependent transcription. Analysis of the phenotypic consequences of modulating either CUL2 or MAF1 protein expression revealed changes in actin cytoskeleton reorganization and altered sensitivity to doxorubicin-induced apoptosis. Repression of RNA pol III-dependent transcription by chemical inhibition or knockdown of BRF1 RNA pol III transcription initiation factor subunit (BRF1) enhanced HCC cell sensitivity to doxorubicin, suggesting that MAF1 regulates doxorubicin resistance in HCC by controlling RNA pol III-dependent transcription. Together, our results identify the ubiquitin proteasome pathway and CUL2 as important regulators of MAF1 levels. They suggest that decreases in MAF1 protein underlie chemoresistance in HCC and perhaps other cancers and point to an important role for MAF1 and RNA pol III-mediated transcription in chemosensitivity and apoptosis.
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Affiliation(s)
- Xianlong Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Aleksandra Rusin
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | - Christopher J Walkey
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
| | | | - Deborah L Johnson
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030
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16
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Faull SV, Lau AMC, Martens C, Ahdash Z, Hansen K, Yebenes H, Schmidt C, Beuron F, Cronin NB, Morris EP, Politis A. Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome. Nat Commun 2019; 10:3814. [PMID: 31444342 PMCID: PMC6707232 DOI: 10.1038/s41467-019-11772-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/02/2019] [Indexed: 12/19/2022] Open
Abstract
Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. Here we present structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single-particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (XL-MS). These structures suggest a conserved mechanism of CSN activation, consisting of conformational clamping of the CRL2 substrate by CSN2/CSN4, release of the catalytic CSN5/CSN6 heterodimer and finally activation of the CSN5 deneddylation machinery. Using hydrogen-deuterium exchange (HDX)-MS we show that CRL2 activates CSN5/CSN6 in a neddylation-independent manner. The presence of NEDD8 is required to activate the CSN5 active site. Overall, by synergising cryo-EM with MS, we identify sensory regions of the CSN that mediate its stepwise activation and provide a framework for understanding the regulatory mechanism of other Cullin family members.
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Affiliation(s)
- Sarah V Faull
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Andy M C Lau
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Chloe Martens
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Zainab Ahdash
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK
| | - Hugo Yebenes
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120, Halle/Saale, Germany
| | - Fabienne Beuron
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Nora B Cronin
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Edward P Morris
- Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK.
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17
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Gorelik M, Sidhu SS. Specific targeting of the deubiquitinase and E3 ligase families with engineered ubiquitin variants. Bioeng Transl Med 2016; 2:31-42. [PMID: 28580429 PMCID: PMC5434665 DOI: 10.1002/btm2.10044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/24/2016] [Indexed: 12/11/2022] Open
Abstract
The ubiquitin proteasome system (UPS) has garnered much attention due to its potential for the development of therapeutics. Following a successful clinical application of general proteasome inhibitors much effort has been devoted to targeting individual UPS components including E3 enzymes and deubiquitinases that control specificity of ubiquitination. Our group has developed a novel approach for targeting the UPS proteins using engineered ubiquitin variants (Ubvs). These drug‐like proteins can serve as valuable tools to study biological function of UPS components and assist in the development of small molecules for clinical use. In this review, we summarize studies of Ubvs targeting members of three major families, including deubiquitinases, HECT E3 ligases, and CRL E3 ligases. In particular, we focus on Ubv binding mechanisms, structural studies, and effects on enzyme function. Furthermore, new insights gained from the Ubvs are discussed in the context of small molecule studies.
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Affiliation(s)
- Maryna Gorelik
- Banting and Best Dept. of Medical Research and the Dept. of Molecular Genetics Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON Canada M5S 3E1
| | - Sachdev S Sidhu
- Banting and Best Dept. of Medical Research and the Dept. of Molecular Genetics Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON Canada M5S 3E1
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