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Di Gregorio J, Di Giuseppe L, Terreri S, Rossi M, Battafarano G, Pagliarosi O, Flati V, Del Fattore A. Protein Stability Regulation in Osteosarcoma: The Ubiquitin-like Modifications and Glycosylation as Mediators of Tumor Growth and as Targets for Therapy. Cells 2024; 13:537. [PMID: 38534381 DOI: 10.3390/cells13060537] [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: 02/14/2024] [Revised: 03/11/2024] [Accepted: 03/16/2024] [Indexed: 03/28/2024] Open
Abstract
The identification of new therapeutic targets and the development of innovative therapeutic approaches are the most important challenges for osteosarcoma treatment. In fact, despite being relatively rare, recurrence and metastatic potential, particularly to the lungs, make osteosarcoma a deadly form of cancer. In fact, although current treatments, including surgery and chemotherapy, have improved survival rates, the disease's recurrence and metastasis are still unresolved complications. Insights for analyzing the still unclear molecular mechanisms of osteosarcoma development, and for finding new therapeutic targets, may arise from the study of post-translational protein modifications. Indeed, they can influence and alter protein structure, stability and function, and cellular interactions. Among all the post-translational modifications, ubiquitin-like modifications (ubiquitination, deubiquitination, SUMOylation, and NEDDylation), as well as glycosylation, are the most important for regulating protein stability, which is frequently altered in cancers including osteosarcoma. This review summarizes the relevance of ubiquitin-like modifications and glycosylation in osteosarcoma progression, providing an overview of protein stability regulation, as well as highlighting the molecular mediators of these processes in the context of osteosarcoma and their possible targeting for much-needed novel therapy.
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Affiliation(s)
- Jacopo Di Gregorio
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Laura Di Giuseppe
- Department of Clinical, Internal, Anaesthesiological and Cardiovascular Sciences, Sapienza University, 00185 Rome, Italy
| | - Sara Terreri
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Michela Rossi
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Giulia Battafarano
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Olivia Pagliarosi
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
| | - Vincenzo Flati
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Andrea Del Fattore
- Bone Physiopathology Research Unit, Translational Pediatrics and Clinical Genetics Research Division, Bambino Gesù Children's Hospital, IRCCS, 00146 Rome, Italy
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2
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Wu W, Huang C. SUMOylation and DeSUMOylation: Prospective therapeutic targets in cancer. Life Sci 2023; 332:122085. [PMID: 37722589 DOI: 10.1016/j.lfs.2023.122085] [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: 08/05/2023] [Revised: 09/05/2023] [Accepted: 09/12/2023] [Indexed: 09/20/2023]
Abstract
The SUMO family is a type of ubiquitin-like protein modification molecule. Its protein modification mechanism is similar to that of ubiquitination: both involve modifier-activating enzyme E1, conjugating enzyme E2 and substrate-specific ligase E3. However, polyubiquitination can lead to the degradation of substrate proteins, while poly-SUMOylation only leads to the degradation of substrate proteins through the proteasome pathway after being recognized by ubiquitin as a signal factor. There are currently five reported subtypes in the SUMO family, namely SUMO1-5. As a reversible dynamic modification, intracellular sentrin/SUMO-specific proteases (SENPs) mainly regulate the reverse reaction pathway of SUMOylation. The SUMOylation modification system affects the localization, activation and turnover of proteins in cells and participates in regulating most nuclear and extranuclear molecular reactions. Abnormal expression of proteins related to the SUMOylation pathway is commonly observed in tumors, indicating that this pathway is closely related to tumor occurrence, metastasis and invasion. This review mainly discusses the composition of members in the protein family related to SUMOylation pathways, mutual connections between SUMOylation and other post-translational modifications on proteins as well as therapeutic drugs developed based on these pathways.
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Affiliation(s)
- Wenyan Wu
- Kunming University of Science and Technology, Medical School, Kunming 650500, China
| | - Chao Huang
- Kunming University of Science and Technology, Medical School, Kunming 650500, China.
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3
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Liu H, Craig SEL, Molchanov V, Floramo JS, Zhao Y, Yang T. SUMOylation in Skeletal Development, Homeostasis, and Disease. Cells 2022; 11:cells11172710. [PMID: 36078118 PMCID: PMC9454984 DOI: 10.3390/cells11172710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/19/2022] [Accepted: 08/27/2022] [Indexed: 11/18/2022] Open
Abstract
The modification of proteins by small ubiquitin-related modifier (SUMO) molecules, SUMOylation, is a key post-translational modification involved in a variety of biological processes, such as chromosome organization, DNA replication and repair, transcription, nuclear transport, and cell signaling transduction. In recent years, emerging evidence has shown that SUMOylation regulates the development and homeostasis of the skeletal system, with its dysregulation causing skeletal diseases, suggesting that SUMOylation pathways may serve as a promising therapeutic target. In this review, we summarize the current understanding of the molecular mechanisms by which SUMOylation pathways regulate skeletal cells in physiological and disease contexts.
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Affiliation(s)
| | | | | | | | | | - Tao Yang
- Laboratory of Skeletal Biology, Department of Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, USA
- Correspondence: ; Tel.: +1-616-234-5820
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4
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Cancer-Associated Dysregulation of Sumo Regulators: Proteases and Ligases. Int J Mol Sci 2022; 23:ijms23148012. [PMID: 35887358 PMCID: PMC9316396 DOI: 10.3390/ijms23148012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
SUMOylation is a post-translational modification that has emerged in recent decades as a mechanism involved in controlling diverse physiological processes and that is essential in vertebrates. The SUMO pathway is regulated by several enzymes, proteases and ligases being the main actors involved in the control of sumoylation of specific targets. Dysregulation of the expression, localization and function of these enzymes produces physiological changes that can lead to the appearance of different types of cancer, depending on the enzymes and target proteins involved. Among the most studied proteases and ligases, those of the SENP and PIAS families stand out, respectively. While the proteases involved in this pathway have specific SUMO activity, the ligases may have additional functions unrelated to sumoylation, which makes it more difficult to study their SUMO-associated role in cancer process. In this review we update the knowledge and advances in relation to the impact of dysregulation of SUMO proteases and ligases in cancer initiation and progression.
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5
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Gomarasca M, Lombardi G, Maroni P. SUMOylation and NEDDylation in Primary and Metastatic Cancers to Bone. Front Cell Dev Biol 2022; 10:889002. [PMID: 35465332 PMCID: PMC9020829 DOI: 10.3389/fcell.2022.889002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 03/25/2022] [Indexed: 12/22/2022] Open
Abstract
Post-translational modifications comprise series of enzymatically-driven chemical modifications, virtually involving the entire cell proteome, that affect the fate of a target protein and, in turn, cell activity. Different classes of modifications can be established ranging from phosphorylation, glycosylation, ubiquitination, acetylation, methylation, lipidation and their inverse reactions. Among these, SUMOylation and NEDDylation are ubiquitin-like multi-enzymatic processes that determine the bound of SUMOs and NEDD8 labels, respectively, on defined amino acidic residues of a specific protein and regulate protein function. As fate-determinants of several effectors and mediators, SUMOylation and NEDDylation play relevant roles in many aspects of tumor cell biology. Bone represents a preferential site of metastasis for solid tumors (e.g., breast and prostate cancers) and the primary site of primitive tumors (e.g., osteosarcoma, chondrosarcoma). Deregulation of SUMOylation and NEDDylation affects different aspects of neoplastic transformation and evolution such as epithelial-mesenchymal transition, adaptation to hypoxia, expression and action of tumor suppressors and oncogenic mediators, and drug resistance. Thereby, they represent potential therapeutic targets. This narrative review aims at describing the involvement and regulation of SUMOylation and NEDDylation in tumor biology, with a specific focus on primary and secondary bone tumors, and to summarize and highlight their potentiality in diagnostics and therapeutic strategies.
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Affiliation(s)
- Marta Gomarasca
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
- Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Polska
- *Correspondence: Giovanni Lombardi,
| | - Paola Maroni
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
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The Next Frontier: Translational Development of Ubiquitination, SUMOylation, and NEDDylation in Cancer. Int J Mol Sci 2022; 23:ijms23073480. [PMID: 35408841 PMCID: PMC8999128 DOI: 10.3390/ijms23073480] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 01/01/2023] Open
Abstract
Post-translational modifications of proteins ensure optimized cellular processes, including proteostasis, regulated signaling, cell survival, and stress adaptation to maintain a balanced homeostatic state. Abnormal post-translational modifications are associated with cellular dysfunction and the occurrence of life-threatening diseases, such as cancer and neurodegenerative diseases. Therefore, some of the frequently seen protein modifications have been used as disease markers, while others are targeted for developing specific therapies. The ubiquitin and ubiquitin-like post-translational modifiers, namely, small ubiquitin-like modifier (SUMO) and neuronal precursor cell-expressed developmentally down-regulated protein 8 (NEDD8), share several features, such as protein structures, enzymatic cascades mediating the conjugation process, and targeted amino acid residues. Alterations in the regulatory mechanisms lead to aberrations in biological processes during tumorigenesis, including the regulation of tumor metabolism, immunological modulation of the tumor microenvironment, and cancer stem cell stemness, besides many more. Novel insights into ubiquitin and ubiquitin-like pathways involved in cancer biology reveal a potential interplay between ubiquitination, SUMOylation, and NEDDylation. This review outlines the current understandings of the regulatory mechanisms and assay capabilities of ubiquitination, SUMOylation, and NEDDylation. It will further highlight the role of ubiquitination, SUMOylation, and NEDDylation in tumorigenesis.
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7
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Tokarz P, Woźniak K. SENP Proteases as Potential Targets for Cancer Therapy. Cancers (Basel) 2021; 13:cancers13092059. [PMID: 33923236 PMCID: PMC8123143 DOI: 10.3390/cancers13092059] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Post-translational modification—the biochemical addition of functional groups or proteins—occurs following protein biosynthesis and contributes to an increase in the functional diversity of the proteome. Post-translational modifications include SUMOylation—the covalent attachment of small ubiquitin-related modifier (SUMO) proteins to substrate proteins. SUMOylation is a reversible modification, which is erased by SUMO-specific proteases (SENPs). Deregulation of SENPs leads to cellular dysfunction and is associated with various diseases, including cancer. The role of SENPs in cancer pathogenesis is expected, and thus these proteins are considered promising targets for drug design and development. In this review, we will discuss the role of SENPs, focusing on DNA repair and the cell cycle—cellular pathways malfunctioning in most cancer cells—and provide an update on advances in the development of SENP-oriented inhibitors. Abstract SUMOylation is a reversible post-translational modification (PTM) involving a covalent attachment of small ubiquitin-related modifier (SUMO) proteins to substrate proteins. SUMO-specific proteases (SENPs) are cysteine proteases with isopeptidase activity facilitating the de-conjugation of SUMO proteins and thus participating in maintaining the balance between the pools of SUMOylated and unSUMOylated proteins and in SUMO recycling. Several studies have reported that SENPs’ aberrant expression is associated with the development and progression of cancer. In this review, we will discuss the role of SENPs in the pathogenesis of cancer, focusing on DNA repair and the cell cycle—cellular pathways malfunctioning in most cancer cells. The plausible role of SENPs in carcinogenesis resulted in the design and development of their inhibitors, including synthetic protein-based, peptide-based, and small molecular weight inhibitors, as well as naturally occurring compounds. Computational methods including virtual screening have been implemented to identify a number of lead structures in recent years. Some inhibitors suppressed the proliferation of prostate cancer cells in vitro and in vivo, confirming that SENPs are suitable targets for anti-cancer treatment. Further advances in the development of SENP-oriented inhibitors are anticipated toward SENP isoform-specific molecules with therapeutic potential.
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Affiliation(s)
- Paulina Tokarz
- Correspondence: ; Tel.: +48-42-635-48-15; Fax: +48-42-635-44-84
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8
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Wang Z, Liu Y, Zhang J, Ullah S, Kang N, Zhao Y, Zhou H. Benzothiophene-2-carboxamide derivatives as SENPs inhibitors with selectivity within SENPs family. Eur J Med Chem 2020; 204:112553. [PMID: 32717481 DOI: 10.1016/j.ejmech.2020.112553] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/02/2020] [Accepted: 06/07/2020] [Indexed: 12/28/2022]
Abstract
The SUMO (small ubiquitin-related modifier)-specific proteases (SENPs) are responsible for the cleavage of SUMO from its target proteins, thus play important roles in the dynamic SUMOylation and deSUMOylation processes. SENPs are related to a variety of human diseases including cancer and represent a new class of potential therapeutic targets with mechanism of action that is likely to be different from that of current clinically used drugs. However, potent inhibitors that are selective within the SENPs family members still remain a challenge due to their high homology. In order to demonstrate the feasibility of developing selective inhibitors within the SENPs family, we chose SENP1/2/5 as representatives, aiming to identify inhibitors with selectivity among the members. Starting from a hit compound ZCL951 from virtual screening, a series of benzothiophene-2-carboxamide inhibitors were designed based on the protein structures of SENP1, 2, and 5. First, an unoccupied hydrophobic pocket was first identified which led to IC50 as low as 0.56 μM. Furthermore, the ethylacetate 77 gave both submicromolar inhibitory activity and 33-fold selectivity for SENP2 versus SENP5. They are the most potent and selective nonpeptidic inhibitor reported so far for the SENPs family, as far as we are aware. Their structure-activity relationship was also discussed.
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Affiliation(s)
- Zhongli Wang
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yunqi Liu
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Jianchen Zhang
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Shafi Ullah
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Ning Kang
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Yaxue Zhao
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Huchen Zhou
- State Key Laboratory of Microbial Metabolism, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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9
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Xiang JW, Xiao Y, Gan Y, Chen H, Liu Y, Wang L, Nie Q, Liu F, Gong X, Fu JL, Qing WJ, Yang L, Xie J, Luo Z, Qi R, Chen Z, Li DWC. Glucose Oxidase- and UVA-Induced Changes in the Expression Patterns of Seven De-sumoylation Enzymes (SENPs) Are Associated with Cataract Development. Curr Mol Med 2020; 19:48-53. [PMID: 30854967 DOI: 10.2174/1566524019666190311094313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 11/28/2018] [Accepted: 02/28/2019] [Indexed: 01/13/2023]
Abstract
OBJECTIVE It has been well established that sumoylation acts as an important regulatory mechanism that controls many different cellular processes. We and others have shown that sumoylation plays an indispensable role during mouse eye development. Whether sumoylation is implicated in ocular pathogenesis remains to be further studied. In the present study, we have examined the expression patterns of the de-sumoylation enzymes (SENPs) in the in vitro cataract models induced by glucose oxidase and UVA irradiation. METHODS Four-week-old C57BL/6J mice were used in our experiments. Lenses were carefully dissected out from mouse eyes and cultured in M199 medium for 12 hours. Transparent lenses (without surgical damage) were selected for experimentation. The lenses were exposed to UVA for 60 min or treated with 20 mU/mL glucose oxidase (GO) to induce cataract formation. The mRNA levels were analyzed with qRT-PCR. The protein levels were determined with western blot analysis and quantitated with Image J. RESULTS GO treatment and UVA irradiation can induce cataract formation in lens cultured in vitro. GO treatment significantly down-regulated the mRNA levels for SENPs from 50% to 85%; on the other hand, expression of seven SENP proteins under GO treatment appeared in 3 situations: upregulation for SENP1, 2 and 6; downregulation for SENP 5 and 8; and unchanged for SENP3 and 7. UVA irradiation upregulates the mRNAs for all seven SENPs; In contrast to the mRNA levels for 7 SENPs, the expression levels for 6 SENPs (SENP1-3, 5-6 and 8) appeared down-regulated from 10% to 50%, and only SENP7 was slightly upregulated. CONCLUSION Our results for the first time established the differentiation expression patterns of 7 de-sumoylation enzymes (SENPs) under treatment by GO or UVA, which provide preliminary data to link sumoylation to stress-induced cataractogenesis.
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Affiliation(s)
- Jia-Wen Xiang
- Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Yuan Xiao
- Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Yuwen Gan
- Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Huimin Chen
- Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Yunfei Liu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Ling Wang
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Qian Nie
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Fangyuan Liu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Xiaodong Gong
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Jia-Ling Fu
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Wen-Jie Qing
- Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Lan Yang
- Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Jie Xie
- Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Zhongwen Luo
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Ruili Qi
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - Zhigang Chen
- The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
| | - David Wan-Cheng Li
- Key Laboratory of Protein Chemistry and Developmental Biology, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, China.,The State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Guangzhou, Guangdong 510230, China
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10
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Pei H, Chen L, Liao QM, Wang KJ, Chen SG, Liu ZJ, Zhang ZC. SUMO-specific protease 2 (SENP2) functions as a tumor suppressor in osteosarcoma via SOX9 degradation. Exp Ther Med 2018; 16:5359-5365. [PMID: 30542495 DOI: 10.3892/etm.2018.6838] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/09/2018] [Indexed: 01/06/2023] Open
Abstract
Osteosarcoma (OS) is the most common primary bone malignancy in children and adolescents, the pathogenesis of which remain largely unknown. Small ubiquitin-like modifier (SUMO)-Specific Protease 2 (SENP2) has been reported to serve as a tumor suppressor in hepatocellular carcinoma cells. The aim of the present study was to investigate the critical role of SENP2 in OS cells. Using reverse transcription-quantitative polymerase chain reaction and western blot assays, it was observed that SENP2 was significantly downregulated in clinical OS tissues compared with adjacent normal samples. Ectopic expression of SENP2 resulted in the suppression of proliferation, migration and invasion in OS cells, whereas SENP2 knockdown by CRISPR-Cas9-based gene editing had the opposite effect. SENP2 is associated with the proteasome-dependent ubiquitination and degradation of SRY-box-9 (SOX9). SOX9 silencing impaired SENP2-depletion-induced accelerated cell growth and migration. Together, these results suggest that SOX9 is a critical downstream effector of the tumor suppressor SENP2 in OS.
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Affiliation(s)
- Hong Pei
- Department of Orthopaedics, Jing Zhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Liang Chen
- Department of Orthopaedics, Jing Zhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Quan-Ming Liao
- Department of Orthopaedics, Jing Zhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Ke-Jun Wang
- Department of Orthopaedics, Jing Zhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Shun-Guang Chen
- Department of Orthopaedics, Jing Zhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Zheng-Jie Liu
- Department of Orthopaedics, Jing Zhou Central Hospital, The Second Clinical Medical College, Yangtze University, Jingzhou, Hubei 434020, P.R. China
| | - Zhi-Cai Zhang
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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11
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Han ZJ, Feng YH, Gu BH, Li YM, Chen H. The post-translational modification, SUMOylation, and cancer (Review). Int J Oncol 2018; 52:1081-1094. [PMID: 29484374 PMCID: PMC5843405 DOI: 10.3892/ijo.2018.4280] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 02/14/2018] [Indexed: 02/07/2023] Open
Abstract
SUMOylation is a reversible post-translational modification which has emerged as a crucial molecular regulatory mechanism, involved in the regulation of DNA damage repair, immune responses, carcinogenesis, cell cycle progression and apoptosis. Four SUMO isoforms have been identified, which are SUMO1, SUMO2/3 and SUMO4. The small ubiquitin-like modifier (SUMO) pathway is conserved in all eukaryotes and plays pivotal roles in the regulation of gene expression, cellular signaling and the maintenance of genomic integrity. The SUMO catalytic cycle includes maturation, activation, conjugation, ligation and de-modification. The dysregulation of the SUMO system is associated with a number of diseases, particularly cancer. SUMOylation is widely involved in carcinogenesis, DNA damage response, cancer cell proliferation, metastasis and apoptosis. SUMO can be used as a potential therapeutic target for cancer. In this review, we briefly outline the basic concepts of the SUMO system and summarize the involvement of SUMO proteins in cancer cells in order to better understand the role of SUMO in human disease.
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Affiliation(s)
- Zhi-Jian Han
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Yan-Hu Feng
- Key Laboratory of the Digestive System Tumors of Gansu Province, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Bao-Hong Gu
- Department of General Surgery, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Yu-Min Li
- Department of General Surgery, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
| | - Hao Chen
- Department of General Surgery, Second Hospital of Lanzhou University, Lanzhou, Gansu 730030, P.R. China
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12
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Identification of novel prognosis-related genes associated with cancer using integrative network analysis. Sci Rep 2018; 8:3233. [PMID: 29459674 PMCID: PMC5818516 DOI: 10.1038/s41598-018-21691-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/08/2018] [Indexed: 12/28/2022] Open
Abstract
Prognosis identifies the seriousness and the chances of survival of a cancer patient. However, it remains a challenge to identify the key cancer genes in prognostic studies. In this study, we collected 2064 genes that were related to prognostic studies by using gene expression measurements curated from published literatures. Among them, 1820 genes were associated with copy number variations (CNVs). The further functional enrichment on 889 genes with frequent copy number gains (CNGs) revealed that these genes were significantly associated with cancer pathways including regulation of cell cycle, cell differentiation and mitogen-activated protein kinase (MAPK) cascade. We further conducted integrative analyses of CNV and their target genes expression using the data from matched tumour samples of The Cancer Genome Atlas (TCGA). Ultimately, 95 key prognosis-related genes were extracted, with concordant CNG events and increased up-regulation in at least 300 tumour samples. These genes, and the number of samples in which they were found, included: ACTL6A (399), ATP6V1C1 (425), EBAG9 (412), FADD (308), MTDH (377), and SENP5 (304). This study provides the first observation of CNV in prognosis-related genes across pan-cancer. The systematic concordance between CNG and up-regulation of gene expression in these novel prognosis-related genes may indicate their prognostic significance.
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de Freitas RCC, Bortolin RH, Lopes MB, Tamborlin L, Meneguello L, Silbiger VN, Hirata RDC, Hirata MH, Luchessi AD, Luchessi AD. Modulation of miR-26a-5p and miR-15b-5p Exosomal Expression Associated with Clopidogrel-Induced Hepatotoxicity in HepG2 Cells. Front Pharmacol 2017; 8:906. [PMID: 29311920 PMCID: PMC5733064 DOI: 10.3389/fphar.2017.00906] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/28/2017] [Indexed: 01/25/2023] Open
Abstract
Clopidogrel is an essential antiplatelet drug used to prevent thrombosis complications associated with atherosclerosis. However, hepatotoxicity is a potential adverse effect related to clopidogrel therapy. Exosome-derived miRNAs may be useful for improved monitoring of drug response and hepatotoxicity risk. In the present study, the expression of several exosomal miRNAs (miR-26a-5p, miR-145-5p, miR-15b-5p, and miR-4701-3p) and cell-derived mRNA targets (PLOD2, SENP5, EIF4G2, HMGA2, STRADB, and TLK1) were evaluated in HepG2 cells treated with clopidogrel (6.25, 12.5, 25, 50, and 100 μM) for 24 and 48 h. Then, clopidogrel cytotoxicity was evaluated by analyzing DNA fragmentation and the cell cycle profile using flow cytometry. Differential expression of exosome-derived miRNAs and cell-derived mRNAs was analyzed by RT-qPCR. Exposure of HepG2 cells to high concentrations of clopidogrel (50 and 100 μM) for 24 h caused significant DNA fragmentation (17.6 and 44.4%, respectively; p < 0.05) and 48 h (26.8 and 48.9%, respectively; p < 0.05), indicating cellular toxicity. Upregulation of miR-26a-5p and downregulation of miR-15b-5p was observed in cells exposed to 100 μM clopidogrel for 24 and 48 h. The miR-26a-5p target mRNAs HMGA2, EIF4G2, STRADB, and SENP5 were downregulated in HepG2 cells following exposure to cytotoxic concentrations of clopidogrel (50 and 100 μM) for 24 h, and HMGA2 levels remained low after 48 h of treatment. TLK1, a target of miR-15b-5p, was downregulated by 50 and 100 μM clopidogrel at 24 h. In conclusion, our results suggest that exposure to high concentrations of clopidogrel modulates the expression of exosomal miR-26a-5p and miR-15b-5p and their target mRNAs in HepG2 cells. Dysregulation of these miRNAs maybe modulate the regulatory pathways involved in clopidogrel-induced liver injury.
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Affiliation(s)
- Renata C Costa de Freitas
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Raul H Bortolin
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Mariana B Lopes
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Letícia Tamborlin
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, Brazil
| | - Letícia Meneguello
- Post graduation in Biological Science, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Vivian N Silbiger
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Rosario D C Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Mário H Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Augusto D Luchessi
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas, Limeira, Brazil.,Post graduation in Biological Science, Institute of Biosciences, São Paulo State University (UNESP), Rio Claro, Brazil
| | - André D Luchessi
- Department of Clinical and Toxicological Analysis, Federal University of Rio Grande do Norte, Natal, Brazil
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Sun Y, Zheng ZP, Li H, Zhang HQ, Ma FQ. ANRIL is associated with the survival rate of patients with colorectal cancer, and affects cell migration and invasion in vitro. Mol Med Rep 2016; 14:1714-20. [PMID: 27314206 DOI: 10.3892/mmr.2016.5409] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 05/20/2016] [Indexed: 01/16/2023] Open
Abstract
Antisense noncoding RNA in the INK4 locus (ANRIL) has been reported to be upregulated in various types of human cancer, and is also highly expressed in normal human tissue. The aim of the present study was to identify whether ANRIL may be a possible target for colorectal cancer (CRC) therapy. Reverse transcription‑quantitative polymerase chain reaction was used to quantify the expression levels of the long noncoding RNA (lncRNA) ANRIL in 97 paired CRC and adjacent non‑neoplastic tissue samples. In addition, the HT29 and RKO human CRC cell lines underwent ANRIL RNA interference, and knockdown efficiency was evaluated by western blotting. Cell viability, and migratory and invasive ability were subsequently assessed. The CRC tissues were revealed to express higher levels of ANRIL lncRNA compared with the adjacent non‑neoplastic tissues (P<0.05). Furthermore, high ANRIL expression was significantly associated with reduced survival rate (P<0.05). ANRIL gene expression was successfully silenced in human CRC cells. ANRIL knockdown decreased proliferation, inhibited migration and invasion, and reduced the colony‑forming ability of the cells. These data indicated that the lncRNA ANRIL is upregulated in CRC tissues, and is associated with CRC cell pathogenesis. Furthermore, the underlying mechanisms of these effects may be exploited for therapeutic benefit.
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Affiliation(s)
- Yi Sun
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Zhao-Peng Zheng
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Hang Li
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Han-Qun Zhang
- Department of Oncology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Fa-Qiang Ma
- Department of Oncology, The Second Affiliated Hospital of Guizhou Medical University, Kaili, Guizhou 556000, P.R. China
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Eifler K, Vertegaal ACO. SUMOylation-Mediated Regulation of Cell Cycle Progression and Cancer. Trends Biochem Sci 2015; 40:779-793. [PMID: 26601932 DOI: 10.1016/j.tibs.2015.09.006] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/16/2015] [Accepted: 09/22/2015] [Indexed: 01/08/2023]
Abstract
Protein conjugation with Small ubiquitin-like modifier (SUMOylation) has critical roles during cell cycle progression. Many important cell cycle regulators, including many oncogenes and tumor suppressors, are functionally regulated via SUMOylation. The dynamic SUMOylation pattern observed throughout the cell cycle is ensured via distinct spatial and temporal regulation of the SUMO machinery. Additionally, SUMOylation cooperates with other post-translational modifications to mediate cell cycle progression. Deregulation of these SUMOylation and deSUMOylation enzymes causes severe defects in cell proliferation and genome stability. Different types of cancer were recently shown to be dependent on a functioning SUMOylation system, a finding that could be exploited in anticancer therapies.
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Affiliation(s)
- Karolin Eifler
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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16
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Moriarity BS, Otto GM, Rahrmann EP, Rathe SK, Wolf NK, Weg MT, Manlove LA, LaRue RS, Temiz NA, Molyneux SD, Choi K, Holly KJ, Sarver AL, Scott MC, Forster CL, Modiano JF, Khanna C, Hewitt SM, Khokha R, Yang Y, Gorlick R, Dyer MA, Largaespada DA. A Sleeping Beauty forward genetic screen identifies new genes and pathways driving osteosarcoma development and metastasis. Nat Genet 2015; 47:615-24. [PMID: 25961939 DOI: 10.1038/ng.3293] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/07/2015] [Indexed: 12/13/2022]
Abstract
Osteosarcomas are sarcomas of the bone, derived from osteoblasts or their precursors, with a high propensity to metastasize. Osteosarcoma is associated with massive genomic instability, making it problematic to identify driver genes using human tumors or prototypical mouse models, many of which involve loss of Trp53 function. To identify the genes driving osteosarcoma development and metastasis, we performed a Sleeping Beauty (SB) transposon-based forward genetic screen in mice with and without somatic loss of Trp53. Common insertion site (CIS) analysis of 119 primary tumors and 134 metastatic nodules identified 232 sites associated with osteosarcoma development and 43 sites associated with metastasis, respectively. Analysis of CIS-associated genes identified numerous known and new osteosarcoma-associated genes enriched in the ErbB, PI3K-AKT-mTOR and MAPK signaling pathways. Lastly, we identified several oncogenes involved in axon guidance, including Sema4d and Sema6d, which we functionally validated as oncogenes in human osteosarcoma.
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Affiliation(s)
- Branden S Moriarity
- 1] Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA. [2] Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA. [3] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - George M Otto
- 1] Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA. [2] Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA. [3] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [4] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Eric P Rahrmann
- 1] Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA. [2] Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA. [3] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [4] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Susan K Rathe
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Natalie K Wolf
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Madison T Weg
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Luke A Manlove
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rebecca S LaRue
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Nuri A Temiz
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Research Foundation, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kevin J Holly
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Aaron L Sarver
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Milcah C Scott
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Veterinary Clinical Sciences, University of Minnesota, St. Paul, Minnesota, USA
| | - Colleen L Forster
- BioNet, Academic Health Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jaime F Modiano
- 1] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [2] Department of Veterinary Clinical Sciences, University of Minnesota, St. Paul, Minnesota, USA. [3] Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Chand Khanna
- Tumor and Metastasis Biology Section, Pediatric Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephen M Hewitt
- Tissue Array Research Program (TARP), Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, USA
| | - Rama Khokha
- Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Yi Yang
- Department of Orthopedic Surgery, Musculoskeletal Tumor Center, People's Hospital, Peking University, Beijing, China
| | - Richard Gorlick
- 1] Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, New York, USA. [2] Department of Molecular Pharmacology, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, New York, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - David A Largaespada
- 1] Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA. [2] Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA. [3] Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA. [4] Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
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Kumar A, Zhang KYJ. Advances in the development of SUMO specific protease (SENP) inhibitors. Comput Struct Biotechnol J 2015; 13:204-11. [PMID: 25893082 PMCID: PMC4397505 DOI: 10.1016/j.csbj.2015.03.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 03/06/2015] [Accepted: 03/16/2015] [Indexed: 12/12/2022] Open
Abstract
Sumoylation is a reversible post-translational modification that involves the covalent attachment of small ubiquitin-like modifier (SUMO) proteins to their substrate proteins. Prior to their conjugation, SUMO proteins need to be proteolytically processed from its precursor form to mature or active form. SUMO specific proteases (SENPs) are cysteine proteases that cleave the pro or inactive form of SUMO at C-terminus using its hydrolase activity to expose two glycine residues. SENPs also catalyze the de-conjugation of SUMO proteins using their isopeptidase activity, which is crucial for recycling of SUMO from substrate proteins. SENPs are important for maintaining the balance between sumoylated and unsumoylated proteins required for normal cellular physiology. Several studies reported the overexpression of SENPs in disease conditions and highlighted their role in the development of various diseases, especially cancer. In this review, we will address the current biological understanding of various SENP isoforms and their role in the pathogenesis of different cancers and other diseases. We will then discuss the advances in the development of protein-based, peptidyl and small molecule inhibitors of various SENP isoforms. Finally, we will summarize successful examples of computational screening that allowed the identification of SENP inhibitors with therapeutic potential.
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Affiliation(s)
- Ashutosh Kumar
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Division of Structural and Synthetic Biology, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
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