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Lu C, Cai Y, Wu S, Wang Y, Li JB, Xu G, Ma J. Deubiquitinating enzyme USP39 promotes the growth and metastasis of gastric cancer cells by modulating the degradation of RNA-binding protein RBM39. J Biol Chem 2024; 300:107751. [PMID: 39260689 DOI: 10.1016/j.jbc.2024.107751] [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: 05/24/2024] [Revised: 08/05/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024] Open
Abstract
It has been revealed recently that the RNA-binding motif protein RBM39 is highly expressed in several cancers, which results in poor patient survival. However, how RBM39 is regulated in gastric cancer cells is unknown. Here, affinity purification-mass spectrometry and a biochemical screening are employed to identify the RBM39-interacting proteins and the deubiquitinating enzymes that regulate the RBM39 protein level. Integration of the data obtained from these two approaches uncovers USP39 as the potential deubiquitinating enzyme that regulates RBM39 stability. Bioinformatic analysis discloses that USP39 is increased in gastric cancer tissues and its elevation shortens the duration of overall survival for gastric cancer patients. Biochemical experiments verify that USP39 and RBM39 interact with each other and highly colocalize in the nucleus. Expression of USP39 elevates while USP39 knockdown attenuates the RBM39 protein level and their interaction regulates this modulation and their colocalization. Mechanistic studies reveal that USP39 reduces the K48-linked polyubiquitin chains on RBM39, thus enhancing its stability and increasing the protein level by preventing its proteasomal degradation. USP39 overexpression promotes while its knockdown attenuates the growth, colony formation, migration, and invasion of gastric cancer cells. Interestingly, overexpression of RBM39 partially restores the impact of USP39 depletion, while RBM39 knockdown partially abolishes the effect of USP39 overexpression on the growth, colony formation, migration, and invasion of gastric cancer cells. Collectively, this work identifies the first DUB for RBM39 and elucidates the regulatory functions and the underlying mechanism, providing a possible alternative approach to suppressing RBM39 by inhibiting USP39 in cancer therapy.
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Affiliation(s)
- Chengpiao Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Yunxin Cai
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Shenglong Wu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Yuhong Wang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jia-Bin Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China; Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China; MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu Province, China.
| | - Jingjing Ma
- Department of Pharmacy, The Fourth Affiliated Hospital of Soochow University, Suzhou Dushu Lake Hospital, Medical Center of Soochow University, Suzhou, Jiangsu, China.
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2
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Ozaki K, Kato R, Yasuhara T, Uchihara Y, Hirakawa M, Abe Y, Shibata H, Kawabata-Iwakawa R, Shakayeva A, Kot P, Miyagawa K, Suzuki K, Matsuda N, Shibata A, Yamauchi M. Involvement of the splicing factor SART1 in the BRCA1-dependent homologous recombination repair of DNA double-strand breaks. Sci Rep 2024; 14:18455. [PMID: 39117746 PMCID: PMC11310344 DOI: 10.1038/s41598-024-68926-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
Although previous studies have reported that pre-mRNA splicing factors (SFs) are involved in the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR), their exact role in promoting HR remains poorly understood. Here, we showed that SART1, an SF upregulated in several types of cancer, promotes DSB end resection, an essential first step of HR. The resection-promoting function of SART1 requires phosphorylation at threonine 430 and 695 by ATM/ATR. SART1 is recruited to DSB sites in a manner dependent on transcription and its RS domain. SART1 is epistatic with BRCA1, a major HR factor, in the promotion of resection, especially transcription-associated resection in the G2 phase. SART1 and BRCA1 accumulate at DSB sites in an interdependent manner, and epistatically counteract the resection blockade posed by 53BP1 and RIF1. Furthermore, chromosome analysis demonstrated that SART1 and BRCA1 epistatically suppressed genomic alterations caused by DSB misrepair in the G2 phase. Collectively, these results indicate that SART1 and BRCA1 cooperatively facilitate resection of DSBs arising in transcriptionally active genomic regions in the G2 phase, thereby promoting faithful repair by HR, and suppressing genome instability.
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Affiliation(s)
- Kie Ozaki
- Hospital Campus Laboratory, Radioisotope Center, Central Institute of Radioisotope Science and Safety Management, Kyushu University, Fukuoka, 812-8582, Japan
| | - Reona Kato
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, 421 Curie Boulevard, Philadelphia, PA, 19104, USA
| | - Takaaki Yasuhara
- Laboratory of Genome Stress Response, Department of Late Effects Studies, Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Sakyo-Ku, Kyoto, 606-8501, Japan
| | - Yuki Uchihara
- Signal Transduction Program, Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Gunma, 371-8511, Japan
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, Tokyo, 105-8512, Japan
| | - Miyako Hirakawa
- Center for Radiation Research and Education, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Yu Abe
- Department of Radiation Biology and Protection, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Reika Kawabata-Iwakawa
- Division of Integrated Oncology Research, Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Gunma, 371-8511, Japan
| | - Aizhan Shakayeva
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- School of Medicine, Nazarbayev University, 010000, Astana, Kazakhstan
| | - Palina Kot
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- Institute of Biochemistry, FB08, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Kiyoshi Miyagawa
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Keiji Suzuki
- Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Naoki Matsuda
- Center for Radiation Research and Education, Nagasaki University, Nagasaki, 852-8523, Japan
- Department of Radiation Biology and Protection, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, 852-8523, Japan
| | - Atsushi Shibata
- Signal Transduction Program, Gunma University Initiative for Advanced Research (GIAR), Gunma University, Maebashi, Gunma, 371-8511, Japan
- Division of Molecular Oncological Pharmacy, Faculty of Pharmacy, Keio University, Tokyo, 105-8512, Japan
| | - Motohiro Yamauchi
- Hospital Campus Laboratory, Radioisotope Center, Central Institute of Radioisotope Science and Safety Management, Kyushu University, Fukuoka, 812-8582, Japan.
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Ding R, Yu X, Hu Z, Dong Y, Huang H, Zhang Y, Han Q, Ni ZY, Zhao R, Ye Y, Zou Q. Lactate modulates RNA splicing to promote CTLA-4 expression in tumor-infiltrating regulatory T cells. Immunity 2024; 57:528-540.e6. [PMID: 38417442 DOI: 10.1016/j.immuni.2024.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/04/2024] [Accepted: 01/30/2024] [Indexed: 03/01/2024]
Abstract
RNA splicing is involved in cancer initiation and progression, but how it influences host antitumor immunity in the metabolically abnormal tumor microenvironment (TME) remains unclear. Here, we demonstrate that lactate modulates Foxp3-dependent RNA splicing to maintain the phenotypic and functional status of tumor-infiltrating regulatory T (Treg) cells via CTLA-4. RNA splicing in Treg cells was correlated with the Treg cell signatures in the TME. Ubiquitin-specific peptidase 39 (USP39), a component of the RNA splicing machinery, maintained RNA-splicing-mediated CTLA-4 expression to control Treg cell function. Mechanistically, lactate promoted USP39-mediated RNA splicing to facilitate CTLA-4 expression in a Foxp3-dependent manner. Moreover, the efficiency of CTLA-4 RNA splicing was increased in tumor-infiltrating Treg cells from patients with colorectal cancer. These findings highlight the immunological relevance of RNA splicing in Treg cells and provide important insights into the environmental mechanism governing CTLA-4 expression in Treg cells.
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Affiliation(s)
- Rui Ding
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaoyan Yu
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhilin Hu
- Department of Immunology, Key Laboratory of Immune Microenvironment and Disease, the School of Basic Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yu Dong
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Haiyan Huang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuerong Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qiaoqiao Han
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhi-Yu Ni
- Clinical Medical College, Hebei University of Engineering, Handan 056038, Hebei, China; Central Laboratory, Hebei Collaborative Innovation Center of Tumor Microecological Metabolism Regulation, Affiliated Hospital of Hebei University, Baoding 071000, Hebei, China; Affiliated Hospital of Hebei Engineering University, Handan 056002, Hebei, China.
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Youqiong Ye
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
| | - Qiang Zou
- Hongqiao International Institute of Medicine, Tongren Hospital & Shanghai Institute of Immunology, State Key Laboratory of Systems Medicine for Cancer, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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Campos Alonso M, Knobeloch KP. In the moonlight: non-catalytic functions of ubiquitin and ubiquitin-like proteases. Front Mol Biosci 2024; 11:1349509. [PMID: 38455765 PMCID: PMC10919355 DOI: 10.3389/fmolb.2024.1349509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/09/2024] Open
Abstract
Proteases that cleave ubiquitin or ubiquitin-like proteins (UBLs) are critical players in maintaining the homeostasis of the organism. Concordantly, their dysregulation has been directly linked to various diseases, including cancer, neurodegeneration, developmental aberrations, cardiac disorders and inflammation. Given their potential as novel therapeutic targets, it is essential to fully understand their mechanisms of action. Traditionally, observed effects resulting from deficiencies in deubiquitinases (DUBs) and UBL proteases have often been attributed to the misregulation of substrate modification by ubiquitin or UBLs. Therefore, much research has focused on understanding the catalytic activities of these proteins. However, this view has overlooked the possibility that DUBs and UBL proteases might also have significant non-catalytic functions, which are more prevalent than previously believed and urgently require further investigation. Moreover, multiple examples have shown that either selective loss of only the protease activity or complete absence of these proteins can have different functional and physiological consequences. Furthermore, DUBs and UBL proteases have been shown to often contain domains or binding motifs that not only modulate their catalytic activity but can also mediate entirely different functions. This review aims to shed light on the non-catalytic, moonlighting functions of DUBs and UBL proteases, which extend beyond the hydrolysis of ubiquitin and UBL chains and are just beginning to emerge.
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Affiliation(s)
- Marta Campos Alonso
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus-Peter Knobeloch
- Institute of Neuropathology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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5
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Pilarte KA, Reichert EC, Green YS, Halberg LMT, McFarland SA, Mimche PN, Golkowski M, Kamdem SD, Maguire KM, Summers SA, Maschek JA, Reelitz JW, Cox JE, Evason KJ, Koh MY. HAF Prevents Hepatocyte Apoptosis and Hepatocellular Carcinoma through Transcriptional Regulation of the NF-κB pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574894. [PMID: 38260413 PMCID: PMC10802431 DOI: 10.1101/2024.01.09.574894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Background Hepatocellular carcinoma (HCC) incidence is increasing worldwide due to the obesity epidemic, which drives metabolic dysfunction-associated steatohepatitis (MASH) that can lead to HCC. However, the molecular pathways that lead to MASH-HCC are poorly understood. We have previously reported that male mice with global haploinsufficiency of hypoxia-associated factor, HAF ( SART1 +/ - ) spontaneously develop MASH/HCC. However, the cell type(s) responsible for HCC associated with HAF loss are unclear. Results SART1 -floxed mice were crossed with mice expressing Cre-recombinase within hepatocytes (Alb-Cre; hepS -/- ) or macrophages (LysM-Cre, macS -/- ). Only hepS -/- mice (both male and female) developed HCC suggesting that HAF protects against HCC primarily within hepatocytes. HAF-deficient macrophages showed decreased P-p65 and P-p50 and in many major components of the NF-κB pathway, which was recapitulated using HAF siRNA in vitro . HAF depletion increased apoptosis both in vitro and in vivo , suggesting that HAF mediates a tumor suppressor role by suppressing hepatocyte apoptosis. We show that HAF regulates NF-κB activity by controlling transcription of TRADD and RIPK1 . Mice fed a high-fat diet (HFD) showed marked suppression of HAF, P-p65 and TRADD within their livers after 26 weeks, but manifest profound upregulation of HAF, P-65 and TRADD within their livers after 40 weeks of HFD, implicating deregulation of the HAF-NF-κB axis in the progression to MASH. In humans, HAF was significantly decreased in livers with simple steatosis but significantly increased in HCC compared to normal liver. Conclusions HAF is novel transcriptional regulator of the NF-κB pathway that protects against hepatocyte apoptosis and is a key determinant of cell fate during progression to MASH and MASH-HCC.
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Yu J, Yuan S, Song J, Yu S. USP39 interacts with SIRT7 to promote cervical squamous cell carcinoma by modulating autophagy and oxidative stress via FOXM1. J Transl Med 2023; 21:807. [PMID: 37957720 PMCID: PMC10641974 DOI: 10.1186/s12967-023-04623-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 10/13/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Sirtuin 7 (SIRT7) is an oncogene that promotes tumor progression in various malignancies, however, its role and regulatory mechanism in cervical squamous cell carcinoma (CSCC) is unknown. Herein, we attempted to investigate the functional role and molecular mechanism of SIRT7 underlying CSCC progression. METHODS SIRT7 expression was evaluated in CSCC cells using various assays. We then used a series of function gain-and-loss experiments to determine the role of SIRT7 in CSCC progression. Furthermore, mechanism experiments were conducted to assess the interaction between SIRT7/USP39/FOXM1 in CSCC cells. Additionally, rescue assays were conducted to explore the regulatory function of USP39/FOXM1 in CSCC cellular processes. RESULTS SIRT7 was highly expressed in CSCC patient tissues and cell lines. SIRT7 deficiency showed significant repression on the proliferation, and autophagy of CSCC cells in vitro and tumorigenesis in vivo. Similarly, apoptosis and ROS production in CSCC cells were accelerated after the SIRT7 knockdown. Moreover, SIRT7 and USP39 were found colocalized in the cell nucleus. Interestingly, SIRT7 was revealed to deacetylate USP39 to promote its protein stability in CSCC cells. USP39 protein was also verified to be upregulated in CSCC tissues and cells. USP39 silencing showed suppressive effects on CSCC cell growth. Mechanistically, USP39 was revealed to upregulate SIRT7 by promoting the transcriptional activity of FOXM1. Rescue assays also indicated that SIRT7 promoted autophagy and inhibited ROS production in CSCC cells by regulating USP39/FOXM1. CONCLUSION The SIRT7/USP39/FOXM1 positive feedback network regulates autophagy and oxidative stress in CSCC, thus providing a new direction for CSCC-targeted therapy.
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Affiliation(s)
- Juanpeng Yu
- Department of Gynecology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, No. 1 Huanghe West Road, Huaiyin District, Huai'an, 223300, Jiangsu, China
| | - Shuai Yuan
- Department of Gynecology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, No. 1 Huanghe West Road, Huaiyin District, Huai'an, 223300, Jiangsu, China
| | - Jinglin Song
- Department of Obstetrics and Gynecology, Langao County Hospital of Traditional Chinese Medicine, Ankang, 725400, Shaanxi, China
| | - Shengsheng Yu
- Department of Gynecology, The Affiliated Huai'an No.1 People's Hospital of Nanjing Medical University, No. 1 Huanghe West Road, Huaiyin District, Huai'an, 223300, Jiangsu, China.
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7
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Cui D, Wang Z, Dang Q, Wang J, Qin J, Song J, Zhai X, Zhou Y, Zhao L, Lu G, Liu H, Liu G, Liu R, Shao C, Zhang X, Liu Z. Spliceosome component Usp39 contributes to hepatic lipid homeostasis through the regulation of autophagy. Nat Commun 2023; 14:7032. [PMID: 37923718 PMCID: PMC10624899 DOI: 10.1038/s41467-023-42461-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023] Open
Abstract
Regulation of alternative splicing (AS) enables a single transcript to yield multiple isoforms that increase transcriptome and proteome diversity. Here, we report that spliceosome component Usp39 plays a role in the regulation of hepatocyte lipid homeostasis. We demonstrate that Usp39 expression is downregulated in hepatic tissues of non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) subjects. Hepatocyte-specific Usp39 deletion in mice leads to increased lipid accumulation, spontaneous steatosis and impaired autophagy. Combined analysis of RNA immunoprecipitation (RIP-seq) and bulk RNA sequencing (RNA-seq) data reveals that Usp39 regulates AS of several autophagy-related genes. In particular, deletion of Usp39 results in alternative 5' splice site selection of exon 6 in Heat shock transcription factor 1 (Hsf1) and consequently its reduced expression. Importantly, overexpression of Hsf1 could attenuate lipid accumulation caused by Usp39 deficiency. Taken together, our findings indicate that Usp39-mediated AS is required for sustaining autophagy and lipid homeostasis in the liver.
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Affiliation(s)
- Donghai Cui
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Zixiang Wang
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Qianli Dang
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Jing Wang
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Junchao Qin
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Jianping Song
- Department of General Surgery, The Second Hospital, Shandong University, Jinan, China
| | - Xiangyu Zhai
- Department of General Surgery, The Second Hospital, Shandong University, Jinan, China
| | - Yachao Zhou
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
- Advanced Medical Research Institute, Shandong University, Jinan, China
| | - Ling Zhao
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China
| | - Gang Lu
- CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hongbin Liu
- Center for Reproductive Medicine, Shandong University, Jinan, China
| | - Gang Liu
- Nephrology Research Institute of Shandong University, The Second Hospital of Shandong University, Jinan, China
| | - Runping Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Changshun Shao
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China.
| | - Xiyu Zhang
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China.
| | - Zhaojian Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, School of Basic Medical Science, Department of Obstetrics and Gynecology, Qilu Hospital, Shandong University, Jinan, China.
- Advanced Medical Research Institute, Shandong University, Jinan, China.
- Nephrology Research Institute of Shandong University, The Second Hospital of Shandong University, Jinan, China.
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8
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Petri BJ, Piell KM, Wahlang B, Head KZ, Rouchka EC, Park JW, Hwang JY, Banerjee M, Cave MC, Klinge CM. Altered splicing factor and alternative splicing events in a mouse model of diet- and polychlorinated biphenyl-induced liver disease. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 103:104260. [PMID: 37683712 PMCID: PMC10591945 DOI: 10.1016/j.etap.2023.104260] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is associated with human environmental exposure to polychlorinated biphenyls (PCBs). Alternative splicing (AS) is dysregulated in steatotic liver disease and is regulated by splicing factors (SFs) and N-6 methyladenosine (m6A) modification. Here integrated analysis of hepatic mRNA-sequencing data was used to identify differentially expressed SFs and differential AS events (ASEs) in the livers of high fat diet-fed C57BL/6 J male mice exposed to Aroclor1260, PCB126, Aroclor1260 + PCB126, or vehicle control. Aroclor1260 + PCB126 co-exposure altered 100 SFs and replicate multivariate analysis of transcript splicing (rMATS) identified 449 ASEs in 366 genes associated with NAFLD pathways. These ASEs were similar to those resulting from experimental perturbations in m6A writers, readers, and erasers. These results demonstrate specific hepatic SF and AS regulatory mechanisms are disrupted by HFD and PCB exposures, contributing to the expression of altered isoforms that may play a role in NAFLD progression to NASH.
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Affiliation(s)
- Belinda J Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Banrida Wahlang
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Kimberly Z Head
- University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Eric C Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; KY INBRE Bioinformatics Core, University of Louisville, USA
| | - Juw Won Park
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; KY INBRE Bioinformatics Core, University of Louisville, USA; Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292 USA
| | - Jae Yeon Hwang
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Mayukh Banerjee
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292 USA
| | - Matthew C Cave
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA.
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Quan J, Zhao X, Xiao Y, Wu H, Di Q, Wu Z, Chen X, Tang H, Zhao J, Guan Y, Xu Y, Chen W. USP39 Regulates NF-κB-Mediated Inflammatory Responses through Deubiquitinating K48-Linked IκBα. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:640-652. [PMID: 36651806 DOI: 10.4049/jimmunol.2200603] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/06/2022] [Indexed: 01/19/2023]
Abstract
IκBα is a critical protein that inhibits NF-κB nuclear translocation and impairs NF-κB-mediated signaling. The abundance of IκBα determines the activation and restoration of the inflammatory response. However, posttranslational regulation of IκBα remains to be fully understood. In this study, we identified ubiquitin-specific protease 39 (USP39) as a negative regulator in the NF-κB inflammatory response by stabilizing basal IκBα. The expression of USP39 in macrophages was reduced under LPS-induced inflammation. Knockdown or knockout of USP39 in macrophages significantly increased the expression and secretion of proinflammatory cytokines upon exposure to LPS or Escherichia coli, whereas reexpression of exogenous USP39 in USP39-deficient macrophages rescued the effect. Moreover, USP39-defective mice were more sensitive to LPS or E. coli-induced systemic sepsis. Mechanistically, USP39 interacted with and stabilized IκBα by reducing K48-linked polyubiquination of IκBα. Taken together, to our knowledge, our study for the first time revealed the inhibitory function of USP39 in the NF-κB inflammatory response, providing a previously unknown mechanism for control of inflammatory cytokine induction in the cellular anti-inflammatory response.
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Affiliation(s)
- Jiazheng Quan
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Xibao Zhao
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Yue Xiao
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Han Wu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Qianqian Di
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Zherui Wu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Xinyi Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Haimei Tang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Jiajing Zhao
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Yonghong Guan
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Yongxian Xu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Weilin Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Institute of Biological Therapy, Department of Immunology, Shenzhen University School of Medicine, Shenzhen, China
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10
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de Luxán-Hernández C, Lohmann J, Tranque E, Chumova J, Binarova P, Salinas J, Weingartner M. MDF is a conserved splicing factor and modulates cell division and stress response in Arabidopsis. Life Sci Alliance 2022; 6:6/1/e202201507. [PMID: 36265897 PMCID: PMC9585968 DOI: 10.26508/lsa.202201507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 02/05/2023] Open
Abstract
The coordination of cell division with stress response is essential for maintaining genome stability in plant meristems. Proteins involved in pre-mRNA splicing are important for these processes in animal and human cells. Based on its homology to the splicing factor SART1, which is implicated in the control of cell division and genome stability in human cells, we analyzed if MDF has similar functions in plants. We found that MDF associates with U4/U6.U5 tri-snRNP proteins and is essential for correct splicing of 2,037 transcripts. Loss of MDF function leads to cell division defects and cell death in meristems and was associated with up-regulation of stress-induced genes and down-regulation of mitotic regulators. In addition, the mdf-1 mutant is hypersensitive to DNA damage treatment supporting its role in coordinating stress response with cell division. Our analysis of a dephosphomutant of MDF suggested how its protein activity might be controlled. Our work uncovers the conserved function of a plant splicing factor and provides novel insight into the interplay of pre-mRNA processing and genome stability in plants.
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Affiliation(s)
| | - Julia Lohmann
- Institute of Plant Sciences and Microbiology, University of Hamburg, Hamburg, Germany
| | - Eduardo Tranque
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas “Margarita Salas” (CSIC), Madrid, Spain
| | - Jana Chumova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pavla Binarova
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas “Margarita Salas” (CSIC), Madrid, Spain
| | - Magdalena Weingartner
- Institute of Plant Sciences and Microbiology, University of Hamburg, Hamburg, Germany
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11
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Zhao J, Guo J, Wang Y, Ma Q, Shi Y, Cheng F, Lu Q, Fu W, Ouyang G, Zhang J, Xu Q, Hu X. Research Progress of DUB Enzyme in Hepatocellular Carcinoma. Front Oncol 2022; 12:920287. [PMID: 35875077 PMCID: PMC9303014 DOI: 10.3389/fonc.2022.920287] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
According to GLOBOCAN 2021 cancer incidence and mortality statistics compiled by the International Agency for Research on Cancer, hepatocellular carcinoma (HCC) is the most common malignancy in the human liver and one of the leading causes of cancer death worldwide. Although there have been great advances in the treatment of HCC, such as regofenib, sorafenib, and lomvatinib, which have been developed and approved for the clinical treatment of advanced or metastatic HCC. However, they only prolong survival by a few months, and patients with advanced liver cancer are susceptible to tumor invasion metastasis and drug resistance. Ubiquitination modification is a type of post-translational modification of proteins. It can affect the physiological activity of cells by regulating the localization, stability and activity of proteins, such as: gene transcription, DNA damage signaling and other pathways. The reversible process of ubiquitination is called de-ubiquitination: it is the process of re-releasing ubiquitinated substrates with the participation of de-ubiquitinases (DUBs) and other active substances. There is growing evidence that many dysregulations of DUBs are associated with tumorigenesis. Although dysregulation of deuquitinase function is often found in HCC and other cancers, The mechanisms of action of many DUBs in HCC have not been elucidated. In this review, we focused on several deubiquitinases (DUBs) associated with hepatocellular carcinoma, including their structure, function, and relationship to hepatocellular carcinoma. hepatocellular carcinoma was highlighted, as well as the latest research reports. Among them, we focus on the USP family and OTU family which are more studied in the HCC. In addition, we discussed the prospects and significance of targeting DUBs as a new strategy for the treatment of hepatocellular carcinoma. It also briefly summarizes the research progress of some DUB-related small molecule inhibitors and their clinical application significance as a treatment for HCC in the future.
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Affiliation(s)
- Jie Zhao
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
| | - Jinhui Guo
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Yanan Wang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiancheng Ma
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yu Shi
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Feng Cheng
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiliang Lu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Wen Fu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | | | - Ji Zhang
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Qiuran Xu
- Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoge Hu, ; Qiuran Xu,
| | - Xiaoge Hu
- Department of Hepatobiliary and Pancreatic Surgery, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical CollegeHangzhou, China
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People’s Hospital, Affiliated People’s Hospital, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoge Hu, ; Qiuran Xu,
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12
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The Deubiquitinase USP39 Promotes Esophageal Squamous Cell Carcinoma Malignancy as a Splicing Factor. Genes (Basel) 2022; 13:genes13050819. [PMID: 35627203 PMCID: PMC9141838 DOI: 10.3390/genes13050819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 02/01/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is an aggressive epithelial malignancy and the underlying molecular mechanisms remain elusive. Here, we identify that the ubiquitin-specific protease 39 (USP39) drives cell growth and chemoresistance by functional screening in ESCC, and that high expression of USP39 correlates with shorter overall survival and progression-free survival. Mechanistically, we provide evidence for the role of USP39 in alternative splicing regulation. USP39 interacts with several spliceosome components. Integrated analysis of RNA-seq and RIP-seq reveals that USP39 regulates the alternative splicing events. Taken together, our results indicate that USP39 functions as an oncogenic splicing factor and acts as a potential therapeutic target for ESCC.
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13
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Kimura-Yoshida C, Mochida K, Kanno SI, Matsuo I. USP39 is essential for mammalian epithelial morphogenesis through upregulation of planar cell polarity components. Commun Biol 2022; 5:378. [PMID: 35440748 PMCID: PMC9018712 DOI: 10.1038/s42003-022-03254-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
Previously, we have shown that the translocation of Grainyhead-like 3 (GRHL3) transcription factor from the nucleus to the cytoplasm triggers the switch from canonical Wnt signaling for epidermal differentiation to non-canonical Wnt signaling for epithelial morphogenesis. However, the molecular mechanism that underlies the cytoplasmic localization of GRHL3 protein and that activates non-canonical Wnt signaling is not known. Here, we show that ubiquitin-specific protease 39 (USP39), a deubiquitinating enzyme, is involved in the subcellular localization of GRHL3 as a potential GRHL3-interacting protein and is necessary for epithelial morphogenesis to up-regulate expression of planar cell polarity (PCP) components. Notably, mouse Usp39-deficient embryos display early embryonic lethality due to a failure in primitive streak formation and apico-basal polarity in epiblast cells, resembling those of mutant embryos of the Prickle1 gene, a crucial PCP component. Current findings provide unique insights into how differentiation and morphogenesis are coordinated to construct three-dimensional complex structures via USP39. The ubiquitin specific protease 39 (USP39) interacts with the transcription factor and cytoplasmic regulator of planar cell polarity (PCP), Grainyheadlike 3 (Grhl3). USP39-dependent PCP gene upregulation contributes to epithelial morphogenesis.
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Affiliation(s)
- Chiharu Kimura-Yoshida
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan.
| | - Kyoko Mochida
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Shin-Ichiro Kanno
- IDAC Fellow Research Group for DNA Repair and Dynamic Proteome, Institute of Development, Aging and Cancer, Tohoku University, Sendai, 980-8575, Japan
| | - Isao Matsuo
- Department of Molecular Embryology, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, 840, Murodo-cho, Izumi, Osaka, 594-1101, Japan. .,Department of Pediatric and Neonatal-Perinatal Research, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.
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14
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Ruan GX, Li Y, Chen W, Huang H, Zhang R, Chen C, Lam KP, Xu S, Ou X. The spliceosome component Usp39 controls B cell development by regulating immunoglobulin gene rearrangement. Cell Rep 2022; 38:110338. [PMID: 35139388 DOI: 10.1016/j.celrep.2022.110338] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 11/18/2021] [Accepted: 01/13/2022] [Indexed: 12/17/2022] Open
Abstract
The spliceosome is a large ribonucleoprotein complex responsible for pre-mRNA splicing and genome stability maintenance. Disruption of the spliceosome activity may lead to developmental disorders and tumorigenesis. However, the physiological role that the spliceosome plays in B cell development and function is still poorly defined. Here, we demonstrate that ubiquitin-specific peptidase 39 (Usp39), a spliceosome component of the U4/U6.U5 tri-snRNP complex, is essential for B cell development. Ablation of Usp39 in B cell lineage blocks pre-pro-B to pro-B cell transition in the bone marrow, leading to a profound reduction of mature B cells in the periphery. We show that Usp39 specifically regulates immunoglobulin gene rearrangement in a spliceosome-dependent manner, which involves modulating chromatin interactions at the Igh locus. Moreover, our results indicate that Usp39 deletion reduces the pre-malignant B cells in Eμ-Myc transgenic mice and significantly improves their survival.
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Affiliation(s)
- Gui-Xin Ruan
- Harbin Institute of Technology, Harbin 150001, China; Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yuxing Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenjing Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hengjun Huang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Rui Zhang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Changxu Chen
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Kong-Peng Lam
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; Departments of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore; Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Shengli Xu
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore 138648, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - Xijun Ou
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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15
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High Expression of Ubiquitin-Specific Protease 39 and Its Roles in Prognosis in Patients with Hepatocellular Carcinoma. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2021:6233175. [PMID: 34987596 PMCID: PMC8723855 DOI: 10.1155/2021/6233175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Ubiquitin-specific protease 39 is mainly involved in mRNA splicing and multiple kinds of tumors. Accumulating evidence has shown that USP39 participated in the proliferation and metastasis of hepatocellular carcinoma (HCC). The present study aimed to demonstrate the association between USP39 expression and clinical features and the diagnostic value in HCC based on the Cancer Genome Atlas (TCGA). METHODS A comprehensive analysis for expression of USP39 in HCC was conducted by using multiple databases. The mRNA level of USP39, clinical features, survival rate, and diagnostic value in HCC were analyzed using data from TCGA. The Gene Set Enrichment Analysis (GSEA) was conducted to analyze signaling pathways correlated with USP39 expression in HCC. RESULTS The mRNA level of USP39 was significantly elevated in HCC. The expression of USP39 showed significant correlation with T stage, pathologic stage, tumor status, age, and histologic grade. Logistic analysis demonstrated that high expression of USP39 was significantly associated with older age, tumor status, advanced pathologic stage, T stage, and higher histologic grade. Univariate Cox regression analysis showed that high expression of USP39 was significantly associated with advanced T stage, pathological stage, and tumor status. Multivariate Cox analysis confirmed the result that USP39 expression was an independent prognostic factor for overall survival (OS) in HCC. Results of Kaplan-Meier curves showed that high expression of USP39 had a significant association with poor OS, disease-free survival (DSS), and progress-free interval (PFI) in HCC. ROC analysis indicated that USP39 could be regarded as a promising marker for distinguishing HCC from nontumor. CONCLUSION The increased USP39 might play roles in the progression, diagnosis, and prognosis of HCC.
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16
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DHX15-independent roles for TFIP11 in U6 snRNA modification, U4/U6.U5 tri-snRNP assembly and pre-mRNA splicing fidelity. Nat Commun 2021; 12:6648. [PMID: 34789764 PMCID: PMC8599867 DOI: 10.1038/s41467-021-26932-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 10/22/2021] [Indexed: 11/29/2022] Open
Abstract
The U6 snRNA, the core catalytic component of the spliceosome, is extensively modified post-transcriptionally, with 2'-O-methylation being most common. However, how U6 2'-O-methylation is regulated remains largely unknown. Here we report that TFIP11, the human homolog of the yeast spliceosome disassembly factor Ntr1, localizes to nucleoli and Cajal Bodies and is essential for the 2'-O-methylation of U6. Mechanistically, we demonstrate that TFIP11 knockdown reduces the association of U6 snRNA with fibrillarin and associated snoRNAs, therefore altering U6 2'-O-methylation. We show U6 snRNA hypomethylation is associated with changes in assembly of the U4/U6.U5 tri-snRNP leading to defects in spliceosome assembly and alterations in splicing fidelity. Strikingly, this function of TFIP11 is independent of the RNA helicase DHX15, its known partner in yeast. In sum, our study demonstrates an unrecognized function for TFIP11 in U6 snRNP modification and U4/U6.U5 tri-snRNP assembly, identifying TFIP11 as a critical spliceosome assembly regulator.
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17
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Kim JJ, Lee SY, Hwang Y, Kim S, Chung JM, Park S, Yoon J, Yun H, Ji JH, Chae S, Cho H, Kim CG, Dawson TM, Kim H, Dawson VL, Kang HC. USP39 promotes non-homologous end-joining repair by poly(ADP-ribose)-induced liquid demixing. Nucleic Acids Res 2021; 49:11083-11102. [PMID: 34614178 PMCID: PMC8565343 DOI: 10.1093/nar/gkab892] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/18/2022] Open
Abstract
Mutual crosstalk among poly(ADP-ribose) (PAR), activated PAR polymerase 1 (PARP1) metabolites, and DNA repair machinery has emerged as a key regulatory mechanism of the DNA damage response (DDR). However, there is no conclusive evidence of how PAR precisely controls DDR. Herein, six deubiquitinating enzymes (DUBs) associated with PAR-coupled DDR were identified, and the role of USP39, an inactive DUB involved in spliceosome assembly, was characterized. USP39 rapidly localizes to DNA lesions in a PAR-dependent manner, where it regulates non-homologous end-joining (NHEJ) via a tripartite RG motif located in the N-terminus comprising 46 amino acids (N46). Furthermore, USP39 acts as a molecular trigger for liquid demixing in a PAR-coupled N46-dependent manner, thereby directly interacting with the XRCC4/LIG4 complex during NHEJ. In parallel, the USP39-associated spliceosome complex controls homologous recombination repair in a PAR-independent manner. These findings provide mechanistic insights into how PAR chains precisely control DNA repair processes in the DDR.
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Affiliation(s)
- Jae Jin Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Life Science, Hallym University, Chuncheon 24252, Republic of Korea
| | - Seo Yun Lee
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Yiseul Hwang
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Soyeon Kim
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Jee Min Chung
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Sangwook Park
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Junghyun Yoon
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Hansol Yun
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Jae-Hoon Ji
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Biochemistry & Structural Biology, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sunyoung Chae
- Institute of Medical Science, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Hyeseong Cho
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
| | - Chan Gil Kim
- Department of Biotechnology, Konkuk University, Chungju 380-701, Republic of Korea
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hongtae Kim
- Center for Genomic Integrity Institute for Basic Science (IBS), Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.,School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ho Chul Kang
- Genomic Instability Research Center, Ajou University School of Medicine, Suwon, Gyeonggi, 16499, Republic of Korea.,Department of Physiology, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea.,Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Gyeonggi 16499, Republic of Korea
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18
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Novel function of SART1 in HNF4α transcriptional regulation contributes to its antiviral role during HBV infection. J Hepatol 2021; 75:1072-1082. [PMID: 34242702 DOI: 10.1016/j.jhep.2021.06.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS Our understanding of the interactions between HBV and its host cells is still quite limited. Spliceosome associated factor 1 (SART1) has recently been found to restrict HCV. Thus, we aimed to dissect its role in HBV infection. METHODS SART1 was knocked down by RNA interference and over-expressed by lentiviral or adeno-associated virus (AAV) vectors in HBV-infected cell cultures and in vivo in HBV-infected mice. Luciferase reporter assays were used to determine viral or host factor promoter activities, and chromatin immunoprecipitation (ChIP) was used to investigate protein-DNA interactions. RESULTS In HBV-infected cell cultures, downregulation of SART1 did not affect covalently closed circular HBV DNA but resulted in markedly enhanced HBV RNA, antigen expression and progeny virus production. On the other hand, HBV transcription and replication were significantly inhibited by overexpression of SART1. Similar results were observed in AAV-HBV-infected mice persistently replicating HBV. Inhibition of Janus kinases had no effect on SART1-mediated inhibition of HBV replication. HBV promoter assays revealed that SART1 reduced HBV core promoter activity. By screening known HBV transcription factors, we found that SART1 specifically suppressed the expression of hepatocyte nuclear factor 4α (HNF4α). Luciferase reporter and ChIP assays demonstrated a direct downregulation of HNF4α expression by association of SART1 with the HNF4α proximal P1 promoter element. CONCLUSIONS We identify SART1 as a novel host factor suppressing HBV cccDNA transcription. Besides its effect on interferon-stimulated genes, SART1 exerts an anti-HBV activity by suppressing HNF4α expression, which is essential for transcription of HBV cccDNA. LAY SUMMARY Hepatitis B virus (HBV) infects hepatocytes and persists in the form of covalently closed circular DNA (cccDNA), which remains a major obstacle to successful antiviral treatment. In this study, using various HBV models, we demonstrate that the protein SART1 restricts HBV cccDNA transcription by suppressing a key transcription factor, HNF4α.
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Khayer N, Jalessi M, Jahanbakhshi A, Tabib Khooei A, Mirzaie M. Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness. Sci Rep 2021; 11:20943. [PMID: 34686726 PMCID: PMC8536755 DOI: 10.1038/s41598-021-00431-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Non-functioning pituitary adenomas (NFPAs) are typical pituitary macroadenomas in adults associated with increased mortality and morbidity. Although pituitary adenomas are commonly considered slow-growing benign brain tumors, numerous of them possess an invasive nature. Such tumors destroy sella turcica and invade the adjacent tissues such as the cavernous sinus and sphenoid sinus. In these cases, the most critical obstacle for complete surgical removal is the high risk of damaging adjacent vital structures. Therefore, the development of novel therapeutic strategies for either early diagnosis through biomarkers or medical therapies to reduce the recurrence rate of NFPAs is imperative. Identification of gene interactions has paved the way for decoding complex molecular mechanisms, including disease-related pathways, and identifying the most momentous genes involved in a specific disease. Currently, our knowledge of the invasion of the pituitary adenoma at the molecular level is not sufficient. The current study aimed to identify critical biomarkers and biological pathways associated with invasiveness in the NFPAs using a three-way interaction model for the first time. In the current study, the Liquid association method was applied to capture the statistically significant triplets involved in NFPAs invasiveness. Subsequently, Random Forest analysis was applied to select the most important switch genes. Finally, gene set enrichment (GSE) and gene regulatory network (GRN) analyses were applied to trace the biological relevance of the statistically significant triplets. The results of this study suggest that "mRNA processing" and "spindle organization" biological processes are important in NFAPs invasiveness. Specifically, our results suggest Nkx3-1 and Fech as two switch genes in NFAPs invasiveness that may be potential biomarkers or target genes in this pathology.
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Affiliation(s)
- Nasibeh Khayer
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Jalessi
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran.
- ENT and Head & Neck Research Center and Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran.
| | - Amin Jahanbakhshi
- Skull Base Research Center, The Five Senses Health Institute, Iran University of Medical Sciences, Tehran, Iran
- Neurology Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Tabib Khooei
- Neurology Department, Hazrat Rasoul Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran.
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20
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Pan XW, Xu D, Chen WJ, Chen JX, Chen WJ, Ye JQ, Gan SS, Zhou W, Song X, Shi L, Cui XG. USP39 promotes malignant proliferation and angiogenesis of renal cell carcinoma by inhibiting VEGF-A 165b alternative splicing via regulating SRSF1 and SRPK1. Cancer Cell Int 2021; 21:486. [PMID: 34544400 PMCID: PMC8454004 DOI: 10.1186/s12935-021-02161-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/18/2021] [Indexed: 01/01/2023] Open
Abstract
Background The benefit of targeted therapy for renal cell carcinoma (RCC) is largely crippled by drug resistance. Rapid disease progression and poor prognosis occur in patients with drug resistance. New treatments demand prompt exploration for clinical therapies. Ubiquitin-specific peptidase 39 (USP39) serves as the pro-tumor factor in several previous studies of other malignant tumors. To investigate the function and mechanism of USP39 in promoting malignant proliferation and angiogenesis of RCC. Methods We applied ONCOMINE database to analyze the correlation between USP39 expression level and the clinical characteristics of RCC. USP39 knockdown or overexpression plasmids were transfected into 786-O and ACHN cells. The HUVEC received cell supernatants of 786-O and ACHN cells with knockdown or overexpression USP39.The effect of USP39 on RCC was evaluated by MTT assay, cell cycle analysis, colony formation assay and tubule formation assay. The interaction between USP39 and VEGF-A alternative splicing was assessed by affinity purification and mass spectrometry, co-immunoprecipitation and Western blot assays. Results The mRNA expression level of USP39 in RCC was significantly higher than that in normal renal tissue (P < 0.001), and negatively correlated with the survival rate of RCC patients (P < 0.01). Silencing of USP39 in 786-O and ACHN cells inhibited cell proliferation and colony formation, and induced S phase arrest. USP39 overexpression significantly increased the number of tubules (P < 0.05) and branches (P < 0.01) formed by HUVEC cells, and USP39 knockdown produced an opposite effect (P < 0.05). The USP39 (101–565) fragment directly mediated its binding to SRSF1 and SRPK1, and promoted the phosphorylation of SRSF1 to regulate VEGF-A alternative splicing. USP39 knockdown upregulated the expression of VEGF-A165b, and USP39 overexpression downregulated the expression of VEGF-A165b significantly (both P < 0.05). Conclusion USP39 acted as a pro-tumor factor by motivating the malignant biological processes of RCC, probably through inhibiting VEGF-A165b alternative splicing and regulating SRSF1 and SRPK1. USP39 may prove to be a potential therapeutic target for RCC. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02161-x.
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Affiliation(s)
- Xiu-Wu Pan
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China.,Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Da Xu
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Wen-Jin Chen
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Jia-Xin Chen
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Wei-Jie Chen
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Jian-Qing Ye
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Si-Shun Gan
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Wang Zhou
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China.
| | - Xu Song
- Department of Urology, Shanghai Seventh People's Hospital, Shandong, 200137, China.
| | - Lei Shi
- Department of Urology, Yantai Yuhuangding Hospital of Qingdao University Medical College, Shandong, 264000, China.
| | - Xin-Gang Cui
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China.
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21
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Dong X, Liu Z, Zhang E, Zhang P, Wang Y, Hang J, Li Q. USP39 promotes tumorigenesis by stabilizing and deubiquitinating SP1 protein in hepatocellular carcinoma. Cell Signal 2021; 85:110068. [PMID: 34197957 DOI: 10.1016/j.cellsig.2021.110068] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 01/17/2023]
Abstract
Deubiquitinating enzyme (DUB) can hydrolyze ubiquitin molecules from the protein bound with ubiquitin, and reversely regulate protein degradation. The ubiquitin-specific proteases (USP) family are cysteine proteases, which owns the largest members and diverse structure among the currently known DUB. The important roles of ubiquitin-specific peptidase39 (USP39) in cancer have been widely investigated. However, little is known about the putative de-ubiquitination function of USP39 in hepatocellular carcinoma (HCC) and the mechanisms of USP39 regulating tumor growth. Here, we used bioinformatics methods to reveal that USP39 expression is significantly upregulated in several cancer database. High expression of USP39 is correlated with poor prognosis of HCC patients. Then, we identify the specificity protein 1 (SP1), as a novel subtract of the USP39. We observe that USP39 stabilizes SP1 protein and prolongs its half-life by promoting its deubiquitylation pathway. In addition, our results show USP39 promotes cell proliferation by SP1-depenet manner in vivo and vitro. Knocking-down of USP39 promotes the cell apoptosis and arrest of the cell cycle, whereas SP1 forcefully reversed these effects. Taken together, our results suggest that USP39 participates the deubiquitylation of SP1 protein, providing new pathway for understand the upstream signaling for oncogene SP1.
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Affiliation(s)
- Xiao Dong
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Zixin Liu
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Navy Military Medical University (Second Military Medical University), Shanghai, China
| | - Encheng Zhang
- Department of Urology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Pingzhao Zhang
- Department of Oncology, Changzhou No.2 People's Hospital, the Affiliated Hospital of Nanjing Medical University, Changzhou, China
| | - Yuqi Wang
- Department of Oncology, Changzhou No.2 People's Hospital, the Affiliated Hospital of Nanjing Medical University, Changzhou, China
| | - Junjie Hang
- Department of Oncology, Changzhou No.2 People's Hospital, the Affiliated Hospital of Nanjing Medical University, Changzhou, China.
| | - Qi Li
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China.
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22
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Li X, Yuan J, Song C, Lei Y, Xu J, Zhang G, Wang W, Song G. Deubiquitinase USP39 and E3 ligase TRIM26 balance the level of ZEB1 ubiquitination and thereby determine the progression of hepatocellular carcinoma. Cell Death Differ 2021; 28:2315-2332. [PMID: 33649471 PMCID: PMC8329202 DOI: 10.1038/s41418-021-00754-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
Emerging evidence suggests that USP39 plays an important role in the development of hepatocellular carcinoma (HCC). However, the molecular mechanism by which USP39 promotes HCC progression has not been well defined, especially regarding its putative ubiquitination function. Zinc-finger E-box-binding homeobox 1 (ZEB1) is a crucial inducer of epithelial-to-mesenchymal transition (EMT) to promote tumor proliferation and metastasis, but the regulatory mechanism of ZEB1 stability in HCC remains enigmatic. Here, we reveal that USP39 is highly expressed in human HCC tissues and correlated with poor prognosis. Moreover, USP39 depletion inhibits HCC cell proliferation and metastasis by promoting ZEB1 degradation. Intriguingly, deubiquitinase USP39 has a direct interaction with the E3 ligase TRIM26 identified by co-immunoprecipitation assays and immunofluorescence staining assays. We further demonstrate that TRIM26 is lowly expressed in human HCC tissues and inhibits HCC cell proliferation and migration. TRIM26 promotes the degradation of ZEB1 protein by ubiquitination in HCC. Deubiquitinase USP39 and E3 ligase TRIM26 function in an antagonistic pattern, but not a competitive pattern, and play key roles in controlling ZEB1 stability to determine the HCC progression. In summary, our data reveal a previously unknown mechanism that USP39 and TRIM26 balance the level of ZEB1 ubiquitination and thereby determine HCC cell proliferation and migration. This novel mechanism may provide new approaches to target treatment for inhibiting HCC development by restoring TRIM26 or suppressing USP39 expression in HCC cases with high ZEB1 protein levels.
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Affiliation(s)
- Xiaomei Li
- grid.12955.3a0000 0001 2264 7233Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
| | - Jiahui Yuan
- grid.12955.3a0000 0001 2264 7233Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
| | - Conghua Song
- grid.12955.3a0000 0001 2264 7233Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
| | - Yongbin Lei
- grid.12955.3a0000 0001 2264 7233Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
| | - Jiajia Xu
- grid.12955.3a0000 0001 2264 7233Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
| | - Gongye Zhang
- grid.12955.3a0000 0001 2264 7233Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
| | - Weiwei Wang
- grid.12955.3a0000 0001 2264 7233Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
| | - Gang Song
- grid.12955.3a0000 0001 2264 7233Cancer Research Center, School of Medicine, Xiamen University, Xiamen, China
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23
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Yildirim A, Mozaffari-Jovin S, Wallisch AK, Schäfer J, Ludwig SEJ, Urlaub H, Lührmann R, Wolfrum U. SANS (USH1G) regulates pre-mRNA splicing by mediating the intra-nuclear transfer of tri-snRNP complexes. Nucleic Acids Res 2021; 49:5845-5866. [PMID: 34023904 PMCID: PMC8191790 DOI: 10.1093/nar/gkab386] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/22/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Splicing is catalyzed by the spliceosome, a compositionally dynamic complex assembled stepwise on pre-mRNA. We reveal links between splicing machinery components and the intrinsically disordered ciliopathy protein SANS. Pathogenic mutations in SANS/USH1G lead to Usher syndrome—the most common cause of deaf-blindness. Previously, SANS was shown to function only in the cytosol and primary cilia. Here, we have uncovered molecular links between SANS and pre-mRNA splicing catalyzed by the spliceosome in the nucleus. We show that SANS is found in Cajal bodies and nuclear speckles, where it interacts with components of spliceosomal sub-complexes such as SF3B1 and the large splicing cofactor SON but also with PRPFs and snRNAs related to the tri-snRNP complex. SANS is required for the transfer of tri-snRNPs between Cajal bodies and nuclear speckles for spliceosome assembly and may also participate in snRNP recycling back to Cajal bodies. SANS depletion alters the kinetics of spliceosome assembly, leading to accumulation of complex A. SANS deficiency and USH1G pathogenic mutations affects splicing of genes related to cell proliferation and human Usher syndrome. Thus, we provide the first evidence that splicing dysregulation may participate in the pathophysiology of Usher syndrome.
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Affiliation(s)
- Adem Yildirim
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Sina Mozaffari-Jovin
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Ann-Kathrin Wallisch
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Jessica Schäfer
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
| | - Sebastian E J Ludwig
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany.,Bioanalytics, Department of Clinical Chemistry, University Medical Center Goettingen, Germany
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany
| | - Uwe Wolfrum
- Molecular Cell Biology, Institute of Molecular Physiology, Johannes Gutenberg-University of Mainz, Germany
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24
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TSSC4 is a component of U5 snRNP that promotes tri-snRNP formation. Nat Commun 2021; 12:3646. [PMID: 34131137 PMCID: PMC8206348 DOI: 10.1038/s41467-021-23934-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/19/2021] [Indexed: 11/29/2022] Open
Abstract
U5 snRNP is a complex particle essential for RNA splicing. U5 snRNPs undergo intricate biogenesis that ensures that only a fully mature particle assembles into a splicing competent U4/U6•U5 tri-snRNP and enters the splicing reaction. During splicing, U5 snRNP is substantially rearranged and leaves as a U5/PRPF19 post-splicing particle, which requires re-generation before the next round of splicing. Here, we show that a previously uncharacterized protein TSSC4 is a component of U5 snRNP that promotes tri-snRNP formation. We provide evidence that TSSC4 associates with U5 snRNP chaperones, U5 snRNP and the U5/PRPF19 particle. Specifically, TSSC4 interacts with U5-specific proteins PRPF8, EFTUD2 and SNRNP200. We also identified TSSC4 domains critical for the interaction with U5 snRNP and the PRPF19 complex, as well as for TSSC4 function in tri-snRNP assembly. TSSC4 emerges as a specific chaperone that acts in U5 snRNP de novo biogenesis as well as post-splicing recycling. The correct assembly and recycling of the multicomponent spliceosome remains largely elusive. Here, the authors show that a previously uncharacterized protein TSSC4 associates with de novo formed spliceosomal U5 snRNP as well as with a post-splicing U5-PRPF19 particle, and that TSSC4 is important for assembly of the splicing competent tri-snRNP.
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25
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Zhao Y, Geng H, Liu G, Ji Q, Cheng X, Li X, Liu W, Thorne RF, Zhang R, Liu X. The Deubiquitinase USP39 Promotes ESCC Tumorigenesis Through Pre-mRNA Splicing of the mTORC2 Component Rictor. Front Oncol 2021; 11:667495. [PMID: 34123832 PMCID: PMC8189149 DOI: 10.3389/fonc.2021.667495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 05/05/2021] [Indexed: 12/24/2022] Open
Abstract
Spliceosomes are large RNA-protein molecular complexes which mediate splicing of pre-mRNA in eukaryotic cells. Their function is frequently altered in cancer, providing opportunities for novel therapeutic approaches. The ubiquitin specific protease 39 (USP39) is a highly conserved deubiquitylation family member that plays an essential role in pre-mRNA splicing where it serves to assemble the mature spliceosome complex. Previous studies have reported that USP39 acts in an oncogenic manner where it contributes to cancer progression and predicts poor prognosis in various human tumor types. Here we report that USP39 is differentially upregulated in human esophageal squamous cell carcinoma (ESCC) and its expression is significantly associated with clinicopathological characteristics including differentiation status and TNM stage. We found the USP39 upregulation was maintained in ESCC cell lines where it functioned to promote cancer cell growth in vitro and in xenografts. RNA-seq analyses identified that mTOR pathway activation was affected by shRNA-mediated silencing of USP39. Subsequent biochemical analyses demonstrated that USP39 regulates the activity of mTORC2 by selectively enhancing the splicing and maturation of Rictor mRNA, although not other key mTORC components. Together, our report proposes USP39 as a biomarker and oncogenic factor in ESCC, with a potential for targeting the USP39/mTOR2/Rictor axis as a therapeutic strategy. Furthermore, our study adds ESCC to the list of cancers where USP39 contributes to tumorigenesis and progression.
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Affiliation(s)
- Yuan Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Huiwu Geng
- Biology Department, School of Life Sciences, Anhui Medical University, Hefei, China
| | - Gang Liu
- Biology Department, School of Life Sciences, Anhui Medical University, Hefei, China
| | - Qiang Ji
- Biology Department, School of Life Sciences, Anhui Medical University, Hefei, China.,Translational Research Institute of Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Molecular Pathology Centre, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiaomin Cheng
- Biology Department, School of Life Sciences, Anhui Medical University, Hefei, China
| | - Xinying Li
- Biology Department, School of Life Sciences, Anhui Medical University, Hefei, China
| | - Wei Liu
- Department of Thoracic Surgery, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Rick F Thorne
- Translational Research Institute of Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Molecular Pathology Centre, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Renquan Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, Anhui Medical University, Hefei, China
| | - Xiaoying Liu
- Biology Department, School of Life Sciences, Anhui Medical University, Hefei, China.,Translational Research Institute of Henan Provincial People's Hospital and People's Hospital of Zhengzhou University, Molecular Pathology Centre, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
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26
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Cerrito MG, Grassilli E. Identifying Novel Actionable Targets in Colon Cancer. Biomedicines 2021; 9:biomedicines9050579. [PMID: 34065438 PMCID: PMC8160963 DOI: 10.3390/biomedicines9050579] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/10/2021] [Accepted: 05/14/2021] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer is the fourth cause of death from cancer worldwide, mainly due to the high incidence of drug-resistance toward classic chemotherapeutic and newly targeted drugs. In the last decade or so, the development of novel high-throughput approaches, both genome-wide and chemical, allowed the identification of novel actionable targets and the development of the relative specific inhibitors to be used either to re-sensitize drug-resistant tumors (in combination with chemotherapy) or to be synthetic lethal for tumors with specific oncogenic mutations. Finally, high-throughput screening using FDA-approved libraries of “known” drugs uncovered new therapeutic applications of drugs (used alone or in combination) that have been in the clinic for decades for treating non-cancerous diseases (re-positioning or re-purposing approach). Thus, several novel actionable targets have been identified and some of them are already being tested in clinical trials, indicating that high-throughput approaches, especially those involving drug re-positioning, may lead in a near future to significant improvement of the therapy for colon cancer patients, especially in the context of a personalized approach, i.e., in defined subgroups of patients whose tumors carry certain mutations.
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27
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Xiao Y, Ma W, Hu W, Di Q, Zhao X, Ma X, Chen X, Sun P, Wu H, Wu Z, Chen W. Ubiquitin-specific peptidase 39 promotes human glioma cells migration and invasion by facilitating ADAM9 mRNA maturation. Mol Oncol 2021; 16:388-404. [PMID: 33811456 PMCID: PMC8763660 DOI: 10.1002/1878-0261.12958] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/03/2021] [Accepted: 03/31/2021] [Indexed: 12/16/2022] Open
Abstract
Glioma cells are characterized by high migration and invasion ability; however, the molecular mechanism behind both processes still remains to be investigated. Several studies have demonstrated that ubiquitin‐specific protease 39 (USP39) plays an oncogenic role in various cancer types. Here, we investigated the expression and function of USP39 in patients with glioma. Oncomine database analysis revealed that high USP39 expression was significantly correlated with poor overall survival in patients with glioma. Knockdown of USP39 in U251 and U87 cell lines significantly inhibited their migration and invasion in vitro. Gene expression profiling of glioma cells transduced with short hairpin RNA (shRNA) against USP39 revealed that disintegrin and metalloproteinase domain‐containing protein 9 (ADAM9), a molecule previously related to tumor cell migration and invasion, was significantly downregulated. Furthermore, USP39 induced ADAM9 messenger RNA (mRNA) maturation and decreased the expression of integrin β1. Additionally, overexpression of ADAM9 inhibited the migration and invasion of glioma cells caused by USP39 depletion in vitro. USP39 promoted the invasion of glioma cells in vivo and reduced the overall survival of the mice. Altogether, our data show that USP39 induces mRNA maturation and elevates the expression of ADAM9 in glioma cells and may thus be considered potential target for treating patients with glioma.
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Affiliation(s)
- Yue Xiao
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
| | - Wenjing Ma
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
| | - Weiwei Hu
- Department of Neurosurgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianqian Di
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
| | - Xibao Zhao
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
| | - Xingyu Ma
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
| | - Xinyi Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
| | - Ping Sun
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
| | - Han Wu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
| | - Zherui Wu
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
| | - Weilin Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Immunology, School of Medicine, Shenzhen University, China
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28
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Wang S, Wang Z, Li J, Qin J, Song J, Li Y, Zhao L, Zhang X, Guo H, Shao C, Kong B, Liu Z. Splicing factor USP39 promotes ovarian cancer malignancy through maintaining efficient splicing of oncogenic HMGA2. Cell Death Dis 2021; 12:294. [PMID: 33731694 PMCID: PMC7969951 DOI: 10.1038/s41419-021-03581-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/16/2022]
Abstract
Aberrant expression of splicing factors was found to promote tumorigenesis and the development of human malignant tumors. Nevertheless, the underlying mechanisms and functional relevance remain elusive. We here show that USP39, a component of the spliceosome, is frequently overexpressed in high-grade serous ovarian carcinoma (HGSOC) and that an elevated level of USP39 is associated with a poor prognosis. USP39 promotes proliferation/invasion in vitro and tumor growth in vivo. Importantly, USP39 was transcriptionally activated by the oncogene protein c-MYC in ovarian cancer cells. We further demonstrated that USP39 colocalizes with spliceosome components in nuclear speckles. Transcriptomic analysis revealed that USP39 deletion led to globally impaired splicing that is characterized by skipped exons and overrepresentation of introns and intergenic regions. Furthermore, RNA immunoprecipitation sequencing showed that USP39 preferentially binds to exon-intron regions near 5' and 3' splicing sites. In particular, USP39 facilitates efficient splicing of HMGA2 and thereby increases the malignancy of ovarian cancer cells. Taken together, our results indicate that USP39 functions as an oncogenic splicing factor in ovarian cancer and represents a potential target for ovarian cancer therapy.
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Affiliation(s)
- Shourong Wang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong Province, China.,Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Zixiang Wang
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong Province, China.,Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jieyin Li
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Junchao Qin
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Jianping Song
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Yingwei Li
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong Province, China
| | - Ling Zhao
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xiyu Zhang
- Molecular Medicine and Genetics, Cheeloo College of Medicine, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong, 250012, China
| | - Haiyang Guo
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, 250012, China
| | - Changshun Shao
- Institutes for Translational Medicine, State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Beihua Kong
- Department of Obstetrics and Gynecology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, 107 Wenhua Xi Road, Jinan, 250012, Shandong Province, China.
| | - Zhaojian Liu
- Key Laboratory of Experimental Teratology, Ministry of Education, Department of Cell Biology, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China.
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29
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Henson HE, Taylor MR. A sart1 Zebrafish Mutant Results in Developmental Defects in the Central Nervous System. Cells 2020; 9:cells9112340. [PMID: 33105605 PMCID: PMC7690441 DOI: 10.3390/cells9112340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 11/16/2022] Open
Abstract
The spliceosome consists of accessory proteins and small nuclear ribonucleoproteins (snRNPs) that remove introns from RNA. As splicing defects are associated with degenerative conditions, a better understanding of spliceosome formation and function is essential. We provide insight into the role of a spliceosome protein U4/U6.U5 tri-snRNP-associated protein 1, or Squamous cell carcinoma antigen recognized by T-cells (Sart1). Sart1 recruits the U4.U6/U5 tri-snRNP complex to nuclear RNA. The complex then associates with U1 and U2 snRNPs to form the spliceosome. A forward genetic screen identifying defects in choroid plexus development and whole-exome sequencing (WES) identified a point mutation in exon 12 of sart1 in Danio rerio (zebrafish). This mutation caused an up-regulation of sart1. Using RNA-Seq analysis, we identified additional upregulated genes, including those involved in apoptosis. We also observed increased activated caspase 3 in the brain and eye and down-regulation of vision-related genes. Although splicing occurs in numerous cells types, sart1 expression in zebrafish was restricted to the brain. By identifying sart1 expression in the brain and cell death within the central nervous system (CNS), we provide additional insights into the role of sart1 in specific tissues. We also characterized sart1's involvement in cell death and vision-related pathways.
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Affiliation(s)
- Hannah E. Henson
- Chemical Biology and Therapeutics Department, St. Jude Children’s Research Hospital, Memphis, TN 38015, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Correspondence: ; Tel.: +1-731-661-5520
| | - Michael R. Taylor
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA;
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30
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Zhang KL, Feng Z, Yang JF, Yang F, Yuan T, Zhang D, Hao GF, Fang YM, Zhang J, Wu C, Chen MX, Zhu FY. Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses. BMC PLANT BIOLOGY 2020; 20:379. [PMID: 32811430 PMCID: PMC7433366 DOI: 10.1186/s12870-020-02570-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/22/2020] [Indexed: 06/01/2023]
Abstract
BACKGROUND Among eukaryotic organisms, alternative splicing is an important process that can generate multiple transcripts from one same precursor messenger RNA, which greatly increase transcriptome and proteome diversity. This process is carried out by a super-protein complex defined as the spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting the 5' and 3' splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoa and mammals. However, its counterpart in plants has been seldomly reported. RESULTS To this end, we conducted a systematic characterization of the SF1 gene family across plant lineages. In this work, a total of 92 sequences from 59 plant species were identified. Phylogenetic relationships of these sequences were constructed, and subsequent bioinformatic analysis suggested that this family likely originated from an ancient gene transposition duplication event. Most plant species were shown to maintain a single copy of this gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this gene family in comparison to their animal and yeast counterparts, indicating that their potential role was preserved in the plant lineage. CONCLUSION Our analysis presents general features of the gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.
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Affiliation(s)
- Kai-Lu Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Zhen Feng
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Jing-Fang Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079 China
| | - Feng Yang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Tian Yuan
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Di Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, 430079 China
| | - Yan-Ming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Jianhua Zhang
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Caie Wu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
| | - Mo-Xian Chen
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 PR China
| | - Fu-Yuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037 Jiangsu Province China
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31
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Dong L, Yu L, Li H, Shi L, Luo Z, Zhao H, Liu Z, Yin G, Yan X, Lin Z. An NAD +-Dependent Deacetylase SIRT7 Promotes HCC Development Through Deacetylation of USP39. iScience 2020; 23:101351. [PMID: 32711345 PMCID: PMC7387830 DOI: 10.1016/j.isci.2020.101351] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 05/14/2020] [Accepted: 06/27/2020] [Indexed: 12/21/2022] Open
Abstract
Ubiquitin specific protease 39 (USP39), an ortholog of Sad1p in yeast, is essential for spliceosome assembly during pre-mRNA splicing in human. Although it is known that USP39 is upregulated and plays an oncogenic role in hepatocellular carcinoma (HCC), the underlying mechanism remains unknown. The results of this study demonstrated that USP39 can be acetylated by the histone acetyltransferase MYST1, which is required for its proteasome-mediated degradation by Von Hippel-Lindau protein. In HCC cells, USP39 interacts with and is deacetylated by the lysine deacetylase sirtuin 7 (SIRT7). Notably, the deacetylation of USP39 by SIRT7 promotes its stability and thereby accelerates HCC cell proliferation and tumorigenesis in vitro and in vivo. Our data demonstrated a novel mechanism by which SIRT7 modulates the deacetylation of USP39 to promote HCC development, thus providing an effective anti-tumor therapeutic strategy for HCC. SIRT7 modulates the deacetylation of USP39 MYST1 promotes the acetyl binding of USP39 USP39 acetylation induces its instability
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Affiliation(s)
- Ling Dong
- School of Life Sciences, Chongqing University, Chongqing 401331, P.R. China
| | - Le Yu
- School of Life Sciences, Chongqing University, Chongqing 401331, P.R. China
| | - Hui Li
- School of Life Sciences, Chongqing University, Chongqing 401331, P.R. China
| | - Lei Shi
- School of Life Sciences, Chongqing University, Chongqing 401331, P.R. China
| | - Zhong Luo
- School of Life Sciences, Chongqing University, Chongqing 401331, P.R. China
| | - Huakan Zhao
- Institute of Cancer, Xinqiao Hospital, Third Military Medical University, Chongqing 400038, P.R. China
| | - Zhaojian Liu
- Department of Cell Biology, Shandong University School of Medicine, Jinan 250012, P.R. China
| | - Guobing Yin
- Department of Breast, Thyroid, Pancreatic Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, P.R. China
| | - Xiaohua Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang 330006, Jiangxi, P.R. China.
| | - Zhenghong Lin
- School of Life Sciences, Chongqing University, Chongqing 401331, P.R. China.
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32
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Tian Y, Wen H, Qi X, Zhang X, Sun Y, Li J, He F, Zhang M, Zhang K, Yang W, Huang Z, Ren Y, Li Y. Alternative splicing (AS) mechanism plays important roles in response to different salinity environments in spotted sea bass. Int J Biol Macromol 2020; 155:50-60. [DOI: 10.1016/j.ijbiomac.2020.03.178] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 01/12/2023]
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33
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Yan C, Yuan J, Xu J, Zhang G, Li X, Zhang B, Hu T, Huang X, Mao Y, Song G. Ubiquitin-specific peptidase 39 regulates the process of proliferation and migration of human ovarian cancer via p53/p21 pathway and EMT. Med Oncol 2019; 36:95. [PMID: 31637536 DOI: 10.1007/s12032-019-1308-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/27/2019] [Indexed: 12/15/2022]
Abstract
Ovarian cancer is one of the most lethal gynecological cancers; owning to its late detection and chemoresistance, understanding the pathogenesis of this malignant tumor is much critical. Previous studies have reported that ubiquitin-specific peptidase 39 (USP39) is generally overexpressed in a variety of cancers, including hepatocellular carcinoma, gastric cancer and so forth. Furthermore, USP39 is proved to be associated with the proliferation of malignant tumors. However, the function and mechanism of USP39 in ovarian cancer have not been elucidated. In the present study, we observed that USP39 was frequently overexpressed in human ovarian cancer and was highly correlated with TNM stage. Suppression of USP39 markedly inhibited the growth and migration of ovarian cancer cell lines HO-8910 and SKOV3 and induced cell cycle G2/M arrest. Moreover, knockdown of USP39 inhibited ovarian tumor growth in a xenograft model. In addition, our findings indicated that cell cycle arrest induced by USP39 knockdown might be involved in p53/p21 signaling pathway. Furthermore, we found that the depletion of USP39 inhibited the migration of ovarian cancer cells via blocking epithelial-mesenchymal transition. Taken together, these results suggest that USP39 may play vital roles in the genesis and progression and may serve as a potential biomarker for diagnosis and therapeutic target of ovarian cancer.
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Affiliation(s)
- Congcong Yan
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Jiahui Yuan
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Jiajia Xu
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Gongye Zhang
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Xiaomei Li
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Bing Zhang
- Department of Basic Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Tianhui Hu
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Xiaohua Huang
- Department of Basic Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China
| | - Yubin Mao
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, 361102, China. .,Department of Basic Medicine, School of Medicine, Xiamen University, Xiamen, 361102, China.
| | - Gang Song
- Cancer Research Center, School of Medicine, Xiamen University, Xiamen, 361102, China.
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34
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Alam MM, Sanchez-Azqueta A, Janha O, Flannery EL, Mahindra A, Mapesa K, Char AB, Sriranganadane D, Brancucci NMB, Antonova-Koch Y, Crouch K, Simwela NV, Millar SB, Akinwale J, Mitcheson D, Solyakov L, Dudek K, Jones C, Zapatero C, Doerig C, Nwakanma DC, Vázquez MJ, Colmenarejo G, Lafuente-Monasterio MJ, Leon ML, Godoi PHC, Elkins JM, Waters AP, Jamieson AG, Álvaro EF, Ranford-Cartwright LC, Marti M, Winzeler EA, Gamo FJ, Tobin AB. Validation of the protein kinase PfCLK3 as a multistage cross-species malarial drug target. Science 2019; 365:365/6456/eaau1682. [PMID: 31467193 DOI: 10.1126/science.aau1682] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 03/15/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022]
Abstract
The requirement for next-generation antimalarials to be both curative and transmission-blocking necessitates the identification of previously undiscovered druggable molecular pathways. We identified a selective inhibitor of the Plasmodium falciparum protein kinase PfCLK3, which we used in combination with chemogenetics to validate PfCLK3 as a drug target acting at multiple parasite life stages. Consistent with a role for PfCLK3 in RNA splicing, inhibition resulted in the down-regulation of more than 400 essential parasite genes. Inhibition of PfCLK3 mediated rapid killing of asexual liver- and blood-stage P. falciparum and blockade of gametocyte development, thereby preventing transmission, and also showed parasiticidal activity against P. berghei and P. knowlesi Hence, our data establish PfCLK3 as a target for drugs, with the potential to offer a cure-to be prophylactic and transmission blocking in malaria.
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Affiliation(s)
- Mahmood M Alam
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Ana Sanchez-Azqueta
- Centre for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Omar Janha
- Centre for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Erika L Flannery
- Novartis Institute for Biomedical Research, Emeryville, CA 94608, USA
| | - Amit Mahindra
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Kopano Mapesa
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, UK
| | - Aditya B Char
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - Dev Sriranganadane
- Structural Genomics Consortium, Universidade Estadual de Campinas, Campinas, São Paulo 13083-886, Brazil
| | - Nicolas M B Brancucci
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland
| | - Yevgeniya Antonova-Koch
- Skaggs School of Pharmaceutical Sciences, UC Health Sciences Center for Immunology, Infection and Inflammation, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Kathryn Crouch
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Nelson Victor Simwela
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Scott B Millar
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Jude Akinwale
- Medical Research Council Toxicology Unit, University of Leicester, Leicester LE1 9HN, UK
| | - Deborah Mitcheson
- Department of Molecular Cell Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Lev Solyakov
- Medical Research Council Toxicology Unit, University of Leicester, Leicester LE1 9HN, UK
| | - Kate Dudek
- Medical Research Council Toxicology Unit, University of Leicester, Leicester LE1 9HN, UK
| | - Carolyn Jones
- Medical Research Council Toxicology Unit, University of Leicester, Leicester LE1 9HN, UK
| | - Cleofé Zapatero
- Diseases of the Developing World, GlaxoSmithKline, 28760 Tres Cantos, Madrid, Spain
| | - Christian Doerig
- Biomedical Science Cluster, School of Health and Biomedical Sciences, Royal Melbourne Institute of Technology, Melbourne, VIC 3000, Australia
| | | | - Maria Jesús Vázquez
- Diseases of the Developing World, GlaxoSmithKline, 28760 Tres Cantos, Madrid, Spain
| | - Gonzalo Colmenarejo
- Biostatistics and Bioinformatics Unit, IMDEA Food Institute, 28049 Madrid, Spain
| | | | - Maria Luisa Leon
- Diseases of the Developing World, GlaxoSmithKline, 28760 Tres Cantos, Madrid, Spain
| | - Paulo H C Godoi
- Structural Genomics Consortium, Universidade Estadual de Campinas, Campinas, São Paulo 13083-886, Brazil
| | - Jon M Elkins
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Andrew P Waters
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | | - Lisa C Ranford-Cartwright
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - Matthias Marti
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8QQ, UK
| | - Elizabeth A Winzeler
- Skaggs School of Pharmaceutical Sciences, UC Health Sciences Center for Immunology, Infection and Inflammation, University of California, San Diego, School of Medicine, La Jolla, CA 92093, USA
| | | | - Andrew B Tobin
- Centre for Translational Pharmacology, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, UK.
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35
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Keiper S, Papasaikas P, Will CL, Valcárcel J, Girard C, Lührmann R. Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns. Nat Commun 2019; 10:3639. [PMID: 31409787 PMCID: PMC6692369 DOI: 10.1038/s41467-019-11293-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 07/01/2019] [Indexed: 12/02/2022] Open
Abstract
Human pre-catalytic spliceosomes contain several proteins that associate transiently just prior to spliceosome activation and are absent in yeast, suggesting that this critical step is more complex in higher eukaryotes. We demonstrate via RNAi coupled with RNA-Seq that two of these human-specific proteins, Smu1 and RED, function both as alternative splicing regulators and as general splicing factors and are required predominantly for efficient splicing of short introns. In vitro splicing assays reveal that Smu1 and RED promote spliceosome activation, and are essential for this step when the distance between the pre-mRNA’s 5′ splice site (SS) and branch site (BS) is sufficiently short. This Smu1-RED requirement can be bypassed when the 5′ and 3′ regions of short introns are physically separated. Our observations suggest that Smu1 and RED relieve physical constraints arising from a short 5′SS-BS distance, thereby enabling spliceosomes to overcome structural challenges associated with the splicing of short introns. Human spliceosome components Smu1 and RED regulate alternative splicing. Here the authors show that Smu1 and RED are also required for constitutive splicing of short introns.
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Affiliation(s)
- Sandra Keiper
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Panagiotis Papasaikas
- Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain.,Friedrich Miescher Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058, Basel, Switzerland.,Swiss Institute of Bioinformatics, 4058, Basel, Switzerland
| | - Cindy L Will
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Juan Valcárcel
- Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology and Universitat Pompeu Fabra, Dr. Aiguader 88, 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys, 08010, Barcelona, Spain
| | - Cyrille Girard
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Reinhard Lührmann
- Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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36
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Jia X, Sun C. Structural dynamics of the N-terminal domain and the Switch loop of Prp8 during spliceosome assembly and activation. Nucleic Acids Res 2019; 46:3833-3840. [PMID: 29635373 PMCID: PMC5934631 DOI: 10.1093/nar/gky242] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/03/2018] [Indexed: 11/13/2022] Open
Abstract
Precursor message RNA (pre-mRNA) splicing is executed by the spliceosome, a large ribonucleoprotein (RNP) machinery that is comparable to the ribosome. Driven by the rapid progress of cryo-electron microscopy (cryo-EM) technology, high resolution structures of the spliceosome in its different splicing stages have proliferated over the past three years, which has greatly facilitated the mechanistic understanding of pre-mRNA splicing. As the largest and most conserved protein in the spliceosome, Prp8 plays a pivotal role within this protein-directed ribozyme. Structure determination of different spliceosomal complexes has revealed intimate and dynamic interactions between Prp8 and catalytic RNAs as well as with other protein factors during splicing. Here we review the structural dynamics of two elements of Prp8, the N-terminal domain (N-domain) and the Switch loop, and delineate the dynamic organisation and underlying functional significance of these two elements during spliceosome assembly and activation. Further biochemical and structural dissections of idiographic splicing stages are much needed for a complete understanding of the spliceosome and pre-mRNA splicing.
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Affiliation(s)
- Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, China
| | - Chengfu Sun
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, China
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37
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Li X, Fan Z, Yan M, Qu J, Xu JR, Jin Q. Spontaneous mutations in FgSAD1 suppress the growth defect of the Fgprp4 mutant by affecting tri-snRNP stability and its docking in Fusarium graminearum. Environ Microbiol 2019; 21:4488-4503. [PMID: 31291045 DOI: 10.1111/1462-2920.14736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/27/2022]
Abstract
FgPrp4, the only kinase in the spliceosome, is not essential for viability, but is important for splicing efficiency in Fusarium graminearum. The Fgprp4 deletion mutant had severe growth defects but often produced spontaneous suppressors with faster growth rate. To better understand the suppression mechanism, we identified and characterized spontaneous mutations in the tri-snRNP-specific protein, FgSad1, which suppressed the growth defects of Fgprp4. The L512P mutation was verified for its suppressive effects on Fgprp4, suggesting that mutations in FgSad1 may have effects involving FgPrp4 phosphorylation on FgSad1. Phosphoproteomics analysis showed that FgSad1 may not be the direct substrate of FgPrp4 kinase. Furthermore, truncation analysis showed that the N-terminal, extra RS-rich region of FgSad1 is critical for its function and is post-translationally modified. The P258S or S269P mutations in FgSad1 increased its interactions with the U5 protein FgPrp8 and the U4/U6 protein FgPrp31, which may result in tri-snRNP stabilization. Additionally, the D76N mutation increased the association of FgSad1 with the U2 snRNP. These data indicate that suppressor mutations in FgSad1 increase the stability of the tri-snRNP and/or the affinity of FgSad1 with U2 snRNP and therefore potentially facilitate the docking of tri-snRNP into the spliceosome.
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Affiliation(s)
- Xiaoping Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhili Fan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Ming Yan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jia Qu
- Microbial Resource Center, Microbiology Institute of Shaanxi, Xi'an, Shaanxi, 710043, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Qiaojun Jin
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
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Ding K, Ji J, Zhang X, Huang B, Chen A, Zhang D, Li X, Wang X, Wang J. RNA splicing factor USP39 promotes glioma progression by inducing TAZ mRNA maturation. Oncogene 2019; 38:6414-6428. [PMID: 31332287 PMCID: PMC6756117 DOI: 10.1038/s41388-019-0888-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 06/06/2019] [Accepted: 07/03/2019] [Indexed: 01/01/2023]
Abstract
Increasing evidence demonstrates that ubiquitin specific protease 39 (USP39) plays an oncogenic role in various human tumors. Here, using expression analysis of the publicly available Oncomine database, clinical glioma patient samples, and glioma cells, we found that USP39 was overexpressed in human gliomas. Knockdown of USP39 in glioma cells demonstrated that the protein promoted cell growth, invasion and migration in vitro and in a tumor model in nude mice. To identify mediators of USP39 growth-promoting properties, we used luciferase reporter constructs under transcriptional control of various promoters specific to seven canonical cancer-associated pathways. Luciferase activity from a synthetic TEAD-dependent YAP/TAZ-responsive reporter, as a direct readout of the Hippo signaling pathway, was decreased by 92% in cells with USP39 knockdown, whereas the luciferase activities from the other six cancer pathways, including MAPK/ERK, MAPK/JNK, NFκB, Notch, TGFβ, and Wnt, remained unchanged. TAZ protein expression however was decreased independent of canonical Hippo signaling. Immunohistochemistry revealed a positive correlation between USP39 and TAZ proteins in orthotopic xenografts derived from modified glioma cells expressing USP39 shRNAs and primary human glioma samples (p < 0.05). Finally, loss of USP39 decreased TAZ pre-mRNA splicing efficiency in glioma cells in vitro, which led to reduced levels of TAZ protein. In summary, USP39 has oncogenic properties that increase TAZ protein levels by inducing maturation of its mRNA. USP39 therefore provides a novel therapeutic target for the treatment of human glioma.
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Affiliation(s)
- Kaikai Ding
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, 250012, Jinan, PR China.,Shandong Key Laboratory of Brain Function Remodeling, 250012, Jinan, PR China
| | - Jianxiong Ji
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, 250012, Jinan, PR China.,Shandong Key Laboratory of Brain Function Remodeling, 250012, Jinan, PR China
| | - Xin Zhang
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, 250012, Jinan, PR China.,Shandong Key Laboratory of Brain Function Remodeling, 250012, Jinan, PR China
| | - Bin Huang
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, 250012, Jinan, PR China.,Shandong Key Laboratory of Brain Function Remodeling, 250012, Jinan, PR China
| | - Anjing Chen
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, 250012, Jinan, PR China.,Shandong Key Laboratory of Brain Function Remodeling, 250012, Jinan, PR China
| | - Di Zhang
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, 250012, Jinan, PR China.,Shandong Key Laboratory of Brain Function Remodeling, 250012, Jinan, PR China
| | - Xingang Li
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, 250012, Jinan, PR China.,Shandong Key Laboratory of Brain Function Remodeling, 250012, Jinan, PR China
| | - Xinyu Wang
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, 250012, Jinan, PR China. .,Shandong Key Laboratory of Brain Function Remodeling, 250012, Jinan, PR China.
| | - Jian Wang
- Department of Neurosurgery, Qilu Hospital of Shandong University and Institute of Brain and Brain-Inspired Science, Shandong University, 250012, Jinan, PR China. .,Shandong Key Laboratory of Brain Function Remodeling, 250012, Jinan, PR China. .,Department of Biomedicine, University of Bergen, 5009, Bergen, Norway.
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An Allosteric Network for Spliceosome Activation Revealed by High-Throughput Suppressor Analysis in Saccharomyces cerevisiae. Genetics 2019; 212:111-124. [PMID: 30898770 DOI: 10.1534/genetics.119.301922] [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: 01/08/2019] [Accepted: 03/15/2019] [Indexed: 12/30/2022] Open
Abstract
Selection of suppressor mutations that correct growth defects caused by substitutions in an RNA or protein can reveal functionally important molecular structures and interactions in living cells. This approach is particularly useful for the study of complex biological pathways involving many macromolecules, such as premessenger RNA (pre-mRNA) splicing. When a sufficiently large number of suppressor mutations is obtained and structural information is available, it is possible to generate detailed models of molecular function. However, the laborious and expensive task of identifying suppressor mutations in whole-genome selections limits the utility of this approach. Here I show that a custom targeted sequencing panel can greatly accelerate the identification of suppressor mutations in the Saccharomyces cerevisiae genome. Using a panel that targets 112 genes encoding pre-mRNA splicing factors, I identified 27 unique mutations in six protein-coding genes that each overcome the cold-sensitive block to spliceosome activation caused by a substitution in U4 small nuclear RNA. When mapped to existing structures of spliceosomal complexes, the identified suppressors implicate specific molecular contacts between the proteins Brr2, Prp6, Prp8, Prp31, Sad1, and Snu114 as functionally important in an early step of catalytic activation of the spliceosome. This approach shows great promise for elucidating the allosteric cascade of molecular interactions that direct accurate and efficient pre-mRNA splicing and should be broadly useful for understanding the dynamics of other complex biological assemblies or pathways.
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Structural and Functional Insights into Human Nuclear Cyclophilins. Biomolecules 2018; 8:biom8040161. [PMID: 30518120 PMCID: PMC6315705 DOI: 10.3390/biom8040161] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 02/05/2023] Open
Abstract
The peptidyl prolyl isomerases (PPI) of the cyclophilin type are distributed throughout human cells, including eight found solely in the nucleus. Nuclear cyclophilins are involved in complexes that regulate chromatin modification, transcription, and pre-mRNA splicing. This review collects what is known about the eight human nuclear cyclophilins: peptidyl prolyl isomerase H (PPIH), peptidyl prolyl isomerase E (PPIE), peptidyl prolyl isomerase-like 1 (PPIL1), peptidyl prolyl isomerase-like 2 (PPIL2), peptidyl prolyl isomerase-like 3 (PPIL3), peptidyl prolyl isomerase G (PPIG), spliceosome-associated protein CWC27 homolog (CWC27), and peptidyl prolyl isomerase domain and WD repeat-containing protein 1 (PPWD1). Each “spliceophilin” is evaluated in relation to the spliceosomal complex in which it has been studied, and current work studying the biological roles of these cyclophilins in the nucleus are discussed. The eight human splicing complexes available in the Protein Data Bank (PDB) are analyzed from the viewpoint of the human spliceophilins. Future directions in structural and cellular biology, and the importance of developing spliceophilin-specific inhibitors, are considered.
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Zahler AM, Rogel LE, Glover ML, Yitiz S, Ragle JM, Katzman S. SNRP-27, the C. elegans homolog of the tri-snRNP 27K protein, has a role in 5' splice site positioning in the spliceosome. RNA (NEW YORK, N.Y.) 2018; 24:1314-1325. [PMID: 30006499 PMCID: PMC6140464 DOI: 10.1261/rna.066878.118] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/12/2018] [Indexed: 05/04/2023]
Abstract
The tri-snRNP 27K protein is a component of the human U4/U6-U5 tri-snRNP and contains an N-terminal phosphorylated RS domain. In a forward genetic screen in C. elegans, we previously identified a dominant mutation, M141T, in the highly-conserved C-terminal region of this protein. The mutant allele promotes changes in cryptic 5' splice site choice. To better understand the function of this poorly characterized splicing factor, we performed high-throughput mRNA sequencing analysis on worms containing this dominant mutation. Comparison of alternative splice site usage between the mutant and wild-type strains led to the identification of 26 native genes whose splicing changes in the presence of the snrp-27 mutation. The changes in splicing are specific to alternative 5' splice sites. Analysis of new alleles suggests that snrp-27 is an essential gene for worm viability. We performed a novel directed-mutation experiment in which we used the CRISPR-cas9 system to randomly generate mutations specifically at M141 of SNRP-27. We identified eight amino acid substitutions at this position that are viable, and three that are homozygous lethal. All viable substitutions at M141 led to varying degrees of changes in alternative 5' splicing of native targets. We hypothesize a role for this SR-related factor in maintaining the position of the 5' splice site as U1snRNA trades interactions at the 5' end of the intron with U6snRNA and PRP8 as the catalytic site is assembled.
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Affiliation(s)
- Alan M Zahler
- Department of MCD Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Lucero E Rogel
- Department of MCD Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Marissa L Glover
- Department of MCD Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Samira Yitiz
- Department of MCD Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - J Matthew Ragle
- Department of MCD Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Sol Katzman
- Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
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Sun M, Zhang Y, Wang Q, Wu C, Jiang C, Xu JR. The tri-snRNP specific protein FgSnu66 is functionally related to FgPrp4 kinase in Fusarium graminearum. Mol Microbiol 2018; 109:494-508. [PMID: 29923654 DOI: 10.1111/mmi.14005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2018] [Indexed: 11/28/2022]
Abstract
Deletion of Prp4, the only kinase among spliceosome components, is not lethal in Fusarium graminearum but Fgprp4 mutants have severe growth defects and produced spontaneous suppressors. To identify novel suppressor mutations of Fgprp4, we sequenced the genome of suppressor S37 that was normal in growth but only partially recovered for intron splicing and identified a tandem duplication of 9-aa in the tri-snRNP component FgSNU66. Among the 19 additional suppressor strains found to have mutations in FgSNU66 (out of 260 screened), five had the same 9-aa duplication event with S37 and another five had the R477H/C mutation. The rest had nonsense or G-to-D mutations in the C-terminal 27-aa (CT27) region of FgSnu66, which is absent in its yeast ortholog. Truncation of this C-terminal region reduced the interaction of FgSnu66 with FgHub1 but increased its interaction with FgPrp8 and FgPrp6. Five phosphorylation sites were identified in FgSnu66 by phosphoproteomic analysis and the T418A-S420A-S422A mutation was shown to reduce virulence. Overall, our results showed that mutations in FgSNU66 can suppress deletion of Fgprp4, which has not been reported in other organisms, and the C-terminal tail of FgSnu66 plays a role in its interaction with key tri-snRNP components during spliceosome activation.
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Affiliation(s)
- Manli Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yimei Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chunlan Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas and NWAFU-Purdue Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China.,Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
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43
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Targeting the spliceosome for cutaneous squamous cell carcinoma therapy: a role for c-MYC and wild-type p53 in determining the degree of tumour selectivity. Oncotarget 2018; 9:23029-23046. [PMID: 29796170 PMCID: PMC5955416 DOI: 10.18632/oncotarget.25196] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 04/04/2018] [Indexed: 12/25/2022] Open
Abstract
We show that suppression of the spliceosome has potential for the treatment of cutaneous squamous cell carcinoma (cSCC). The small-molecule inhibitors of the spliceosome at the most advanced stage of development target the splicing factor SF3B1/SF3b155. The majority of cSCC cell lines are more sensitive than normal skin cells to death induced by the SF3B1 inhibitor pladienolide B. Knockdown of SF3B1 and a range of other splicing factors with diverse roles in the spliceosome can also selectively kill cSCC cells. We demonstrate that endogenous c-MYC participates in conferring sensitivity to spliceosome inhibition. c-MYC expression is elevated in cSCC lines and its knockdown reduces alterations in mRNA splicing and attenuates cell death caused by interference with the spliceosome. In addition, this study provides further support for a key role of the p53 pathway in the response to spliceosome disruption. SF3B1 inhibition causes wild-type p53 upregulation associated with altered mRNA splicing and reduced protein expression of both principal p53 negative regulators MDMX/MDM4 and MDM2. We observed that wild-type p53 can promote pladienolide B-induced death in tumour cells. However, p53 is commonly inactivated by mutation in cSCCs and p53 participates in killing normal skin cells at high concentrations of pladienolide B. This may limit the therapeutic window of SF3B1 inhibitors for cSCC. We provide evidence that, while suppression of SF3B1 has promise for treating cSCCs with mutant p53, inhibitors which target the spliceosome through SF3B1-independent mechanisms could have greater cSCC selectivity as a consequence of reduced p53 upregulation in normal cells.
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Xing Z, Sun F, He W, Wang Z, Song X, Zhang F. Downregulation of ubiquitin-specific peptidase 39 suppresses the proliferation and induces the apoptosis of human colorectal cancer cells. Oncol Lett 2018; 15:5443-5450. [PMID: 29556295 PMCID: PMC5844003 DOI: 10.3892/ol.2018.8061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 10/20/2017] [Indexed: 02/07/2023] Open
Abstract
Ubiquitin-specific peptidase 39 (USP39) has been reported to participate in the mitotic spindle checkpoint and the process of cytokinesis. and has been identified as a therapeutic target for various types of cancer. However, the effect of USP39 in colorectal cancer (CRC) has not been investigated. To explore the functional role of USP39 in CRC cell growth, lentivirus-mediated RNA interference was applied to inhibit USP39 expression in SW1116 and HCT116 cells. The relative USP39 mRNA and protein expression levels were significantly reduced in the USP39 knockdown cells, as verified by reverse transcription-quantitative polymerase chain reaction and western blot analysis. USP39 knockdown significantly reduced the proliferation and colony formation abilities of CRC cells, and induced apoptosis and cell cycle arrest in the G2/M phases, as determined by an MTT assay, a colony formation assay and flow cytometry analysis. Furthermore, western blot analysis demonstrated that USP39 knockdown may have induced apoptosis through the upregulation of p53, p-p53, PARP and caspase-3 expression in SW1116 cells. In conclusion, USP39 may be a novel biological marker for targeted therapy against CRC, and requires further investigation.
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Affiliation(s)
- Zhiyuan Xing
- Department of General Surgery, The Second Affiliated Hospital of Qingdao University Medical College, Qingdao, Shandong 266000, P.R. China
| | - Fengbo Sun
- Department of General Surgery, Qingdao Haici Medical Group, Qingdao, Shandong 266000, P.R. China
| | - Wang He
- Department of Hepatopathy, Qingdao Sixth People's Hospital, Qingdao, Shandong 266000, P.R. China
| | - Zhiwei Wang
- Department of General Surgery, The Second Affiliated Hospital of Qingdao University Medical College, Qingdao, Shandong 266000, P.R. China
| | - Xiuqi Song
- Department of General Surgery, The Second Affiliated Hospital of Qingdao University Medical College, Qingdao, Shandong 266000, P.R. China
| | - Fengjuan Zhang
- Department of Infection, The Second Affiliated Hospital of Qingdao University Medical College, Qingdao, Shandong 266000, P.R. China
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Xu Y, Zhu MR, Zhang JY, Si GM, Lv JJ. Knockdown of ubiquitin‑specific peptidase 39 inhibits the malignant progression of human renal cell carcinoma. Mol Med Rep 2018; 17:4729-4735. [PMID: 29328477 DOI: 10.3892/mmr.2018.8421] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/04/2017] [Indexed: 11/06/2022] Open
Abstract
Ubiquitin specific peptidase 39 (USP39) serves important roles in mRNA processing and is involved in tumorigenesis of multiple solid malignancies. However, the influence and underlying mechanism of USP39 on human renal cell carcinomas (RCC) remain to be elucidated. The current study investigated the functional roles of USP39 in human RCC cell lines. siRNA‑mediated RNA interference was used to downregulate USP39 in RCC cells. CCK‑8, wound healing and invasion assays were performed to assess the proliferative ability and metastatic potential. The cell cycle distribution and apoptosis were evaluated by flow cytometry. The activity of signaling pathways and the expression of cell cycle‑related proteins were detected by western blot analysis. The siRNA‑directed RNA interference targeting USP39 could effectively downregulate the expression level of USP39 in two RCC cell lines. Depletion of USP39 by siRNA significantly suppressed cell growth and decreased invasive capacity of RCC cells. Silencing of USP39 induced cell apoptosis and cell cycle arrest at G2/M phase. Additionally, the expression levels of apoptotic and G2/M phase‑related proteins were notably decreased following depletion of USP39. Mechanistically, downregulation of USP39 blocked the activation of Akt and extracellular signal regulated kinase signaling pathways in RCC cells. These findings indicate that USP39 may serve as an oncogenic factor in RCC and could be a potential therapeutic candidate for human RCCs.
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Affiliation(s)
- Yuan Xu
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Mei-Rong Zhu
- Department of Urology, Jinan Central Hospital, Shandong University, Jinan, Shandong 250013, P.R. China
| | - Jing-Yong Zhang
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Guo-Min Si
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, P.R. China
| | - Jia-Ju Lv
- Department of Urology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong 250021, P.R. China
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Overexpression of USP39 predicts poor prognosis and promotes tumorigenesis of prostate cancer via promoting EGFR mRNA maturation and transcription elongation. Oncotarget 2017; 7:22016-30. [PMID: 26959883 PMCID: PMC5008341 DOI: 10.18632/oncotarget.7882] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/23/2016] [Indexed: 12/14/2022] Open
Abstract
Castration resistance is a serious problem facing clinical treatment of prostate cancer (PCa). The underlying molecular mechanisms of acquired proliferation ability of tumor cells upon androgen deprivation are largely undetermined. In the present study, we identified that ubiquitin specific peptidase 39 (USP39) was significantly upregulated in PCa samples and cell lines. Elevated USP39 expression was positively correlated with Gleason score, predicted a poor outcome, and functioned as an independent risk factor for biochemical recurrence (BCR) especially in patients with a Gleason score ≤7. Our cell-based study showed that the expression level of USP39 was the highest in AR-negative PCa cell lines. Knockdown of USP39 in PCa cells inhibited cancer colony formation and tumor cell growth, and induced G2/M arrest and cell apoptosis. Microarray analysis suggested that knockdown of USP39 caused a reduced expression of EGFR. Silencing of USP39 inhibited the expression of EGFR 3′-end, and presented a remarkable block to the maturation of EGFR mRNA, suggesting that silencing of USP39 decreased the transcriptional elongation and maturation of EGFR mRNA. Oncomine datasets analysis showed that USP39 expression was positively correlated with EGFR level. The above findings suggest that USP39 plays a vital oncogenic role in the tumorigenesis of PCa and may prove to be a potential biomarker for predicting the prognosis of PCa patients.
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47
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Chen Z, Gui B, Zhang Y, Xie G, Li W, Liu S, Xu B, Wu C, He L, Yang J, Yi X, Yang X, Sun L, Liang J, Shang Y. Identification of a 35S U4/U6.U5 tri-small nuclear ribonucleoprotein (tri-snRNP) complex intermediate in spliceosome assembly. J Biol Chem 2017; 292:18113-18128. [PMID: 28878014 DOI: 10.1074/jbc.m117.797357] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/28/2017] [Indexed: 11/06/2022] Open
Abstract
The de novo assembly and post-splicing reassembly of the U4/U6.U5 tri-snRNP remain to be investigated. We report here that ZIP, a protein containing a CCCH-type zinc finger and a G-patch domain, as characterized by us previously, regulates pre-mRNA splicing independent of RNA binding. We found that ZIP physically associates with the U4/U6.U5 tri-small nuclear ribonucleoprotein (tri-snRNP). Remarkably, the ZIP-containing tri-snRNP, which has a sedimentation coefficient of ∼35S, is a tri-snRNP that has not been described previously. We also found that the 35S tri-snRNP contains hPrp24, indicative of a state in which the U4/U6 di-snRNP is integrating with the U5 snRNP. We found that the 35S tri-snRNP is enriched in the Cajal body, indicating that it is an assembly intermediate during 25S tri-snRNP maturation. We showed that the 35S tri-snRNP also contains hPrp43, in which ATPase/RNA helicase activities are stimulated by ZIP. Our study identified, for the first time, a tri-snRNP intermediate, shedding new light on the de novo assembly and recycling of the U4/U6.U5 tri-snRNP.
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Affiliation(s)
- Zhe Chen
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bin Gui
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Guojia Xie
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Wanjin Li
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shumeng Liu
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bosen Xu
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chongyang Wu
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xia Yi
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaohan Yang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jing Liang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongfeng Shang
- From the Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China, .,the Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China, and.,the Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
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Kim YD, Lee J, Kim HS, Lee MO, Son MY, Yoo CH, Choi JK, Lee SC, Cho YS. The unique spliceosome signature of human pluripotent stem cells is mediated by SNRPA1, SNRPD1, and PNN. Stem Cell Res 2017; 22:43-53. [PMID: 28595116 DOI: 10.1016/j.scr.2017.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/25/2017] [Accepted: 05/26/2017] [Indexed: 12/21/2022] Open
Abstract
Spliceosomes are the core host of pre-mRNA splicing, allowing multiple protein isoforms to be produced from a single gene. Herein, we reveal that spliceosomes are more abundant in human pluripotent stem cells (hPSs), including human embryonic stem cells (hESs) and human induced pluripotent stem cells (hiPSs), than non-hPSs, and their presence is associated with high transcriptional activity. Supportively, spliceosomal components involved in the catalytically active pre-mRNA splicing step were mainly co-localized with hPS spliceosomes. By profiling the gene expression of 342 selected splicing factors, we found that 71 genes were significantly altered during the reprogramming of human somatic cells into hiPSs. Among them, SNRPA1, SNRPD1, and PNN were significantly up-regulated during the early stage of reprogramming, identified as hub genes by interaction network and cluster analysis. SNRPA1, SNRPD1, or PNN depletion led to a pronounced loss of pluripotency and significantly blocked hiPS generation. SNRPA1, SNRPD1, and PNN co-localized with the hPS spliceosomes, physically interacted with each other, and positively influenced the appearance of hPS spliceosomes. Our data suggest that SNRPA1, SNRPD1, and PNN are key players in the regulation of pluripotency-specific spliceosome assembly and the acquisition and maintenance of pluripotency.
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Affiliation(s)
- Young-Dae Kim
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jungwoon Lee
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Han-Seop Kim
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Mi-Ok Lee
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Mi-Young Son
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Chae Hwa Yoo
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung-Kyun Choi
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Bioscience, KRIBB School, University of Science & Technology, 113 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Sang Chul Lee
- Research Center for Metabolic Regulation, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Yee Sook Cho
- Stem Cell Research Laboratory, Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Bioscience, KRIBB School, University of Science & Technology, 113 Gwahak-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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Gan Z, Han K, Lin S, Hu H, Shen Z, Min D. Knockdown of ubiquitin-specific peptidase 39 inhibited the growth of osteosarcoma cells and induced apoptosis in vitro. Biol Res 2017; 50:15. [PMID: 28403900 PMCID: PMC5389082 DOI: 10.1186/s40659-017-0121-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 04/07/2017] [Indexed: 11/10/2022] Open
Abstract
Background Ubiquitin specific peptidase 39 (USP39), an essential factor in the assembly of the mature spliceosome complex, has an aberrant expression in several cancer. However, its function and the corresponding mechanism on human osteosarcoma has not been fully explored yet. Methods The mRNA and DNA copies of USP39 were increased in osteosarcoma cancer tissues compared with the one in human normal tissues according to datasets from the publicly available Oncomine database. A further western blot analysis also demonstrated an aberrant endogenous expression of USP39 in three different osteosarcoma cells. Then lentivirus-mediated short hairpin RNA (shRNA) was designed to silence USP39 in human osteosarcoma cell line U2OS, which is used to test the impact of USP39-silencing on cellular proliferation, colony formation, cell cycle distribution and apoptosis. Results Knockdown of USP39 expression in U2OS cell significantly decreased cell proliferation, impaired colony formation ability. A further analysis indicated suppression of USP39 arrested cell cycle progression at G2/M phase via p21 dependent way. In addition, the results of Annexin V/7-AAD staining suggested the knockdown of USP39 could promote U2OS cell apoptosis through PARP cleavage. Conclusions These results uncover the critical role of USP39 in regulating cancer cell mitosis and indicate USP39 is critical for osteosarcoma tumorigenesis.
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Affiliation(s)
- Zhihua Gan
- Department of Medical Oncology, The Affiliated 6th People's Hospital of Shanghai Jiaotong University, Shanghai, 200223, China
| | - Kun Han
- Department of Medical Oncology, The Affiliated 6th People's Hospital of Shanghai Jiaotong University, Shanghai, 200223, China
| | - Shuchen Lin
- Department of Medical Oncology, The Affiliated 6th People's Hospital of Shanghai Jiaotong University, Shanghai, 200223, China
| | - Haiyan Hu
- Department of Medical Oncology, The Affiliated 6th People's Hospital of Shanghai Jiaotong University, Shanghai, 200223, China
| | - Zan Shen
- Department of Medical Oncology, The Affiliated 6th People's Hospital of Shanghai Jiaotong University, Shanghai, 200223, China
| | - Daliu Min
- Department of Medical Oncology, The Affiliated 6th People's Hospital of Shanghai Jiaotong University, Shanghai, 200223, China.
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50
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PKR activation and eIF2α phosphorylation mediate human globin mRNA splicing at spliceosome assembly. Cell Res 2017; 27:688-704. [PMID: 28374749 DOI: 10.1038/cr.2017.39] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 11/20/2016] [Accepted: 12/30/2016] [Indexed: 02/01/2023] Open
Abstract
Short elements in mammalian mRNA can control gene expression by activating the RNA-dependent protein kinase PKR that attenuates translation by phosphorylating cytoplasmic eukaryotic initiation factor 2α (eIF2α). We demonstrate a novel, positive role for PKR activation and eIF2α phosphorylation in human globin mRNA splicing. PKR localizes in splicing complexes and associates with splicing factor SC35. Splicing and early-stage spliceosome assembly on β-globin pre-mRNA depend strictly on activation of PKR by a codon-containing RNA fragment within exon 1 and on phosphorylation of nuclear eIF2α on Serine 51. Nonphosphorylatable mutant eIF2αS51A blocked β-globin mRNA splicing in cells and nuclear extract. Mutations of the β-globin RNA activator abrogated PKR activation and profoundly affected mRNA splicing efficiency. PKR depletion abrogated splicing and spliceosome assembly; recombinant PKR effectively restored splicing. Excision of the first intron of β-globin induces strand displacement within the RNA activator of PKR by a sequence from exon 2, a structural rearrangement that silences the ability of spliced β-globin mRNA to activate PKR. Thus, the ability to activate PKR is transient, serving solely to enable splicing. α-Globin pre-mRNA splicing is controlled likewise but positions of PKR activator and silencer are reversed, demonstrating evolutionary flexibility in how PKR activation regulates globin mRNA splicing through eIF2α phosphorylation.
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