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Zhang X, Cong P, Tian L, Zheng Y, Zhang H, Liu Q, Wu T, Zhang Q, Wu H, Huang X, Xiong L. Genomic gain/methylation modification/hsa-miR-132-3p increases RRS1 overexpression in liver hepatocellular carcinoma. Cancer Sci 2023; 114:4329-4342. [PMID: 37705317 PMCID: PMC10637089 DOI: 10.1111/cas.15933] [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: 05/30/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
This study aimed to determine the upstream regulatory factors affecting ribosome biogenesis regulator 1 homolog (RRS1) expression and the development and prognosis of liver hepatocellular carcinoma (LIHC). The expression profiles of RRS1 were evaluated in pan-cancer tissues and liver tumor cell lines. The associations of RRS1 with pan-cancer survival, immune infiltrations, immune checkpoints, and drug sensitivity were identified. We explored the potential upstream regulatory mechanisms of RRS1 expression. Hsa-miR-132-3p knockdown, CCK-8 assays, transwell, and wound healing assays were performed to validate the regulatory effect of hsa-miR-132-3p on RRS1 expression and the development of LIHC. Our findings demonstrated that RRS1 was significantly elevated in 27 types of cancers. RRS1 predicts a poor outcome of LIHC, lung adenocarcinoma, head and neck cancer, and kidney papillary cell carcinoma. RRS1 expression showed a significant association with immune cell infiltrates and the expression of immune checkpoints-related genes in LIHC tissues. Increased RRS1 expression may have a negative effect on these anticancer drugs of LIHC. Low methylation of the RRS1 promoter and its genomic gain may elevate RRS1 expression and predict poor prognosis for LIHC. Increased hsa-miR-132-3p expression may elevate RRS1 expression and result in poor prognosis for LIHC. Hsa-miR-132-3p inhibition can decrease RRS1 expression and the development of liver tumor cell lines. Low methylation of the RRS1 promoter, RRS1 genomic gain, and hsa-miR-132-3p upregulation in LIHC may promote RRS1 upregulation and thus lead to the development and poor prognosis for LIHC. RRS1 is a promising therapeutic target for LIHC.
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Affiliation(s)
- Xiaoxia Zhang
- Department of Hospital Infection Management, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Peilin Cong
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Li Tian
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Yinggang Zheng
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Hong Zhang
- Department of Rehabilitation Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Qiong Liu
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Tingmei Wu
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Qian Zhang
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Huanghui Wu
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Xinwei Huang
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Lize Xiong
- Clinical Research Center for Anesthesiology and Perioperative MedicineTongji UniversityShanghaiChina
- Shanghai Key Laboratory of Anesthesiology and Brain Functional ModulationShanghaiChina
- Translational Research Institute of Brain and Brain‐Like Intelligence, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
- Department of Anesthesiology and Perioperative Medicine, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
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Du YX, Zhou Y, Zheng XH, Duan YJ, Gu ZT, Yin YF, Wang CF. Subcellular localization of nucleolar protein 14 and its proliferative function mediated by miR-17-5p and E2F4 in pancreatic cancer. Aging (Albany NY) 2023; 15:7308-7323. [PMID: 37506248 PMCID: PMC10415562 DOI: 10.18632/aging.204915] [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: 11/12/2022] [Accepted: 06/22/2023] [Indexed: 07/30/2023]
Abstract
Pancreatic cancer is one of the most lethal malignancies worldwide. Acquiring infinite proliferation ability is a key hallmark and basis of tumorigenesis. NOP14 is an identified ribosome biogenesis protein that plays potential roles in cell proliferation. However, the function and molecular mechanism of NOP14 remain ambiguous in most human cancers. In this study, we first investigated the subcellular localization and expression of NOP14 by multiple quantitative assays in pancreatic cancer. We confirmed that NOP14 was mainly localized in nucleolus in human pancreatic cancer cells. Then we studied the regulatory effects of this nucleolus protein on tumor cell proliferation in vitro. NOP14 was demonstrated to play a dominant pro-proliferation role in pancreatic cancer. Furthermore, we identified miR17-5p as a downstream target of NOP14. Transfection of miR17-5p mimics or inhibitors rescued the down- or upregulated effect of NOP14 on cell proliferation by regulating expression of P130. In addition, NOP14 induced expression of transcription factor E2F4 independent of miR17-5p/P130 signaling, which simultaneously activated a set of targeted genes, such as CCNE1, PIM1, AKT1 etc., to promote tumor proliferation. These findings might provide novel insights for better understanding the diverse function of NOP14 in human malignancies to develop new strategies for targeted therapy.
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Affiliation(s)
- Yong-Xing Du
- Department of Pancreatic and Gastric Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People’s Republic of China
| | - Ying Zhou
- Department of Endocrinology, China-Japan Friendship Hospital, Beijing 100029, People’s Republic of China
| | - Xiao-Hao Zheng
- Department of Pancreatic and Gastric Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People’s Republic of China
| | - Yun-Jie Duan
- Department of Pancreatic and Gastric Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People’s Republic of China
| | - Zong-Ting Gu
- Department of Pancreatic and Gastric Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People’s Republic of China
| | - Ye-Feng Yin
- Department of Colorectal Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People’s Republic of China
| | - Cheng-Feng Wang
- Department of Pancreatic and Gastric Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People’s Republic of China
- Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan 030013, Shanxi, People’s Republic of China
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3
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Jacobs RQ, Fuller KB, Cooper SL, Carter ZI, Laiho M, Lucius AL, Schneider DA. RNA Polymerase I Is Uniquely Vulnerable to the Small-Molecule Inhibitor BMH-21. Cancers (Basel) 2022; 14:5544. [PMID: 36428638 PMCID: PMC9688676 DOI: 10.3390/cancers14225544] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/09/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer cells require robust ribosome biogenesis to maintain rapid cell growth during tumorigenesis. Because RNA polymerase I (Pol I) transcription of the ribosomal DNA (rDNA) is the first and rate-limiting step of ribosome biogenesis, it has emerged as a promising anti-cancer target. Over the last decade, novel cancer therapeutics targeting Pol I have progressed to clinical trials. BMH-21 is a first-in-class small molecule that inhibits Pol I transcription and represses cancer cell growth. Several recent studies have uncovered key mechanisms by which BMH-21 inhibits ribosome biosynthesis but the selectivity of BMH-21 for Pol I has not been directly measured. Here, we quantify the effects of BMH-21 on Pol I, RNA polymerase II (Pol II), and RNA polymerase III (Pol III) in vitro using purified components. We found that BMH-21 directly impairs nucleotide addition by Pol I, with no or modest effect on Pols II and III, respectively. Additionally, we found that BMH-21 does not affect the stability of any of the Pols' elongation complexes. These data demonstrate that BMH-21 directly exploits unique vulnerabilities of Pol I.
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Affiliation(s)
- Ruth Q. Jacobs
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kaila B. Fuller
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Stephanie L. Cooper
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Aaron L. Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David A. Schneider
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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4
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Ribosome-Directed Therapies in Cancer. Biomedicines 2022; 10:biomedicines10092088. [PMID: 36140189 PMCID: PMC9495564 DOI: 10.3390/biomedicines10092088] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 12/29/2022] Open
Abstract
The human ribosomes are the cellular machines that participate in protein synthesis, which is deeply affected during cancer transformation by different oncoproteins and is shown to provide cancer cell proliferation and therefore biomass. Cancer diseases are associated with an increase in ribosome biogenesis and mutation of ribosomal proteins. The ribosome represents an attractive anti-cancer therapy target and several strategies are used to identify specific drugs. Here we review the role of different drugs that may decrease ribosome biogenesis and cancer cell proliferation.
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Ding L, Zhang Z, Zhao C, Chen L, Chen Z, Zhang J, Liu Y, Nie Y, He Y, Liao K, Zhang X. Ribosomal L1 domain-containing protein 1 coordinates with HDM2 to negatively regulate p53 in human colorectal Cancer cells. J Exp Clin Cancer Res 2021; 40:245. [PMID: 34362424 PMCID: PMC8344204 DOI: 10.1186/s13046-021-02057-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/31/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ribosomal L1 domain-containing protein 1 (RSL1D1) is a nucleolar protein that is essential in cell proliferation. In the current opinion, RSL1D1 translocates to the nucleoplasm under nucleolar stress and inhibits the E3 ligase activity of HDM2 via direct interaction, thereby leading to stabilization of p53. METHODS Gene knockdown was achieved in HCT116p53+/+, HCT116p53-/-, and HCT-8 human colorectal cancer (CRC) cells by siRNA transfection. A lentiviral expression system was used to establish cell strains overexpressing genes of interest. The mRNA and protein levels in cells were evaluated by qRT-PCR and western blot analyses. Cell proliferation, cell cycle, and cell apoptosis were determined by MTT, PI staining, and Annexin V-FITC/PI double staining assays, respectively. The level of ubiquitinated p53 protein was assessed by IP. The protein-RNA interaction was investigated by RIP. The subcellular localization of proteins of interest was determined by IFA. Protein-protein interaction was investigated by GST-pulldown, BiFC, and co-IP assays. The therapeutic efficacy of RSL1D1 silencing on tumor growth was evaluated in HCT116 tumor-bearing nude mice. RESULTS RSL1D1 distributed throughout the nucleus in human CRC cells. Silencing of RSL1D1 gene induced cell cycle arrest at G1/S and cell apoptosis in a p53-dependent manner. RSL1D1 directly interacted with and recruited p53 to HDM2 to form a ternary RSL1D1/HDM2/p53 protein complex and thereby enhanced p53 ubiquitination and degradation, leading to a decrease in the protein level of p53. Destruction of the ternary complex increased the level of p53 protein. RSL1D1 also indirectly decreased the protein level of p53 by stabilizing HDM2 mRNA. Consequently, the negative regulation of p53 by RSL1D1 facilitated cell proliferation and survival and downregulation of RSL1D1 remarkably inhibited the growth of HCT116p53+/+ tumors in a nude mouse model. CONCLUSION We report, for the first time, that RSL1D1 is a novel negative regulator of p53 in human CRC cells and more importantly, a potential molecular target for anticancer drug development.
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Affiliation(s)
- Li Ding
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Zhiping Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Chenhong Zhao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Lei Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Zhiqiang Chen
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jie Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yaxian Liu
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yesen Nie
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yanzhi He
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Kai Liao
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xinyue Zhang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China. .,Joint International Research Laboratory of Agriculture & Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, 225009, Jiangsu, China. .,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agrifood Safety and Quality, The Ministry of Agriculture of China, Yangzhou University (26116120), Yangzhou, 225009, Jiangsu, China. .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, Jiangsu, China.
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6
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Gao LF, Jia S, Zhang QM, Xia YF, Li CJ, Li YH. MicroRNA-802 promotes the progression of osteosarcoma through targeting p27 and activating PI3K/AKT pathway. Clin Transl Oncol 2021; 24:266-275. [PMID: 34318428 DOI: 10.1007/s12094-021-02683-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/08/2021] [Indexed: 11/27/2022]
Abstract
PURPOSE Increasing evidences suggest dysfunctions of microRNAs (miRNAs) are playing important part in tumors. Therefore, the role of miR-802 in osteosarcoma (OS) was exploited. The object was to evaluate the effect of miR-802 and verify its influence on p27 Kip1 (p27) in OS. METHODS RT-qPCR experiment was used to detect miR-802 and p27 expression in OS tissues and cells. We explored the function of miR-802 through Transwell assays. The phosphoinositide 3-kinase (PI3K)/AKT serine/threonine kinase pathway and epithelial-mesenchymal transition (EMT) was detected by Western blot assays. Luciferase assay was used to testify the target of miR-802. RESULTS MiR-802 expression was elevated in OS, which was related to poor clinical outcome in OS patients. MiR-802 overexpression promoted OS migration, invasion and EMT. Further, p27 is a direct target of miR-802. P27 elevation counteracted the promotion effect of OS on EMT, migration and invasion induced by miR-802. In addition, miR-802 overexpression inactivated PI3K/AKT pathway via targeting p27 in OS. CONCLUSION MiR-802 promoted the progress of EMT, migration and invasion in OS via targeting p27. This newly identified miR-802/p27/PI3K/AKT axis may represent potential targets for OS.
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Affiliation(s)
- L F Gao
- Department of Clinical Laboratory, Weifang Weiyi Tumor Hospital, Affiliated Hospital of Weifang Medical University, Weifang, 261061, China
| | - S Jia
- No.1 Department of Orthopedics, Traditional Chinese Medical Hospital of Huangdao District, Qingdao, 266500, China
| | - Q M Zhang
- Emergency Ward, Qingdao Hospital of Traditional Chinese Medicine, Qingdao Hiser Medical Group, Qingdao, 266033, China
| | - Y F Xia
- Department of Imaging, Zhangqiu District People's Hospital, Jinan, 250200, China
| | - C J Li
- Department of Imaging, Zhangqiu District People's Hospital, Jinan, 250200, China
| | - Y H Li
- Department of Spine Surgery, Qingdao Hospital of Traditional Chinese Medicine, Qingdao Hiser Medical Group, 4 Renmin Road, Shibei District, Qingdao, 266033, China.
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7
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Ladelfa MF, Peche LY, Amato GE, Escalada MC, Zampieri S, Pascucci FA, Benevento AF, Do Porto DF, Dardis A, Schneider C, Monte M. Expression of the tumor-expressed protein MageB2 enhances rRNA transcription. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119015. [PMID: 33741433 DOI: 10.1016/j.bbamcr.2021.119015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 02/22/2021] [Accepted: 03/12/2021] [Indexed: 11/17/2022]
Abstract
An essential requirement for cells to sustain a high proliferating rate is to be paired with enhanced protein synthesis through the production of ribosomes. For this reason, part of the growth-factor signaling pathways, are devoted to activate ribosome biogenesis. Enhanced production of ribosomes is a hallmark in cancer cells, which is boosted by different mechanisms. Here we report that the nucleolar tumor-protein MageB2, whose expression is associated with cell proliferation, also participates in ribosome biogenesis. Studies carried out in both siRNA-mediated MageB2 silenced cells and CRISPR/CAS9-mediated MageB2 knockout (KO) cells showed that its expression is linked to rRNA transcription increase independently of the cell proliferation status. Mechanistically, MageB2 interacts with phospho-UBF, a protein which causes the recruitment of RNA Pol I pre-initiation complex required for rRNA transcription. In addition, cells expressing MageB2 displays enhanced phospho-UBF occupancy at the rDNA gene promoter. Proteomic studies performed in MageB2 KO cells revealed impairment in ribosomal protein (RPs) content. Functionally, enhancement in rRNA production in MageB2 expressing cells, was directly associated with an increased dynamic in protein synthesis. Altogether our results unveil a novel function for a tumor-expressed protein from the MAGE-I family. Findings reported here suggest that nucleolar MageB2 might play a role in enhancing ribosome biogenesis as part of its repertoire to support cancer cell proliferation.
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Affiliation(s)
- María Fátima Ladelfa
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Leticia Yamila Peche
- Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie, Area Science Park, Trieste, Italy
| | - Gastón Ezequiel Amato
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Micaela Carolina Escalada
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Stefania Zampieri
- Centro di Coordinamento Regionale per le Malattie Rare, Ospedale Universitario Santa Maria Della Misericordia, Udine, Italy
| | - Franco Andrés Pascucci
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Andres Fernandez Benevento
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Pabellón 2, Ciudad Universitaria, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
| | - Dario Fernandez Do Porto
- Plataforma de Bioinformática Argentina, Instituto de Cálculo, Pabellón 2, Ciudad Universitaria, Facultad de Ciencias Exactas y Naturales, UBA, Buenos Aires, Argentina
| | - Andrea Dardis
- Centro di Coordinamento Regionale per le Malattie Rare, Ospedale Universitario Santa Maria Della Misericordia, Udine, Italy
| | - Claudio Schneider
- Laboratorio Nazionale del Consorzio Interuniversitario per le Biotecnologie, Area Science Park, Trieste, Italy; Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, p.le Kolbe 4, Udine, Italy
| | - Martin Monte
- Lab. Oncología Molecular, Departamento de Química Biológica, IQUIBICEN-UBA/CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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8
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Qi X, Liu Z, Zhang Q, Yang M, Wan Y, Huang J, Xu L. Systematic analysis of the function and prognostic value of RNA binding proteins in Colon Adenocarcinoma. J Cancer 2021; 12:2537-2549. [PMID: 33854615 PMCID: PMC8040719 DOI: 10.7150/jca.50407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 02/17/2021] [Indexed: 12/22/2022] Open
Abstract
Background: Abnormal expression of RNA-binding proteins (RBPs) is closely related to tumorigenesis, progression, and prognosis. This study performed systematic bioinformatic analysis of RBPs abnormally expressed in colon adenocarcinoma (COAD) using the Cancer Genome Atlas (TCGA) database to screen prognostic markers and potential therapeutic targets. Methods: First, the gene expression data from COAD samples were used to screen out differentially expressed RBPs for functional enrichment analysis and to visualize interaction relationships. Second, RBPs that were significantly related to prognosis were screened through univariate and multivariate Cox regression analysis to construct a prognostic model. The prediction performance of the prognostic model was evaluated by survival analysis and receiver operating characteristic (ROC) curve analysis. It addition, it was verified in the test cohort. The Human Protein Atlas (HPA) online database was used to verify the expression levels of RBPs in the prognostic model. Results: The study identified 181 differentially expressed RBPs and analyzed their interaction and functional enrichment, which were mainly related to non-coding RNA processing, ribosome biogenesis, RNA metabolic processes, RNA phosphodiester bond hydrolysis, and alternative mRNA splicing. Five RBPs related to prognosis were used to construct a prognostic model, and its predictive ability was verified by the test cohort. ROC curve analysis showed that the prognostic model had good sensitivity and specificity. Independent prognostic analysis showed that risk scores could be used as independent prognostic factors for COAD. Conclusion: This study constructed a reliable prognostic model by analyzing COAD differentially expressed RBPs, facilitating the screening of COAD prognostic markers and therapeutic targets.
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Affiliation(s)
- Xuewei Qi
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zeyu Liu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Qiaoli Zhang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ming Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yuxiang Wan
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jinchang Huang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China.,Institute of Acupuncture and Moxibustion in Cancer Care, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Lin Xu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing 100029, China
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9
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Hua Y, Song J, Peng C, Wang R, Ma Z, Zhang J, Zhang Z, Li N, Hou L. Advances in the Relationship Between Regulator of Ribosome Synthesis 1 (RRS1) and Diseases. Front Cell Dev Biol 2021; 9:620925. [PMID: 33718361 PMCID: PMC7947238 DOI: 10.3389/fcell.2021.620925] [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: 11/14/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
A regulator of ribosome synthesis 1 (RRS1) was discovered in yeast and is mainly localized in the nucleolus and endoplasmic reticulum. It regulates ribosomal protein, RNA biosynthesis, and protein secretion and is closely involved in cellular senescence, cell cycle regulation, transcription, translation, oncogenic transformation etc., Mutations in the RRS1 gene are associated with the occurrence and development of Huntington’s disease and cancer, and overexpression of RRS1 promotes tumor growth and metastasis. In this review, the structure, function, and mechanisms of RRS1 in various diseases are discussed.
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Affiliation(s)
- Yanan Hua
- Department of Neurobiology, Basic Medical College, Qingdao University, Qingdao, China
| | - Jinlian Song
- Department of Laboratory, Women and Children's Hospital of Qingdao, Qingdao, China
| | - Cuixiu Peng
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Runze Wang
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Zhongliang Ma
- Department of Breast Surgery, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Jinyu Zhang
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Zheng Zhang
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Ning Li
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Lin Hou
- Department of Biochemistry and Molecular Biology, Basic Medical College, Qingdao University, Qingdao, China
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10
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Mazloumi Gavgani F, Karlsson T, Tangen IL, Morovicz AP, Arnesen VS, Turcu DC, Ninzima S, Spang K, Krakstad C, Guillermet-Guibert J, Lewis AE. Nuclear upregulation of class I phosphoinositide 3-kinase p110β correlates with high 47S rRNA levels in cancer cells. J Cell Sci 2021; 134:jcs.246090. [PMID: 33536247 DOI: 10.1242/jcs.246090] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 12/24/2020] [Indexed: 12/12/2022] Open
Abstract
The class I phosphoinositide 3-kinase (PI3K) catalytic subunits p110α and p110β are ubiquitously expressed but differently targeted in tumours. In cancer, PIK3CB (encoding p110β) is seldom mutated compared with PIK3CA (encoding p110α) but can contribute to tumorigenesis in certain PTEN-deficient tumours. The underlying molecular mechanisms are, however, unclear. We have previously reported that p110β is highly expressed in endometrial cancer (EC) cell lines and at the mRNA level in primary patient tumours. Here, we show that p110β protein levels are high in both the cytoplasmic and nuclear compartments in EC cells. Moreover, high nuclear:cytoplasmic staining ratios were detected in high-grade primary tumours. High levels of phosphatidylinositol (3,4,5)-trisphosphate [PtdIns(3,4,5)P 3] were measured in the nucleus of EC cells, and pharmacological and genetic approaches showed that its production was partly dependent upon p110β activity. Using immunofluorescence staining, p110β and PtdIns(3,4,5)P 3 were localised in the nucleolus, which correlated with high levels of 47S pre-rRNA. p110β inhibition led to a decrease in both 47S rRNA levels and cell proliferation. In conclusion, these results present a nucleolar role for p110β that may contribute to tumorigenesis in EC.This article has an associated First Person interview with Fatemeh Mazloumi Gavgani, joint first author of the paper.
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Affiliation(s)
| | - Thomas Karlsson
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
| | - Ingvild L Tangen
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen 5021, Norway.,Department of Gynaecology and Obstetrics, Haukeland University Hospital, Bergen 5021, Norway
| | | | | | - Diana C Turcu
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
| | - Sandra Ninzima
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
| | - Katharina Spang
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
| | - Camilla Krakstad
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen 5021, Norway.,Department of Gynaecology and Obstetrics, Haukeland University Hospital, Bergen 5021, Norway
| | - Julie Guillermet-Guibert
- Inserm U1037, Centre de Recherches en Cancérologie de Toulouse (CRCT), Institut National de la Santé et de la Recherche Médicale (INSERM), Université Toulouse III Paul Sabatier, 31037 Toulouse, France
| | - Aurélia E Lewis
- Department of Biological Sciences, University of Bergen, Bergen 5008, Norway
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11
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Mastrogamvraki N, Zaravinos A. Signatures of co-deregulated genes and their transcriptional regulators in colorectal cancer. NPJ Syst Biol Appl 2020; 6:23. [PMID: 32737302 PMCID: PMC7395738 DOI: 10.1038/s41540-020-00144-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
The deregulated genes in colorectal cancer (CRC) vary significantly across different studies. Thus, a systems biology approach is needed to identify the co-deregulated genes (co-DEGs), explore their molecular networks, and spot the major hub proteins within these networks. We reanalyzed 19 GEO gene expression profiles to identify and annotate CRC versus normal signatures, single-gene perturbation, and single-drug perturbation signatures. We identified the co-DEGs across different studies, their upstream regulating kinases and transcription factors (TFs). Connectivity Map was used to identify likely repurposing drugs against CRC within each group. The functional changes of the co-upregulated genes in the first category were mainly associated with negative regulation of transforming growth factor β production and glomerular epithelial cell differentiation; whereas the co-downregulated genes were enriched in cotranslational protein targeting to the membrane. We identified 17 hub proteins across the co-upregulated genes and 18 hub proteins across the co-downregulated genes, composed of well-known TFs (MYC, TCF3, PML) and kinases (CSNK2A1, CDK1/4, MAPK14), and validated most of them using GEPIA2 and HPA, but also through two signature gene lists composed of the co-up and co-downregulated genes. We further identified a list of repurposing drugs that can potentially target the co-DEGs in CRC, including camptothecin, neostigmine bromide, emetine, remoxipride, cephaeline, thioridazine, and omeprazole. Similar analyses were performed in the co-DEG signatures in single-gene or drug perturbation experiments in CRC. MYC, PML, CDKs, CSNK2A1, and MAPKs were common hub proteins among all studies. Overall, we identified the critical genes in CRC and we propose repurposing drugs that could be used against them.
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Affiliation(s)
- Natalia Mastrogamvraki
- Department of Life Sciences, School of Sciences, European University Cyprus, 1516, Nicosia, Cyprus
| | - Apostolos Zaravinos
- Department of Basic Medical Sciences, College of Medicine, Member of QU Health, Qatar University, Doha, Qatar.
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12
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Elsharawy KA, Toss MS, Raafat S, Ball G, Green AR, Aleskandarany MA, Dalton LW, Rakha EA. Prognostic significance of nucleolar assessment in invasive breast cancer. Histopathology 2020; 76:671-684. [PMID: 31736094 DOI: 10.1111/his.14036] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/07/2019] [Accepted: 11/14/2019] [Indexed: 12/17/2022]
Abstract
AIMS Nucleolar morphometric features have a potential role in the assessment of the aggressiveness of many cancers. However, the role of nucleoli in invasive breast cancer (BC) is still unclear. The aims of this study were to investigate the optimal method for scoring nucleoli in IBC and their prognostic significance, and to refine the grading of breast cancer (BC) by incorporating nucleolar score. METHODS AND RESULTS Digital images acquired from haematoxylin and eosin-stained sections from a large BC cohort were divided into training (n = 400) and validation (n = 1200) sets for use in this study. Four different assessment methods were evaluated in the training set to identify the optimal method associated with the best performance and significant prognostic value. These were: (i) a modified Helpap method; (ii) counting prominent nucleoli (size ≥2.5 µm) in 10 field views (FVs); (iii) counting prominent nucleoli in five FVs; and (iv) counting prominent nucleoli in one FV. The optimal method was applied to the validation set and to an external validation set, i.e. data from The Cancer Genome Atlas (n = 743). Scoring prominent nucleoli in five FVs showed the highest interobserver concordance rate (intraclass correlation coefficient of 0.8) and a significant association with BC-specific survival (P < 0.0001). A high nucleolar score was associated with younger age, larger tumour size, and higher grade. Incorporation of nucleolar score in the Nottingham grading system resulted in a higher significant association with survival than the conventional grade. CONCLUSIONS Quantification of nucleolar prominence in five FVs is a cost-efficient and reproducible morphological feature that can predict BC behaviour and can provide an alternative to pleomorphism to improve BC grading performance.
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Affiliation(s)
- Khloud A Elsharawy
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK.,Department of Zoology, Faculty of Science, Damietta University, Damietta, Egypt
| | - Michael S Toss
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Sara Raafat
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Andrew R Green
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Mohammed A Aleskandarany
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Leslie W Dalton
- Department of Histopathology, South Austin Hospital, Austin, TX, USA
| | - Emad A Rakha
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
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13
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Smekalova EM, Gerashchenko MV, O'Connor PBF, Whittaker CA, Kauffman KJ, Fefilova AS, Zatsepin TS, Bogorad RL, Baranov PV, Langer R, Gladyshev VN, Anderson DG, Koteliansky V. In Vivo RNAi-Mediated eIF3m Knockdown Affects Ribosome Biogenesis and Transcription but Has Limited Impact on mRNA-Specific Translation. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 19:252-266. [PMID: 31855834 PMCID: PMC6926209 DOI: 10.1016/j.omtn.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 10/20/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
Abstract
Translation is an essential biological process, and dysregulation is associated with a range of diseases including ribosomopathies, diabetes, and cancer. Here, we examine translation dysregulation in vivo using RNAi to knock down the m-subunit of the translation initiation factor eIF3 in the mouse liver. Transcriptome sequencing, ribosome profiling, whole proteome, and phosphoproteome analyses show that eIF3m deficiency leads to the transcriptional response and changes in cellular translation that yield few detectable differences in the translation of particular mRNAs. The transcriptional response fell into two main categories: ribosome biogenesis (increased transcription of ribosomal proteins) and cell metabolism (alterations in lipid, amino acid, nucleic acid, and drug metabolism). Analysis of ribosome biogenesis reveals inhibition of rRNA processing, highlighting decoupling of rRNA synthesis and ribosomal protein gene transcription in response to eIF3m knockdown. Interestingly, a similar reduction in eIF3m protein levels is associated with induction of the mTOR pathway in vitro but not in vivo. Overall, this work highlights the utility of a RNAi-based in vivo approach for studying the regulation of mammalian translation in vivo.
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Affiliation(s)
- Elena M Smekalova
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Patrick B F O'Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland
| | - Charles A Whittaker
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Kevin J Kauffman
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Anna S Fefilova
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia
| | - Timofei S Zatsepin
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia; Department of Chemistry and Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Roman L Bogorad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork T12 YN60, Ireland; Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia
| | - Robert Langer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Victor Koteliansky
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow, 121205, Russia.
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14
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Kakoti S, Yamauchi M, Gu W, Kato R, Yasuhara T, Hagiwara Y, Laskar S, Oike T, Sato H, Held KD, Nakano T, Shibata A. p53 deficiency augments nucleolar instability after ionizing irradiation. Oncol Rep 2019; 42:2293-2302. [PMID: 31578593 PMCID: PMC6826308 DOI: 10.3892/or.2019.7341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 08/20/2019] [Indexed: 11/06/2022] Open
Abstract
Ribosomes are important cellular components that maintain cellular homeostasis through overall protein synthesis. The nucleolus is a prominent subnuclear structure that contains ribosomal DNA (rDNA) encoding ribosomal RNA (rRNA), an essential component of ribosomes. Despite the significant role of the rDNA‑rRNA‑ribosome axis in cellular homeostasis, the stability of rDNA in the context of the DNA damage response has not been fully investigated. In the present study, the number and morphological changes of nucleolin, a marker of the nucleolus, were examined following ionizing radiation (IR) in order to investigate the impact of DNA damage on nucleolar stability. An increase in the number of nucleoli per cell was found in HCT116 and U2OS cells following IR. Interestingly, the IR‑dependent increase in nucleolar fragmentation was enhanced by p53 deficiency. In addition, the morphological analysis revealed several distinct types of nucleolar fragmentation following IR. The pattern of nucleolar morphology differed between HCT116 and U2OS cells, and the p53 deficiency altered the pattern of nucleolar morphology. Finally, a significant decrease in rRNA synthesis was observed in HCT116 p53‑/‑ cells following IR, suggesting that severe nucleolar fragmentation downregulates rRNA transcription. The findings of the present study suggest that p53 plays a key role in protecting the transcriptional activity of rDNA in response to DNA damage.
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Affiliation(s)
- Sangeeta Kakoti
- Gunma University Initiative for Advanced Research (GIAR), Maebashi, Gunma 371-8511, Japan
- Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Motohiro Yamauchi
- Department of Radiation Biology and Protection, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki 852-8523, Japan
| | - Wenchao Gu
- Gunma University Initiative for Advanced Research (GIAR), Maebashi, Gunma 371-8511, 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
| | - Takaaki Yasuhara
- Laboratory of Molecular Radiology, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
| | - Yoshihiko Hagiwara
- Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Siddhartha Laskar
- Department of Radiation Oncology, Tata Memorial Hospital, Mumbai 400012, India
| | - Takahiro Oike
- Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Hiro Sato
- Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Kathryn D. Held
- Department of Radiation Oncology, Massachusetts General Hospital/Harvard Medical School, Boston, MA 02114, USA
- International Open Laboratory, Gunma University Initiative for Advanced Research (GIAR), Maebashi, Gunma 371-8511, Japan
| | - Takashi Nakano
- Department of Radiation Oncology, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan
| | - Atsushi Shibata
- Gunma University Initiative for Advanced Research (GIAR), Maebashi, Gunma 371-8511, Japan
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15
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Carotenuto P, Pecoraro A, Palma G, Russo G, Russo A. Therapeutic Approaches Targeting Nucleolus in Cancer. Cells 2019; 8:E1090. [PMID: 31527430 PMCID: PMC6770360 DOI: 10.3390/cells8091090] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/08/2019] [Accepted: 09/13/2019] [Indexed: 01/08/2023] Open
Abstract
The nucleolus is a distinct sub-cellular compartment structure in the nucleus. First observed more than 200 years ago, the nucleolus is detectable by microscopy in eukaryotic cells and visible during the interphase as a sub-nuclear structure immersed in the nucleoplasm, from which it is not separated from any membrane. A huge number of studies, spanning over a century, have identified ribosome biogenesis as the main function of the nucleolus. Recently, novel functions, independent from ribosome biogenesis, have been proposed by several proteomic, genomic, and functional studies. Several works have confirmed the non-canonical role for nucleoli in regulating important cellular processes including genome stability, cell-cycle control, the cellular senescence, stress responses, and biogenesis of ribonucleoprotein particles (RNPs). Many authors have shown that both canonical and non-canonical functions of the nucleolus are associated with several cancer-related processes. The association between the nucleolus and cancer, first proposed by cytological and histopathological studies showing that the number and shape of nucleoli are commonly altered in almost any type of cancer, has been confirmed at the molecular level by several authors who demonstrated that numerous mechanisms occurring in the nucleolus are altered in tumors. Recently, therapeutic approaches targeting the nucleolus in cancer have started to be considered as an emerging "hallmark" of cancer and several therapeutic interventions have been developed. This review proposes an up-to-date overview of available strategies targeting the nucleolus, focusing on novel targeted therapeutic approaches. Finally, a target-based classification of currently available treatment will be proposed.
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Affiliation(s)
- Pietro Carotenuto
- The Institute of Cancer Research, Cancer Therapeutic Unit, London SM2 5NG, UK.
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli 80078, Italy.
| | - Annalisa Pecoraro
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy.
| | - Gaetano Palma
- Department of Advanced Biomedical Science, School of Medicine, University of Naples Federico II, 80131 Naples, Italy.
| | - Giulia Russo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy.
| | - Annapina Russo
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy.
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16
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Penzo M, Montanaro L, Treré D, Derenzini M. The Ribosome Biogenesis-Cancer Connection. Cells 2019; 8:cells8010055. [PMID: 30650663 PMCID: PMC6356843 DOI: 10.3390/cells8010055] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/08/2019] [Accepted: 01/14/2019] [Indexed: 01/05/2023] Open
Abstract
Multifaceted relations link ribosome biogenesis to cancer. Ribosome biogenesis takes place in the nucleolus. Clarifying the mechanisms involved in this nucleolar function and its relationship with cell proliferation: (1) allowed the understanding of the reasons for the nucleolar changes in cancer cells and their exploitation in tumor pathology, (2) defined the importance of the inhibition of ribosome biogenesis in cancer chemotherapy and (3) focused the attention on alterations of ribosome biogenesis in the pathogenesis of cancer. This review summarizes the research milestones regarding these relevant relationships between ribosome biogenesis and cancer. The structure and function of the nucleolus will also be briefly described.
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Affiliation(s)
- Marianna Penzo
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
| | - Davide Treré
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, 40138 Bologna, Italy.
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17
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Derenzini E, Rossi A, Treré D. Treating hematological malignancies with drugs inhibiting ribosome biogenesis: when and why. J Hematol Oncol 2018; 11:75. [PMID: 29855342 PMCID: PMC5984324 DOI: 10.1186/s13045-018-0609-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/26/2018] [Indexed: 01/05/2023] Open
Abstract
It is well known that chemotherapy can cure only some cancers in advanced stage, mostly those with an intact p53 pathway. Hematological cancers such as lymphoma and certain forms of leukemia are paradigmatic examples of such scenario. Recent evidence indicates that the efficacy of many of the alkylating and intercalating agents, antimetabolites, topoisomerase, and kinase inhibitors used in cancer therapy is largely due to p53 stabilization and activation consequent to the inhibition of ribosome biogenesis. In this context, innovative drugs specifically hindering ribosome biogenesis showed preclinical activity and are currently in early clinical development in hematological malignancies. The mechanism of p53 stabilization after ribosome biogenesis inhibition is a multistep process, depending on specific factors that can be altered in tumor cells, which can affect the antitumor efficacy of ribosome biogenesis inhibitors (RiBi). In the present review, the basic mechanisms underlying the anticancer activity of RiBi are discussed based on the evidence deriving from available preclinical and clinical studies, with the purpose of defining when and why the treatment with drugs inhibiting ribosomal biogenesis could be highly effective in hematological malignancies.
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Affiliation(s)
- Enrico Derenzini
- European Institute of Oncology, Via Ripamonti 435, 20141, Milan, Italy.
| | - Alessandra Rossi
- European Institute of Oncology, Via Ripamonti 435, 20141, Milan, Italy
| | - Davide Treré
- DIMES, Università di Bologna, Via Massarenti 9, Bologna, Italy.
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18
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Liu X, Wu J, Zhang D, Wang K, Duan X, Meng Z, Zhang X. Network Pharmacology-Based Approach to Investigate the Mechanisms of Hedyotis diffusa Willd. in the Treatment of Gastric Cancer. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2018; 2018:7802639. [PMID: 29853970 PMCID: PMC5954954 DOI: 10.1155/2018/7802639] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 03/27/2018] [Accepted: 04/01/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Hedyotis diffusa Willd. (HDW) is one of the renowned herbs often used in the treatment of gastric cancer (GC). However, its curative mechanism has not been fully elucidated. OBJECTIVE To systematically investigate the mechanisms of HDW in GC. METHODS A network pharmacology approach mainly comprising target prediction, network construction, and module analysis was adopted in this study. RESULTS A total of 353 targets of the 32 bioactive compounds in HDW were obtained. The network analysis showed that CA isoenzymes, p53, PIK3CA, CDK2, P27Kip1, cyclin D1, cyclin B1, cyclin A2, AKT1, BCL2, MAPK1, and VEGFA were identified as key targets of HDW in the treatment of GC. The functional enrichment analysis indicated that HDW probably produced the therapeutic effects against GC by synergistically regulating many biological pathways, such as nucleotide excision repair, apoptosis, cell cycle, PI3K/AKT/mTOR signaling pathway, VEGF signaling pathway, and Ras signaling pathway. CONCLUSIONS This study holistically illuminates the fact that the pharmacological mechanisms of HDW in GC might be strongly associated with its synergic modulation of apoptosis, cell cycle, differentiation, proliferation, migration, invasion, and angiogenesis.
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Affiliation(s)
- Xinkui Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Jiarui Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Dan Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Kaihuan Wang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Xiaojiao Duan
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Ziqi Meng
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
| | - Xiaomeng Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102, China
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19
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Galbiati A, Penzo M, Bacalini MG, Onofrillo C, Guerrieri AN, Garagnani P, Franceschi C, Treré D, Montanaro L. Epigenetic up-regulation of ribosome biogenesis and more aggressive phenotype triggered by the lack of the histone demethylase JHDM1B in mammary epithelial cells. Oncotarget 2018; 8:37091-37103. [PMID: 28415746 PMCID: PMC5514893 DOI: 10.18632/oncotarget.16181] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 03/03/2017] [Indexed: 01/08/2023] Open
Abstract
The alterations of ribosome biogenesis and protein synthesis play a direct role in the development of tumors. The accessibility and transcription of ribosomal genes is controlled at several levels, with their epigenetic regulation being one of the most important. Here we explored the JmjC domain-containing histone demethylase 1B (JHDM1B) function in the epigenetic control of rDNA transcription. Since JHDM1B is a negative regulator of gene transcription, we focused on the effects induced by JHDM1B knock-down (KD). We studied the consequences of stable inducible JHDM1B silencing in cell lines derived from transformed and untransformed mammary epithelial cells. In these cellular models, prolonged JHDM1B downregulation triggered a surge of 45S pre-rRNA transcription and processing, associated with a re-modulation of the H3K36me2 levels at rDNA loci and with changes in DNA methylation of specific CpG sites in rDNA genes. We also found that after JHDM1B KD, cells showed a higher ribosome content: which were engaged in mRNA translation. JHDM1B KD and the consequent stimulation of ribosomes biogenesis conferred more aggressive features to the tested cellular models, which acquired a greater clonogenic, staminal and invasive potential. Taken together, these data indicate that the reduction of JHDM1B leads to a more aggressive cellular phenotype in mammary gland cells, by virtue of its negative regulatory activity on ribosome biogenesis.
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Affiliation(s)
- Alice Galbiati
- Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Marianna Penzo
- Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Carmine Onofrillo
- Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Ania Naila Guerrieri
- Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Davide Treré
- Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic, and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
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20
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The pre-existing population of 5S rRNA effects p53 stabilization during ribosome biogenesis inhibition. Oncotarget 2018; 8:4257-4267. [PMID: 28032591 PMCID: PMC5354829 DOI: 10.18632/oncotarget.13833] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 12/03/2016] [Indexed: 12/14/2022] Open
Abstract
Pre-ribosomal complex RPL5/RPL11/5S rRNA (5S RNP) is considered the central MDM2 inhibitory complex that control p53 stabilization during ribosome biogenesis inhibition. Despite its role is well defined, the dynamic of 5S RNP assembly still requires further characterization. In the present work, we report that MDM2 inhibition is dependent by a pre-existing population of 5S rRNA.
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21
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Zhou G, Lu MQ, Li DJ, Gao BA, Guo R. Identification of differentially expressed molecular functions associated with breast cancer using Gibbs sampling. Oncol Lett 2017; 14:7489-7494. [PMID: 29344193 DOI: 10.3892/ol.2017.7158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/27/2017] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to identify differentially expressed molecular functions (DEMFs) for breast cancer using the Gibbs sampling approach. Molecular functions (MFs) were obtained on the basis of the Bayesian Approach for Geneset Selection package. Subsequently, MFs were converted into Markov chains (MCs) prior to calculating their probabilities, utilizing the MC Monte Carlo algorithm. DEMFs were identified with probabilities ≥0.8 and the gene compositions were studied. Finally, a co-expression network was constructed via the empirical Bayes method and a pathway enrichment analysis of genes in DEMFs was performed. A total of 396 MFs were identified and all transformed to MCs. With the threshold, 2 DEMFs (structural molecule activity and protein heterodimerization activity) were obtained. The DEMFs were comprised of 297 genes, 259 of which were mapped to the co-expression network. These 297 genes were identified to be enriched in 10 pathways, and ribosome was the most significant pathway. The results of the present study revealed 2 DEMFs (structural molecule activity and protein heterodimerization activity) which may be associated with the pathological molecular mechanisms underlying breast cancer, based on Gibbs sampling.
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Affiliation(s)
- Gang Zhou
- Internal Medicine, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, Hubei 443003, P.R. China
| | - Ming-Qian Lu
- Department of Oncology, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, Hubei 443003, P.R. China
| | - Dao-Jun Li
- Department of Oncology, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, Hubei 443003, P.R. China
| | - Bao-An Gao
- Department of Respiration, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, Hubei 443003, P.R. China
| | - Rong Guo
- Department of Oncology, The First College of Clinical Medical Science, China Three Gorges University, Yichang Central People's Hospital, Yichang, Hubei 443003, P.R. China
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22
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Guo H, Zeng W, Feng L, Yu X, Li P, Zhang K, Zhou Z, Cheng S. Integrated transcriptomic analysis of distance-related field cancerization in rectal cancer patients. Oncotarget 2017; 8:61107-61117. [PMID: 28977850 PMCID: PMC5617410 DOI: 10.18632/oncotarget.17864] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/07/2017] [Indexed: 12/18/2022] Open
Abstract
Field cancerization (FC) occurs in various epithelial carcinomas, including colorectal cancer, which indicates that the molecular events in carcinogenesis might occur in normal tissues extending from tumors. However, the transcriptomic characteristics of FC in colorectal cancer (CRC) remain largely unexplored. To investigate the changes in gene expression associated with proximity to the tumor, we analyzed the global gene expression profiles of cancer tissues and histologically normal tissues taken at various distances from the tumor (1 cm, 5 cm and the proximal end of the resected sample) from 32 rectal cancer patients. Significantly differentially expressed genes related to the distance from the tumor were screened by linear mixed effects analysis using the lme4 package in R. The distance-related differentially expressed genes that were gradually up-regulated (n=302) or gradually down-regulated (n=568) from normal tissues to the tumor were used to construct protein-protein interaction (PPI) networks. Three subnetworks among the gradually up-regulated genes and four subnetworks among the gradually down-regulated genes were identified using the MCODE plugin in the Cytoscape software program. The most significantly enriched Gene Ontology (GO) biological process terms were "ribosome biogenesis", "mRNA splicing via spliceosome", and "positive regulation of leukocyte migration" for the gradually up-regulated subnetworks and "cellular calcium ion homeostasis", "cell separation after cytokinesis", "cell junction assembly", and "fatty acid metabolic process" for the gradually down-regulated subnetworks. Combined with the previously constructed multistep carcinogenesis model used for the analysis, 50.59% of the genes in the subnetworks (43/85) displayed identical changes in expression from normal colon tissues to adenoma and colon cancer. We focused on the 7 genes associated with fatty acid metabolic processes in the distance-related down-regulated subnetwork. Survival analysis of patients in the CRC dataset from The Cancer Genome Atlas (TCGA) revealed that higher expression of these 7 genes, especially CPT2, ACAA2 and ACADM, was associated with better prognosis (p = 0.034, p = 0.00058, p = 0.039, p = 0.04). Cox proportional hazards regression analysis revealed that CPT2 was an independent prognostic factor (p = 0.004131). Our results demonstrate that field cancerization occurs in CRC and affects gene expression in normal tissues extending from the tumor, which may provide new insights into CRC oncogenesis and patient progression.
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Affiliation(s)
- Honglin Guo
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Weigen Zeng
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xuexin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Ping Li
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhixiang Zhou
- Department of Colorectal Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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23
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Wang J, Li Z, Zuo C, Xie Q, Li H, Jia J, Zhen Z, Qi R, Li Z, Liu D, Sun B. Knockdown of RRS1 by lentiviral-mediated RNAi promotes apoptosis and suppresses proliferation of human hepatocellular carcinoma cells. Oncol Rep 2017; 38:2166-2172. [PMID: 28849112 PMCID: PMC5652961 DOI: 10.3892/or.2017.5906] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/03/2017] [Indexed: 12/02/2022] Open
Abstract
In recent years it was found that the synthesis and biological activity of ribosomes are closely associated with tumor cell growth, tumorigenesis, and malignant transformation. However, the role of regulator of ribosome synthesis 1 (RRS1) in hepatocellular carcinoma (HCC) has not yet been reported. In the present study, we aimed to examine the potential role of RRS1 in tumor cell growth by using a lentivirus-mediated RNA interference (RNAi) system in the HCC cell line SMMC-7721 in vitro. Compared with that of the negative control group (Lv-shCon), the mRNA and protein expression levels of RRS1 in SMMC-7721 cells transfected with Lv-shRRS1 were significantly decreased. Further experiments found that silencing of RRS1 gene expression in SMMC-7721 cells significantly suppressed cell proliferation, inhibited colony formation capacity, increased apoptosis and arrested cells in the G1 phase. These results suggest that the RRS1 gene plays a critical role in cell proliferation, colony formation, cell apoptosis and cell cycle distribution in human HCC cells, and that silencing of RRS1 by RNAi is a promising therapeutic approach for the treatment of HCC, and should be further developed.
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Affiliation(s)
- Jitao Wang
- Department of Hepatobiliary Surgery, The Affiliated Xingtai People's Hospital of Hebei Medical University; Institute of Tumor Disease of Xingtai City, Xingtai, Hebei 054001, P.R. China
| | - Zhi Li
- Department of Medicine, General Hospital of Jizhong Energy Xingtai Mining Group Limited Liability Company, Xingtai, Hebei 054000, P.R. China
| | - Changzeng Zuo
- Department of Hepatobiliary Surgery, The Affiliated Xingtai People's Hospital of Hebei Medical University; Institute of Tumor Disease of Xingtai City, Xingtai, Hebei 054001, P.R. China
| | - Qingfan Xie
- Department of Hepatobiliary Surgery, The Affiliated Xingtai People's Hospital of Hebei Medical University; Institute of Tumor Disease of Xingtai City, Xingtai, Hebei 054001, P.R. China
| | - Hui Li
- Department of Hepatobiliary Surgery, The Affiliated Xingtai People's Hospital of Hebei Medical University; Institute of Tumor Disease of Xingtai City, Xingtai, Hebei 054001, P.R. China
| | - Junhong Jia
- Department of Hepatobiliary Surgery, The Affiliated Xingtai People's Hospital of Hebei Medical University; Institute of Tumor Disease of Xingtai City, Xingtai, Hebei 054001, P.R. China
| | - Zhongguang Zhen
- Department of Hepatobiliary Surgery, The Affiliated Xingtai People's Hospital of Hebei Medical University; Institute of Tumor Disease of Xingtai City, Xingtai, Hebei 054001, P.R. China
| | - Ruizhao Qi
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Zhiwei Li
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
| | - Dengxiang Liu
- Department of Hepatobiliary Surgery, The Affiliated Xingtai People's Hospital of Hebei Medical University; Institute of Tumor Disease of Xingtai City, Xingtai, Hebei 054001, P.R. China
| | - Baijun Sun
- Department of Hepatobiliary Surgery, Beijing 302 Hospital, Beijing 100039, P.R. China
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24
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Lee HC, Wang H, Baladandayuthapani V, Lin H, He J, Jones RJ, Kuiatse I, Gu D, Wang Z, Ma W, Lim J, O'Brien S, Keats J, Yang J, Davis RE, Orlowski RZ. RNA Polymerase I Inhibition with CX-5461 as a Novel Therapeutic Strategy to Target MYC in Multiple Myeloma. Br J Haematol 2017; 177:80-94. [PMID: 28369725 DOI: 10.1111/bjh.14525] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/12/2016] [Indexed: 12/15/2022]
Abstract
Dysregulation of MYC is frequently implicated in both early and late myeloma progression events, yet its therapeutic targeting has remained a challenge. Among key MYC downstream targets is ribosomal biogenesis, enabling increases in protein translational capacity necessary to support the growth and self-renewal programmes of malignant cells. We therefore explored the selective targeting of ribosomal biogenesis with the small molecule RNA polymerase (pol) I inhibitor CX-5461 in myeloma. CX-5461 induced significant growth inhibition in wild-type (WT) and mutant TP53 myeloma cell lines and primary samples, in association with increases in downstream markers of apoptosis. Moreover, Pol I inhibition overcame adhesion-mediated drug resistance and resistance to conventional and novel agents. To probe the TP53-independent mechanisms of CX-5461, gene expression profiling was performed on isogenic TP53 WT and knockout cell lines and revealed reduction of MYC downstream targets. Mechanistic studies confirmed that CX-5461 rapidly suppressed both MYC protein and MYC mRNA levels. The latter was associated with an increased binding of the RNA-induced silencing complex (RISC) subunits TARBP2 and AGO2, the ribosomal protein RPL5, and MYC mRNA, resulting in increased MYC transcript degradation. Collectively, these studies provide a rationale for the clinical translation of CX-5461 as a novel therapeutic approach to target MYC in myeloma.
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Affiliation(s)
- Hans C Lee
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hua Wang
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Heather Lin
- The Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jin He
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard J Jones
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Isere Kuiatse
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dongmin Gu
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhiqiang Wang
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wencai Ma
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Lim
- Senhwa Biosciences, Inc., San Diego, CA, USA
| | | | - Jonathan Keats
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jing Yang
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Richard E Davis
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert Z Orlowski
- The Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,The Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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25
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LncRNAs2Pathways: Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method. Sci Rep 2017; 7:46566. [PMID: 28425476 PMCID: PMC5397852 DOI: 10.1038/srep46566] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 03/22/2017] [Indexed: 02/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to play essential roles in diverse cellular processes and biological functions. Exploring the functions associated with lncRNAs may help provide insight into their underlying biological mechanisms. The current methods primarily focus on investigating the functions of individual lncRNAs; however, essential biological functions may be affected by the combinatorial effects of multiple lncRNAs. Here, we have developed a novel computational method, LncRNAs2Pathways, to identify the functional pathways influenced by the combinatorial effects of a set of lncRNAs of interest based on a global network propagation algorithm. A new Kolmogorov–Smirnov-like statistical measure weighted by the network propagation score, which considers the expression correlation among lncRNAs and coding genes, was used to evaluate the biological pathways influenced by the lncRNAs of interest. We have described the LncRNAs2Pathways methodology and illustrated its effectiveness by analyzing three lncRNA sets associated with glioma, prostate and pancreatic cancers. We further analyzed the reproducibility and robustness and compared our results with those of two other methods. Based on these analyses, we showed that LncRNAs2Pathways can effectively identify the functional pathways associated with lncRNA sets. Finally, we implemented this method as a freely available R-based tool.
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26
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Mihailovic MK, Chen A, Gonzalez-Rivera JC, Contreras LM. Defective Ribonucleoproteins, Mistakes in RNA Processing, and Diseases. Biochemistry 2017; 56:1367-1382. [PMID: 28206738 DOI: 10.1021/acs.biochem.6b01134] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ribonucleoproteins (RNPs) are vital to many cellular events. To this end, many neurodegenerative diseases and cancers have been linked to RNP malfunction, particularly as this relates to defective processing of cellular RNA. The connection of RNPs and diseases has also propagated a shift of focus onto RNA targeting from traditional protein targeting treatments. However, therapeutic development in this area has been limited by incomplete molecular insight into the specific contributions of RNPs to disease. This review outlines the role of several RNPs in diseases, focusing on molecular defects in processes that affect proper RNA handling in the cell. This work also evaluates the contributions of recently developed methods to understanding RNP association and function. We review progress in this area by focusing on molecular malfunctions of RNPs associated with the onset and progression of several neurodegenerative diseases and cancer and conclude with a brief discussion of RNA-based therapeutic efforts.
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Affiliation(s)
- Mia K Mihailovic
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Angela Chen
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Juan C Gonzalez-Rivera
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin , 200 East. Dean Keeton Street, Stop C0400, Austin, Texas 78712, United States
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27
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Wang Y, Zeng J, Pan J, Geng X, Liu Y, Wu J, Song P, Wang Y, Jia J, Wang L. MicroRNA-200c is involved in proliferation of gastric cancer by directly repressing p27 Kip1. Biochem Biophys Rep 2016; 8:227-233. [PMID: 28955960 PMCID: PMC5613965 DOI: 10.1016/j.bbrep.2016.09.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 08/10/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022] Open
Abstract
P27Kip1, also known as Cyclin-dependent kinase inhibitor 1B, is an important check-point protein in the cell cycle. It has been identified that although as a tumor suppressor, P27Kip1 is expressed in different cancer cell types, which shows the therapeutic potential in tumor genesis. In this study, we examined the upstream regulatory mechanism of P27Kip1 at the microRNA (miRNA) level in gastric carcinogenesis. We used bioinformatics to predict that microRNA-200c (miR-200c) might be a direct upstream regulator of P27Kip1. It was also verified in gastric epithelial-derived cell lines that overexpression of miR-200c significantly inhibited the expression levels of P27Kip1, whereas knockdown of miR-200c promoted P27Kip1 expression in AGS and BGC-823 cells. Furthermore, we identified the direct binding of miR-200c on the P27Kip1 3′ -UTR sequence by luciferase assay. MiR-200c could enhance the colony formation of cells by repressing P27Kip1 expression. In addition, the negative correlation between P27Kip1 and miR-200c in human gastric cancer tissues and matched normal tissues further supported the tumor-promoting action of miR-200c in vivo. Our finding suggested that miR-200c directly regulates the expression of P27Kip1 and promotes cell growth in gastric cancer as an oncogene, which may provide new clues to treatment. miR-200c is involved in the proliferation of gastric cancer cell lines. P27Kip1 is a direct downstream target of miR-200c. miR-200c is determined an oncogene in human gastric cancer tissue species.
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Affiliation(s)
- Yangyang Wang
- Department of Pharmocology, Shandong University School of Medicine, Jinan 250012, PR China
| | - Jiping Zeng
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan 250012, PR China
| | - Jianyong Pan
- Department of Hepatobiliary Surgery, Qilu Hospital of Shandong University, Jinan 250012, PR China
| | - Xue Geng
- Department of Pharmocology, Shandong University School of Medicine, Jinan 250012, PR China
| | - Yansong Liu
- Shandong Tumor's Hospital and Institute, Jinan 250117, PR China
| | - Jing Wu
- Department of Pharmocology, Shandong University School of Medicine, Jinan 250012, PR China
| | - Ping Song
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan 250012, PR China
| | - Ying Wang
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan 250012, PR China
| | - Jihui Jia
- Department of Microbiology/Key Laboratory for Experimental Teratology of Chinese Ministry of Education, Shandong University School of Medicine, Jinan 250012, PR China
| | - Lixiang Wang
- Department of Pharmocology, Shandong University School of Medicine, Jinan 250012, PR China
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28
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Bai D, Zhang J, Li T, Hang R, Liu Y, Tian Y, Huang D, Qu L, Cao X, Ji J, Zheng X. The ATPase hCINAP regulates 18S rRNA processing and is essential for embryogenesis and tumour growth. Nat Commun 2016; 7:12310. [PMID: 27477389 PMCID: PMC4974663 DOI: 10.1038/ncomms12310] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/20/2016] [Indexed: 12/29/2022] Open
Abstract
Dysfunctions in ribosome biogenesis cause developmental defects and increased cancer susceptibility; however, the connection between ribosome assembly and tumorigenesis remains unestablished. Here we show that hCINAP (also named AK6) is required for human 18S rRNA processing and 40S subunit assembly. Homozygous CINAP−/− mice show embryonic lethality. The heterozygotes are viable and show defects in 18S rRNA processing, whereas no delayed cell growth is observed. However, during rapid growth, CINAP haploinsufficiency impairs protein synthesis. Consistently, hCINAP depletion in fast-growing cancer cells inhibits ribosome assembly and abolishes tumorigenesis. These data demonstrate that hCINAP reduction is a specific rate-limiting controller during rapid growth. Notably, hCINAP is highly expressed in cancers and correlated with a worse prognosis. Genome-wide polysome profiling shows that hCINAP selectively modulates cancer-associated translatome to promote malignancy. Our results connect the role of hCINAP in ribosome assembly with tumorigenesis. Modulation of hCINAP expression may be a promising target for cancer therapy. Perturbations in ribosome biogenesis affect development and increase cancer susceptibility. Here, the authors show that hCINAP is required for 18S rRNA processing, is highly expressed in cancers, and promotes cancer cell growth by upregulating the translation of cancer-associated genes.
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Affiliation(s)
- Dongmei Bai
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Jinfang Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Tingting Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Runlai Hang
- State key Laboratory of Plant Genetics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Yong Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Yonglu Tian
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Dadu Huang
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Linglong Qu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
| | - Xiaofeng Cao
- State key Laboratory of Plant Genetics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Surgery, Peking University Caner Hospital and Institute, Beijing 100142, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Yiheyuan Road No. 5, Beijing 100871, China
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29
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Xu HM, Deng HT, Liu CD, Chen YL, Zhang ZY. Phosphoproteomics Analysis of Endometrium in Women with or without Endometriosis. Chin Med J (Engl) 2016; 128:2617-24. [PMID: 26415800 PMCID: PMC4736851 DOI: 10.4103/0366-6999.166022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background: The molecular mechanisms underlying the endometriosis are still not completely understood. In order to test the hypothesis that the approaches in phosphoproteomics might contribute to the identification of key biomarkers to assess disease pathogenesis and drug targets, we carried out a phosphoproteomics analysis of human endometrium. Methods: A large-scale differential phosphoproteome analysis, using peptide enrichment of titanium dioxide purify and sequential elution from immobilized metal affinity chromatography with linear trap quadrupole-tandem mass spectrometry, was performed in endometrium tissues from 8 women with or without endometriosis. Results: The phosphorylation profiling of endometrium from endometriosis patients had been obtained, and found that identified 516 proteins were modified at phosphorylation level during endometriosis. Gene ontology annotation analysis showed that these proteins were enriched in cellular processes of binding and catalytic activity. Further pathway analysis showed that ribosome pathway and focal adhesion pathway were the top two pathways, which might be deregulated during the development of endometriosis. Conclusions: That large-scale phosphoproteome quantification has been successfully identified in endometrium tissues of women with or without endometriosis will provide new insights to understand the molecular mechanisms of the development of endometriosis.
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Affiliation(s)
| | | | | | | | - Zhen-Yu Zhang
- Department of Obstetrics and Gynecology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
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30
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Eliopoulos AG, Volarevic S. TPL2-NPM-p53 pathway monitors nucleolar stress. Oncoscience 2015; 2:892-3. [PMID: 26697512 PMCID: PMC4675775 DOI: 10.18632/oncoscience.254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 09/27/2015] [Indexed: 11/30/2022] Open
Affiliation(s)
- Aristides G Eliopoulos
- Division of Basic Sciences, University of Crete Medical School, 71003 Heraklion, Crete, Greece
| | - Sinisa Volarevic
- Division of Basic Sciences, University of Crete Medical School, 71003 Heraklion, Crete, Greece
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31
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Esposito D, Crescenzi E, Sagar V, Loreni F, Russo A, Russo G. Human rpL3 plays a crucial role in cell response to nucleolar stress induced by 5-FU and L-OHP. Oncotarget 2015; 5:11737-51. [PMID: 25473889 PMCID: PMC4294388 DOI: 10.18632/oncotarget.2591] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/11/2014] [Indexed: 11/25/2022] Open
Abstract
Recent evidence showed that a variety of DNA damaging agents including 5-FU and L-OHP impairs ribosomal biogenesis activating a ribosomal stress pathway. Here, we demonstrate that in lung and colon cancer cell lines devoid of p53, the efficacy of 5-FU and L-OHP chemotherapy depends on rpL3 status. Specifically, we demonstrate that ribosomal stress induced by 5-FU and L-OHP is associated to up-regulation of rpL3 and its accumulation as ribosome-free form. We show that rpL3 participates in the cell response to chemotherapy acting as a critical regulator of cell cycle, apoptosis and DNA repair, by modulating p21 expression. Moreover, we demonstrate that rpL3 is able to control DNA repair also independently from p21 status of cell. It is noteworthy that silencing of rpL3 abolishes the cytotoxic effects of 5-FU and L-OH indicating that the loss of rpL3 makes chemotherapy drugs ineffective. Taking together our results shed light on 5-FU and L-OHP mechanism of action and contribute to more effective clinical use of these drugs in cancer therapy.
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Affiliation(s)
- Davide Esposito
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples 80131, Italy. Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elvira Crescenzi
- Institute of Experimental Endocrinology and Oncology-CNR, Naples 80131, Italy
| | - Vinay Sagar
- Department of Biology, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Fabrizio Loreni
- Department of Biology, University of Rome 'Tor Vergata', Rome 00133, Italy
| | - Annapina Russo
- Department of Pharmacy, University of Naples "Federico II", Naples 80131, Italy
| | - Giulia Russo
- Department of Pharmacy, University of Naples "Federico II", Naples 80131, Italy
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Õunap K, Leetsi L, Matsoo M, Kurg R. The Stability of Ribosome Biogenesis Factor WBSCR22 Is Regulated by Interaction with TRMT112 via Ubiquitin-Proteasome Pathway. PLoS One 2015. [PMID: 26214185 PMCID: PMC4516353 DOI: 10.1371/journal.pone.0133841] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human WBSCR22 protein is a 18S rRNA methyltransferase involved in pre-rRNA processing and ribosome 40S subunit biogenesis. Recent studies have shown that the protein function in ribosome synthesis is independent of its enzymatic activity. In this work, we have studied the WBSCR22 protein interaction partners by SILAC-coupled co-immunoprecipitation assay and identified TRMT112 as the interaction partner of WBSCR22. Knock-down of TRMT112 expression decreased the WBSCR22 protein level in mammalian cells, suggesting that the stability of WBSCR22 is regulated through the interaction with TRMT112. The localization of the TRMT112 protein is determined by WBSCR22, and the WBSCR22-TRMT112 complex is localized in the cell nucleus. We provide evidence that the interaction between WBSCR22/Bud23 and TRMT112/Trm112 is conserved between mammals and yeast, suggesting that the function of TRMT112 as a co-activator of methyltransferases is evolutionarily conserved. Finally, we show that the transiently expressed WBSCR22 protein is ubiquitinated and degraded through the proteasome pathway, revealing the tight control of the WBSCR22 protein level in the cells.
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Affiliation(s)
- Kadri Õunap
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Lilian Leetsi
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Maarja Matsoo
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Reet Kurg
- Institute of Technology, University of Tartu, Tartu, Estonia
- * E-mail:
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Chaillou T, Kirby TJ, McCarthy JJ. Ribosome biogenesis: emerging evidence for a central role in the regulation of skeletal muscle mass. J Cell Physiol 2014; 229:1584-94. [PMID: 24604615 DOI: 10.1002/jcp.24604] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Accepted: 03/04/2014] [Indexed: 12/17/2022]
Abstract
The ribosome is a supramolecular ribonucleoprotein complex that functions at the heart of the translation machinery to convert mRNA into protein. Ribosome biogenesis is the primary determinant of translational capacity of the cell and accordingly has an essential role in the control of cell growth in eukaryotes. Cumulative evidence supports the hypothesis that ribosome biogenesis has an important role in the regulation of skeletal muscle mass. The purpose of this review is to, first, summarize the main mechanisms known to regulate ribosome biogenesis and, second, put forth the hypothesis that ribosome biogenesis is a central mechanism used by skeletal muscle to regulate protein synthesis and control skeletal muscle mass in response to anabolic and catabolic stimuli. The mTORC1 and Wnt/β-catenin/c-myc signaling pathways are discussed as the major pathways that work in concert with each of the three RNA polymerases (RNA Pol I, II, and III) in regulating ribosome biogenesis. Consistent with our hypothesis, activation of these two pathways has been shown to be associated with ribosome biogenesis during skeletal muscle hypertrophy. Although further study is required, the finding that ribosome biogenesis is altered under catabolic states, in particular during disuse atrophy, suggests that its activation represents a novel therapeutic target to reduce or prevent muscle atrophy. Lastly, the emerging field of ribosome specialization is discussed and its potential role in the regulation of gene expression during periods of skeletal muscle plasticity.
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Affiliation(s)
- Thomas Chaillou
- Center for Muscle Biology, University of Kentucky, Lexington, Kentucky; Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky
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Wong YH, Li CW, Chen BS. Evolution of network biomarkers from early to late stage bladder cancer samples. BIOMED RESEARCH INTERNATIONAL 2014; 2014:159078. [PMID: 25309904 PMCID: PMC4189772 DOI: 10.1155/2014/159078] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/09/2014] [Accepted: 07/10/2014] [Indexed: 11/29/2022]
Abstract
We use a systems biology approach to construct protein-protein interaction networks (PPINs) for early and late stage bladder cancer. By comparing the networks of these two stages, we find that both networks showed very significantly different mechanisms. To obtain the differential network structures between cancer and noncancer PPINs, we constructed cancer PPIN and noncancer PPIN network structures for the two bladder cancer stages using microarray data from cancer cells and their adjacent noncancer cells, respectively. With their carcinogenesis relevance values (CRVs), we identified 152 and 50 significant proteins and their PPI networks (network markers) for early and late stage bladder cancer by statistical assessment. To investigate the evolution of network biomarkers in the carcinogenesis process, primary pathway analysis showed that the significant pathways of early stage bladder cancer are related to ordinary cancer mechanisms, while the ribosome pathway and spliceosome pathway are most important for late stage bladder cancer. Their only intersection is the ubiquitin mediated proteolysis pathway in the whole stage of bladder cancer. The evolution of network biomarkers from early to late stage can reveal the carcinogenesis of bladder cancer. The findings in this study are new clues specific to this study and give us a direction for targeted cancer therapy, and it should be validated in vivo or in vitro in the future.
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Affiliation(s)
- Yung-Hao Wong
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Cheng-Wei Li
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Bor-Sen Chen
- Lab of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
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Madden JM, Mueller KL, Bollig-Fischer A, Stemmer P, Mattingly RR, Boerner JL. Abrogating phosphorylation of eIF4B is required for EGFR and mTOR inhibitor synergy in triple-negative breast cancer. Breast Cancer Res Treat 2014; 147:283-93. [PMID: 25129346 DOI: 10.1007/s10549-014-3102-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 08/10/2014] [Indexed: 11/27/2022]
Abstract
Triple-negative breast cancer (TNBC) patients suffer from a highly malignant and aggressive disease. They have a high rate of relapse and often develop resistance to standard chemotherapy. Many TNBCs have elevated epidermal growth factor receptor (EGFR) but are resistant to EGFR inhibitors as monotherapy. In this study, we sought to find a combination therapy that could sensitize TNBC to EGFR inhibitors. Phospho-mass spectrometry was performed on the TNBC cell line, BT20, treated with 0.5 μM gefitinib. Immunoblotting measured protein levels and phosphorylation. Colony formation and growth assays analyzed the treatment on cell proliferation, while MTT assays determined the synergistic effect of inhibitor combination. A Dual-Luciferase reporter gene plasmid measured translation. All statistical analysis was done on CalucuSyn and GraphPad Prism using ANOVAs. Phospho-proteomics identified the mTOR pathway to be of interest in EGFR inhibitor resistance. In our studies, combining gefitinib and temsirolimus decreased cell growth and survival in a synergistic manner. Our data identified eIF4B, as a potentially key fragile point in EGFR and mTOR inhibitor synergy. Decreased eIF4B phosphorylation correlated with drops in growth, viability, clonogenic survival, and cap-dependent translation. Taken together, these data suggest EGFR and mTOR inhibitors abrogate growth, viability, and survival via disruption of eIF4B phosphorylation leading to decreased translation in TNBC cell lines. Further, including an mTOR inhibitor along with an EGFR inhibitor in TNBC with increased EGFR expression should be further explored. Additionally, translational regulation may play an important role in regulating EGFR and mTOR inhibitor synergy and warrant further investigation.
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Affiliation(s)
- Julie M Madden
- Departments of Oncology, Wayne State University, 4100 John R. St, Detroit, MI, 48201, USA
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Rocchi L, Barbosa AJM, Onofrillo C, Del Rio A, Montanaro L. Inhibition of human dyskerin as a new approach to target ribosome biogenesis. PLoS One 2014; 9:e101971. [PMID: 25010840 PMCID: PMC4092089 DOI: 10.1371/journal.pone.0101971] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 06/13/2014] [Indexed: 11/19/2022] Open
Abstract
The product of the DKC1 gene, dyskerin, is required for both ribosome biogenesis and telomerase complex stabilization. Targeting these cellular processes has been explored for the development of drugs to selectively or preferentially kill cancer cells. Presently, intense research is conducted involving the identification of new biological targets whose modulation may simultaneously interfere with multiple cellular functions that are known to be hyper-activated by neoplastic transformations. Here, we report, for the first time, the computational identification of small molecules able to inhibit dyskerin catalytic activity. Different insilico techniques were applied to select compounds and analyze the binding modes and the interaction patterns of ligands in the human dyskerin catalytic site. We also describe a newly developed and optimized fast real-time PCR assay that was used to detect dyskerin pseudouridylation activity invitro. The identification of new dyskerin inhibitors constitutes the first proof of principle that the pseudouridylation activity can be modulated by means of small molecule agents. Therefore, the presented results, obtained through the usage of computational tools and experimental validation, indicate an alternative therapeutic strategy to target ribosome biogenesis pathway.
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Affiliation(s)
- Laura Rocchi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Surgical Pathology Unit, University Hospital of Parma, Parma, Italy
| | - Arménio J. M. Barbosa
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Carmine Onofrillo
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- “Giorgio Prodi” Interdepartmental Cancer Research Centre, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Alberto Del Rio
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Institute for Organic Chemistry and Photoreactivity, National Research Council, Bologna, Italy
- * E-mail: (ADR); (LM)
| | - Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- * E-mail: (ADR); (LM)
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The nucleolar size is associated to the methylation status of ribosomal DNA in breast carcinomas. BMC Cancer 2014; 14:361. [PMID: 24884608 PMCID: PMC4062283 DOI: 10.1186/1471-2407-14-361] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/30/2014] [Indexed: 01/21/2023] Open
Abstract
Background There is a body of evidence that shows a link between tumorigenesis and ribosome biogenesis. The precursor of mature 18S, 28S and 5.8S ribosomal RNAs is transcribed from the ribosomal DNA gene (rDNA), which exists as 300–400 copies in the human diploid genome. Approximately one half of these copies are epigenetically silenced, but the exact role of epigenetic regulation on ribosome biogenesis is not completely understood. In this study we analyzed the methylation profiles of the rDNA promoter and of the 5’ regions of 18S and 28S in breast cancer. Methods We analyzed rDNA methylation in 68 breast cancer tissues of which the normal counterpart was partially available (45/68 samples) using the MassARRAY EpiTYPER assay, a sensitive and quantitative method with single base resolution. Results We found that rDNA locus tended to be hypermethylated in tumor compared to matched normal breast tissues and that the DNA methylation level of several CpG units within the rDNA locus was associated to nuclear grade and to nucleolar size of tumor tissues. In addition we identified a subgroup of samples in which large nucleoli were associated with very limited or absent rDNA hypermethylation in tumor respect to matched normal tissue. Conclusions In conclusion, we suggest that rDNA is an important target of epigenetic regulation in breast tumors and that rDNA methylation level is associated to nucleolar size.
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Knight JRP, Allison SJ, Milner J. Active regulator of SIRT1 is required for cancer cell survival but not for SIRT1 activity. Open Biol 2013; 3:130130. [PMID: 24258275 PMCID: PMC3843821 DOI: 10.1098/rsob.130130] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 10/25/2013] [Indexed: 01/30/2023] Open
Abstract
The NAD(+)-dependent deacetylase SIRT1 is involved in diverse cellular processes, and has also been linked with multiple disease states. Among these, SIRT1 expression negatively correlates with cancer survival in both laboratory and clinical studies. Active regulator of SIRT1 (AROS) was the first reported post-transcriptional regulator of SIRT1 activity, enhancing SIRT1-mediated deacetylation and downregulation of the SIRT1 target p53. However, little is known regarding the role of AROS in regulation of SIRT1 during disease. Here, we report the cellular and molecular effects of RNAi-mediated AROS suppression, comparing this with the role of SIRT1 in a panel of human cell lines of both cancerous and non-cancerous origins. Unexpectedly, AROS is found to vary in its modulation of p53 acetylation according to cell context. AROS suppresses p53 acetylation only following the application of cell damaging stress, whereas SIRT1 suppresses p53 under all conditions analysed. This supplements the original characterization of AROS but indicates that SIRT1 activity can persist following suppression of AROS. We also demonstrate that knockdown of AROS induces apoptosis in three cancer cell lines, independent of p53 activation. Importantly, AROS is not required for the viability of three non-cancer cell lines indicating a putative role for AROS in specifically promoting cancer cell survival.
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39
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Thapa M, Bommakanti A, Shamsuzzaman M, Gregory B, Samsel L, Zengel JM, Lindahl L. Repressed synthesis of ribosomal proteins generates protein-specific cell cycle and morphological phenotypes. Mol Biol Cell 2013; 24:3620-33. [PMID: 24109599 PMCID: PMC3842990 DOI: 10.1091/mbc.e13-02-0097] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Cell stress caused by repression of 54 individual ribosomal genes in Saccharomyces cerevisiae is analyzed. Cell cycle progression and cell morphology responses are specific to the protein whose synthesis is repressed but bud site selection is not. Proteins that generate G2/M and G1 phenotypes map to separate areas of the ribosomal particle. The biogenesis of ribosomes is coordinated with cell growth and proliferation. Distortion of the coordinated synthesis of ribosomal components affects not only ribosome formation, but also cell fate. However, the connection between ribosome biogenesis and cell fate is not well understood. To establish a model system for inquiries into these processes, we systematically analyzed cell cycle progression, cell morphology, and bud site selection after repression of 54 individual ribosomal protein (r-protein) genes in Saccharomyces cerevisiae. We found that repression of nine 60S r-protein genes results in arrest in the G2/M phase, whereas repression of nine other 60S and 22 40S r-protein genes causes arrest in the G1 phase. Furthermore, bud morphology changes after repression of some r-protein genes. For example, very elongated buds form after repression of seven 60S r-protein genes. These genes overlap with, but are not identical to, those causing the G2/M cell cycle phenotype. Finally, repression of most r-protein genes results in changed sites of bud formation. Strikingly, the r-proteins whose repression generates similar effects on cell cycle progression cluster in the ribosome physical structure, suggesting that different topological areas of the precursor and/or mature ribosome are mechanistically connected to separate aspects of the cell cycle.
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Affiliation(s)
- Mamata Thapa
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250 Flow Cytometry Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892
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40
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Boncristiani HF, Evans JD, Chen Y, Pettis J, Murphy C, Lopez DL, Simone-Finstrom M, Strand M, Tarpy DR, Rueppell O. In vitro infection of pupae with Israeli acute paralysis virus suggests disturbance of transcriptional homeostasis in honey bees (Apis mellifera). PLoS One 2013; 8:e73429. [PMID: 24039938 PMCID: PMC3764161 DOI: 10.1371/journal.pone.0073429] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 07/19/2013] [Indexed: 01/08/2023] Open
Abstract
The ongoing decline of honey bee health worldwide is a serious economic and ecological concern. One major contributor to the decline are pathogens, including several honey bee viruses. However, information is limited on the biology of bee viruses and molecular interactions with their hosts. An experimental protocol to test these systems was developed, using injections of Israeli Acute Paralysis Virus (IAPV) into honey bee pupae reared ex-situ under laboratory conditions. The infected pupae developed pronounced but variable patterns of disease. Symptoms varied from complete cessation of development with no visual evidence of disease to rapid darkening of a part or the entire body. Considerable differences in IAPV titer dynamics were observed, suggesting significant variation in resistance to IAPV among and possibly within honey bee colonies. Thus, selective breeding for virus resistance should be possible. Gene expression analyses of three separate experiments suggest IAPV disruption of transcriptional homeostasis of several fundamental cellular functions, including an up-regulation of the ribosomal biogenesis pathway. These results provide first insights into the mechanisms of IAPV pathogenicity. They mirror a transcriptional survey of honey bees afflicted with Colony Collapse Disorder and thus support the hypothesis that viruses play a critical role in declining honey bee health.
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Affiliation(s)
- Humberto F. Boncristiani
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, United States of America
- * E-mail:
| | - Jay D. Evans
- Bee Research Laboratory, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Yanping Chen
- Bee Research Laboratory, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Jeff Pettis
- Bee Research Laboratory, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Charles Murphy
- Soybean Genomics and Improvement, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Dawn L. Lopez
- Bee Research Laboratory, Agricultural Research Service of the United States Department of Agriculture, Beltsville, Maryland, United States of America
| | - Michael Simone-Finstrom
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Micheline Strand
- United States Army Research Office, Division of Life Sciences, Research Triangle Park, North Carolina, United States of America
| | - David R. Tarpy
- Department of Entomology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Olav Rueppell
- Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, United States of America
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Jacob MD, Audas TE, Uniacke J, Trinkle-Mulcahy L, Lee S. Environmental cues induce a long noncoding RNA-dependent remodeling of the nucleolus. Mol Biol Cell 2013; 24:2943-53. [PMID: 23904269 PMCID: PMC3771955 DOI: 10.1091/mbc.e13-04-0223] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Environmental signals, such heat shock and acidosis, induce a structural and functional remodeling of the nucleolus. This process, which depends on the expression of intergenic long noncoding RNA, reversibly converts the nucleolus from a transcriptionally active ribosome factory into a transcriptionally inert prison for proteins. The nucleolus is a plurifunctional organelle in which structure and function are intimately linked. Its structural plasticity has long been appreciated, particularly in response to transcriptional inhibition and other cellular stresses, although the mechanism and physiological relevance of these phenomena are unclear. Using MCF-7 and other mammalian cell lines, we describe a structural and functional adaptation of the nucleolus, triggered by heat shock or physiological acidosis, that depends on the expression of ribosomal intergenic spacer long noncoding RNA (IGS lncRNA). At the heart of this process is the de novo formation of a large subnucleolar structure, termed the detention center (DC). The DC is a spatially and dynamically distinct region, characterized by an 8-anilino-1-naphthalenesulfonate–positive hydrophobic signature. Its formation is accompanied by redistribution of nucleolar factors and arrest in ribosomal biogenesis. Silencing of regulatory IGS lncRNA prevents the creation of this structure and allows the nucleolus to retain its tripartite organization and transcriptional activity. Signal termination causes a decrease in IGS transcript levels and a return to the active nucleolar conformation. We propose that the induction of IGS lncRNA by environmental signals operates as a molecular switch that regulates the structure and function of the nucleolus.
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Affiliation(s)
- Mathieu D Jacob
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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Montanaro L, Treré D, Derenzini M. The emerging role of RNA polymerase I transcription machinery in human malignancy: a clinical perspective. Onco Targets Ther 2013; 6:909-16. [PMID: 23888116 PMCID: PMC3722134 DOI: 10.2147/ott.s36627] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Ribosome biogenesis – the complex and highly coordinated cellular process leading to the production of ribosomes – is strictly dependent on the activity of RNA polymerase I (Pol I) transcriptional machinery. Pol I activity is continually increased in proliferating cells to sustain the increased demand for ribosome production and protein synthesis, which are necessary for appropriate cell growth and division. The integrity of the process of ribosome biogenesis represents an important sensor of cellular stress: when this process is altered, a tumor suppressor response is triggered, which leads to proliferative arrest. The present review focuses on the possible implications of Pol I targeting in the treatment of human malignancies.
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Affiliation(s)
- Lorenzo Montanaro
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, ItalyAlma Mater Studiorum, University of Bologna, Bologna, Italy
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Zhao WT, Zhou CF, Li XB, Zhang YF, Fan L, Pelletier J, Fang J. The von Hippel-Lindau protein pVHL inhibits ribosome biogenesis and protein synthesis. J Biol Chem 2013; 288:16588-16597. [PMID: 23612971 DOI: 10.1074/jbc.m113.455121] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
pVHL, the product of von Hippel-Lindau (VHL) tumor suppressor gene, functions as the substrate recognition component of an E3-ubiquitin ligase complex that targets hypoxia inducible factor α (HIF-α) for ubiquitination and degradation. Besides HIF-α, pVHL also interacts with other proteins and has multiple functions. Here, we report that pVHL inhibits ribosome biogenesis and protein synthesis. We find that pVHL associates with the 40S ribosomal protein S3 (RPS3) but does not target it for destruction. Rather, the pVHL-RPS3 association interferes with the interaction between RPS3 and RPS2. Expression of pVHL also leads to nuclear retention of pre-40S ribosomal subunits, diminishing polysomes and 18S rRNA levels. We also demonstrate that pVHL suppresses both cap-dependent and cap-independent protein synthesis. Our findings unravel a novel function of pVHL and provide insight into the regulation of ribosome biogenesis by the tumor suppressor pVHL.
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Affiliation(s)
- Wen-Ting Zhao
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng-Fu Zhou
- Department of Surgery, Zhongshan Hospital, Fudan University School of Medicine, Shanghai 200030, China
| | - Xue-Bing Li
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yun-Fang Zhang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Li Fan
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Jing Fang
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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Knight JRP, Willis AE, Milner J. Active regulator of SIRT1 is required for ribosome biogenesis and function. Nucleic Acids Res 2013; 41:4185-97. [PMID: 23462953 PMCID: PMC3627601 DOI: 10.1093/nar/gkt129] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Active regulator of SIRT1 (AROS) binds and upregulates SIRT1, an NAD(+)-dependent deacetylase. In addition, AROS binds RPS19, a structural ribosomal protein, which also functions in ribosome biogenesis and is implicated in multiple disease states. The significance of AROS in relation to ribosome biogenesis and function is unknown. Using human cells, we now show that AROS localizes to (i) the nucleolus and (ii) cytoplasmic ribosomes. Co-localization with nucleolar proteins was verified by confocal immunofluorescence of endogenous protein and confirmed by AROS depletion using RNAi. AROS association with cytoplasmic ribosomes was analysed by sucrose density fractionation and immunoprecipitation, revealing that AROS selectively associates with 40S ribosomal subunits and also with polysomes. RNAi-mediated depletion of AROS leads to deficient ribosome biogenesis with aberrant precursor ribosomal RNA processing, reduced 40S subunit ribosomal RNA and 40S ribosomal proteins (including RPS19). Together, this results in a reduction in 40S subunits and translating polysomes, correlating with reduced overall cellular protein synthesis. Interestingly, knockdown of AROS also results in a functionally significant increase in eIF2α phosphorylation. Overall, our results identify AROS as a factor with a role in both ribosome biogenesis and ribosomal function.
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Affiliation(s)
- John R P Knight
- Department of Biology, University of York, Wentworth Way, York, YO10 5DD, UK
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Saiselet M, Floor S, Tarabichi M, Dom G, Hébrant A, van Staveren WCG, Maenhaut C. Thyroid cancer cell lines: an overview. Front Endocrinol (Lausanne) 2012; 3:133. [PMID: 23162534 PMCID: PMC3499787 DOI: 10.3389/fendo.2012.00133] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 10/23/2012] [Indexed: 01/09/2023] Open
Abstract
Human thyroid cancer cell lines are the most used models for thyroid cancer studies. They must be used with detailed knowledge of their characteristics. These in vitro cell lines originate from differentiated and dedifferentiated in vivo human thyroid tumors. However, it has been shown that mRNA expression profiles of these cell lines were closer to dedifferentiated in vivo thyroid tumors (anaplastic thyroid carcinoma, ATC) than to differentiated ones. Here an overview of the knowledge of these models was made. The mutational status of six human thyroid cancer cell lines (WRO, FTC133, BCPAP, TPC1, K1, and 8505C) was in line with previously reported findings for 10 genes frequently mutated in thyroid cancer. However, the presence of a BRAF mutation (T1799A: V600E) in WRO questions the use of this cell line as a model for follicular thyroid carcinoma (FTC). Next, to investigate the biological meaning of the modulated mRNAs in these cells, a pathway analysis on previously obtained mRNA profiles was performed on five cell lines. In five cell lines, the MHC class II pathway was down-regulated and in four of them, ribosome biosynthesis and translation pathways were up-regulated. mRNA expression profiles of the cell lines were also compared to those of the different types of thyroid cancers. Three datasets originating from different microarray platforms and derived from distinct laboratories were used. This meta-analysis showed a significant higher correlation between the profiles of the thyroid cancer cell lines and ATC, than to differentiated thyroid tumors (i.e., PTC or FTC) specifically for DNA replication. This already observed higher correlation was obtained here with an increased number of in vivo tumors and using different platforms. In summary, this would suggest that some papillary thyroid carcinoma or follicular thyroid carcinoma (PTC or FTC) cell lines (i.e., TPC-1) might have partially lost their original DNA synthesis/replication regulation mechanisms during their in vitro cell adaptation/evolution.
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Affiliation(s)
- Manuel Saiselet
- School of Medicine, IRIBHM, Université Libre de BruxellesBrussels, Belgium
- *Correspondence: Manuel Saiselet, IRIBHM, Faculté de Médecine CP602, Université Libre de Bruxelles, Campus Erasme Bat. C, 4-177A, 808 Route de Lennik, 1070 Bruxelles, Belgium. e-mail:
| | - Sébastien Floor
- School of Medicine, IRIBHM, Université Libre de BruxellesBrussels, Belgium
| | - Maxime Tarabichi
- School of Medicine, IRIBHM, Université Libre de BruxellesBrussels, Belgium
| | - Geneviève Dom
- School of Medicine, IRIBHM, Université Libre de BruxellesBrussels, Belgium
| | - Aline Hébrant
- School of Medicine, IRIBHM, Université Libre de BruxellesBrussels, Belgium
| | | | - Carine Maenhaut
- School of Medicine, IRIBHM, Université Libre de BruxellesBrussels, Belgium
- Welbio - Université Libre de BruxellesBrussels, Belgium
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