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An G, Liu Y, Hou Y, Lei Y, Bai J, He L, Liu Y. RRP12 suppresses cell migration and invasion in colorectal cancer cell via regulation of epithelial-mesenchymal transition. J Gastrointest Oncol 2023; 14:2111-2123. [PMID: 37969827 PMCID: PMC10643574 DOI: 10.21037/jgo-23-254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/13/2023] [Indexed: 11/17/2023] Open
Abstract
Background The survival of patients with advanced colorectal cancer (CRC) is variable. The high rates of recurrence, metastasis, and drug resistance make clinical treatment difficult, which needs to further develop therapeutic and prognostic targets. Ribosomal RNA processing 12 homolog (RRP12), as a nucleolar protein involved in ribosome subunit maturation and export, plays important roles in cell cycle-related processes and the response to DNA damage, and regulates the occurrence and development of various cancers. The primary aim of this study was to identify the function of RRP12 in the process of epithelial-mesenchymal transition (EMT) in CRC. Methods In this study, the expression of RRP12 in tissue samples and the association with clinicopathological features in CRC was evaluated, and the correlation between RRP12 expression and aggressiveness of CRC was detected. After knockdown of RRP12 gene, the relationship between RRP12 and EMT-related indicators was verified in vivo and in vitro of CRC cells. Identification of RRP12-related genes and pathways through bioinformatic-based analyses was performed to find its potential mechanism. Results RRP12 is highly expressed in CRC cell lines and clinical samples and is associated with poor survival in CRC patients. RRP12 expression was positively associated with lymph node metastasis, tumor-node-metastasis (TNM) stage, and poor differentiation. Knockdown of RRP12 was found to suppress migration and invasion of CRC cells. RRP12 contributed to the EMT process of CRC cell lines in a ZEB1-mediated manner. RRP12 knockdown was found to reverse metastasis of CRC cells in vivo. Bioinformatic-based analyses indicated that RRP12 could serve as a potential biomarker for prognostic assessment of CRC patients. Conclusions RRP12 is involved in the tumorigenesis and metastasis of CRC by regulating the EMT process through ZEB1. Thus, RRP12 could be a potential therapeutic target for CRC therapy.
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Affiliation(s)
- Gaili An
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
- Department of Oncology, the First Affiliated Hospital of Xi’an Jiaotong University Xi’an, China
| | - Ying Liu
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Yinyin Hou
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Yu Lei
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Jun Bai
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Li He
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Yi Liu
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
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2
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Zhong W, Liu H, Li F, lin Y, Ye Y, Xu L, Li S, Chen H, Li C, Lin Y, Zhuang W, Lin Y, Wang Q. Elevated expression of LIF predicts a poor prognosis and promotes cell migration and invasion of clear cell renal cell carcinoma. Front Oncol 2022; 12:934128. [PMID: 35992780 PMCID: PMC9382297 DOI: 10.3389/fonc.2022.934128] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background Renal cell carcinoma (RCC) is the seventh most common cancer in humans, of which clear cell renal cell carcinoma (ccRCC) accounts for the majority. Recently, although there have been significant breakthroughs in the treatment of ccRCC, the prognosis of targeted therapy is still poor. Leukemia inhibitory factor (LIF) is a pleiotropic protein, which is overexpressed in many cancers and plays a carcinogenic role. In this study, we explored the expression and potential role of LIF in ccRCC. Methods The expression levels and prognostic effects of the LIF gene in ccRCC were detected using TCGA, GEO, ICGC, and ArrayExpress databases. The function of LIF in ccRCC was investigated using a series of cell function approaches. LIF-related genes were identified by weighted gene correlation network analysis (WGCNA). GO and KEGG analyses were performed subsequently. Cox univariate and LASSO analyses were used to develop risk signatures based on LIF-related genes, and the prognostic model was validated in the ICGC and E-MTAB-1980 databases. Then, a nomogram model was constructed for survival prediction and validation of ccRCC patients. To further explore the drug sensitivity between LIF-related genes, we also conducted a drug sensitivity analysis based on the GDSC database. Results The mRNA and protein expression levels of LIF were significantly increased in ccRCC patients. In addition, a high expression of LIF has a poor prognostic effect in ccRCC patients. LIF knockdown can inhibit the migration and invasion of ccRCC cells. By using WGCNA, 97 LIF-related genes in ccRCC were identified. Next, a prognostic risk prediction model including eight LIF-related genes (TOB2, MEPCE, LIF, RGS2, RND3, KLF6, RRP12, and SOCS3) was developed and validated. Survival analysis and ROC curve analysis indicated that the eight LIF-related-gene predictive model had good performance in evaluating patients’ prognosis in different subgroups of ccRCC. Conclusion Our study revealed that LIF plays a carcinogenic role in ccRCC. In addition, we firstly integrated multiple LIF-related genes to set up a risk-predictive model. The model could accurately predict the prognosis of ccRCC, which offers clinical implications for risk stratification, drug screening, and therapeutic decision.
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Affiliation(s)
- Wenting Zhong
- Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Hongxia Liu
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Feng Li
- Department of Pathology, Fujian Provincial Hospital, Fuzhou, China
| | - Youyu lin
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yan Ye
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Luyun Xu
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - ShengZhao Li
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Hui Chen
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Chengcheng Li
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Yuxuan Lin
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Wei Zhuang
- Department of Urology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China
- *Correspondence: Qingshui Wang, ; Yao Lin, ; ; Wei Zhuang,
| | - Yao Lin
- Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- *Correspondence: Qingshui Wang, ; Yao Lin, ; ; Wei Zhuang,
| | - Qingshui Wang
- Central Laboratory at the Second Affiliated Hospital of Fujian Traditional Chinese Medical University, Fujian-Macao Science and Technology Cooperation Base of Traditional Chinese Medicine-Oriented Chronic Disease Prevention and Treatment, Innovation and Transformation Center, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- College of Life Sciences, Fujian Normal University, Fuzhou, China
- *Correspondence: Qingshui Wang, ; Yao Lin, ; ; Wei Zhuang,
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3
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Wei C, Wang B, Chen ZH, Xiao H, Tang L, Guan JF, Yuan RF, Yu X, Hu ZG, Wu HJ, Dai Z, Wang K. Validating RRP12 Expression and Its Prognostic Significance in HCC Based on Data Mining and Bioinformatics Methods. Front Oncol 2022; 12:812009. [PMID: 35178347 PMCID: PMC8844371 DOI: 10.3389/fonc.2022.812009] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/11/2022] [Indexed: 12/26/2022] Open
Abstract
RRP12 (ribosomal RNA processing 12 homolog) is a nucleolar protein involved in the maturation and transport of eukaryotic ribosomal subunits and is a type of RNA binding protein. In recent years, considerable research has indicated that RRP12 is associated with the occurrence and development of multiple cancers. However, there is no research on RRP12 in hepatocellular carcinoma. Herein, we aimed to explore the role and significance of RRP12 in hepatocellular carcinoma.We used the TIMER and GEPIA databases to perform pan-cancer analyses of RRP12. The impact of RRP12 on the prognosis was analyzed through the GEPIA database. The relationship between RRP12 and immune cell infiltration was investigated by TIMER and GEPIA databases. Moreover, the expression of RRP12 in various liver cancer cells was evaluated by Western Blot to determine the cell line for the next experiment. Scratch test, Transwell test, and Edu tests were applied to validate the effects of RRP12 on the function of liver cancer cells. And the data were statistically analyzed.Pan-cancer analysis found that RPP12 was significantly upregulated in many cancers. Moreover, the prognostic analysis revealed that the difference in the expression of RRP12 has statistical significance for the overall survival rate and disease-free survival rate of liver cancer patients. In order to analyze the correlation between the expression level of RRP12 and clinical parameters, it was found that there was a significant negative correlation with tumor stage, tumor grade and tumor size. Univariate and multivariate analysis showed that RRP12 could be used as an independent prognostic factor for patients with hepatocellular carcinoma. Cellular experiments have proved that knocking down RRP12 can inhibit the proliferation, invasion, and metastasis of liver cancer cells.Therefore, RRP12 significantly affects the occurrence and development of HCC. Hence, RRP12 can become a potential target and prognostic biomarker for the treatment of hepatocellular carcinoma.
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Affiliation(s)
- Chao Wei
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China
| | - Ben Wang
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China
| | - Zhong-Huo Chen
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China
| | - Han Xiao
- Department of Hepato-Biliary-Pancreatic Surgery, Jiujiang First People's Hospital, Jiujiang, China
| | - Lei Tang
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Key Laboratory of Molecular Medicine, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China
| | - Jia-Fu Guan
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China
| | - Rong-Fa Yuan
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Provincial Clinical Research Center for General Surgery Disease, Nanchang, China
| | - Xin Yu
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Provincial Clinical Research Center for General Surgery Disease, Nanchang, China
| | - Zhi-Gang Hu
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Provincial Clinical Research Center for General Surgery Disease, Nanchang, China
| | - Hua-Jun Wu
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Provincial Clinical Research Center for General Surgery Disease, Nanchang, China
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Kai Wang
- Hepato-Biliary-Pancreatic Surgery Division, Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Province Engineering Research Center of Hepatobiliary Disease, Nanchang, China.,Second Affiliated Hospital of Nanchang University, Jiangxi Provincial Clinical Research Center for General Surgery Disease, Nanchang, China
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4
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Nieto B, Gaspar SG, Moriggi G, Pestov DG, Bustelo XR, Dosil M. Identification of distinct maturation steps involved in human 40S ribosomal subunit biosynthesis. Nat Commun 2020; 11:156. [PMID: 31919354 PMCID: PMC6952385 DOI: 10.1038/s41467-019-13990-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 12/11/2019] [Indexed: 02/02/2023] Open
Abstract
Technical problems intrinsic to the purification of preribosome intermediates have limited our understanding of ribosome biosynthesis in humans. Addressing this issue is important given the implication of this biological process in human disease. Here we report a preribosome purification and tagging strategy that overcomes some of the existing technical difficulties. Using these tools, we find that the pre-40S precursors go through two distinct maturation phases inside the nucleolus and follow a regulatory step that precedes late maturation in the cytoplasm. This regulatory step entails the intertwined actions of both PARN (a metazoan-specific ribonuclease) and RRP12 (a phylogenetically conserved 40S biogenesis factor that has acquired additional functional features in higher eukaryotes). Together, these results demonstrate the usefulness of this purification method for the dissection of ribosome biogenesis in human cells. They also identify distinct maturation stages and metazoan-specific regulatory mechanisms involved in the generation of the human 40S ribosomal subunit. Ribosome synthesis is a complex multi-step process. Here the authors present a method that allows the efficient isolation and characterization of the preribosomal complexes formed along the entire ribosome synthesis pathway in human cells.
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Affiliation(s)
- Blanca Nieto
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Sonia G Gaspar
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Giulia Moriggi
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Dimitri G Pestov
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08084, USA
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Mercedes Dosil
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), CSIC-University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain. .,Departamento de Bioquímica y Biología Molecular, University of Salamanca, Campus Unamuno, 37007, Salamanca, Spain.
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5
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Iacovella MG, Bremang M, Basha O, Giacò L, Carotenuto W, Golfieri C, Szakal B, Dal Maschio M, Infantino V, Beznoussenko GV, Joseph CR, Visintin C, Mironov AA, Visintin R, Branzei D, Ferreira-Cerca S, Yeger-Lotem E, De Wulf P. Integrating Rio1 activities discloses its nutrient-activated network in Saccharomyces cerevisiae. Nucleic Acids Res 2019; 46:7586-7611. [PMID: 30011030 PMCID: PMC6125641 DOI: 10.1093/nar/gky618] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 06/28/2018] [Indexed: 12/14/2022] Open
Abstract
The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subunit biogenesis and has not been characterized globally. We show that Rio1 manages directly and via a series of regulators, an essential signaling network at the protein, chromatin and RNA levels. Rio1 orchestrates growth and division depending on resource availability, in parallel to the nutrient-activated Tor1 kinase. To define the Rio1 network, we identified its physical interactors, profiled its target genes/transcripts, mapped its chromatin-binding sites and integrated our data with yeast’s protein–protein and protein–DNA interaction catalogs using network computation. We experimentally confirmed network components and localized Rio1 also to mitochondria and vacuoles. Via its network, Rio1 commands protein synthesis (ribosomal gene expression, assembly and activity) and turnover (26S proteasome expression), and impinges on metabolic, energy-production and cell-cycle programs. We find that Rio1 activity is conserved to humans and propose that pathological RIOK1 may fuel promiscuous transcription, ribosome production, chromosomal instability, unrestrained metabolism and proliferation; established contributors to cancer. Our study will advance the understanding of numerous processes, here revealed to depend on Rio1 activity.
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Affiliation(s)
- Maria G Iacovella
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Michael Bremang
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Current address: Proteome Sciences Plc, Hamilton House, Mabledon Place, London, United Kingdom
| | - Omer Basha
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Luciano Giacò
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Walter Carotenuto
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Cristina Golfieri
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Barnabas Szakal
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Marianna Dal Maschio
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Valentina Infantino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Galina V Beznoussenko
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Chinnu R Joseph
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Clara Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Alexander A Mironov
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy
| | - Rosella Visintin
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Dana Branzei
- The FIRC Institute of Molecular Oncology (IFOM), Via Adamello 16, 20139 Milan, Italy.,Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Via Abbiategrasso 207, 27100 Pavia, Italy
| | - Sébastien Ferreira-Cerca
- Lehrstuhl für Biochemie III, Universität Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany
| | - Esti Yeger-Lotem
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, POB 653, Beer-Sheva 84105, Israel
| | - Peter De Wulf
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139 Milan, Italy.,Centre for Integrative Biology (CIBIO), University of Trento, Via Sommarive 9, 38123 Trento, Italy
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6
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Monteiro LF, Forti FL. Network analysis of DUSP12 partners in the nucleus under genotoxic stress. J Proteomics 2019; 197:42-52. [PMID: 30779967 DOI: 10.1016/j.jprot.2019.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/23/2019] [Accepted: 02/12/2019] [Indexed: 01/01/2023]
Abstract
Dual Specificity Phosphatase 12 is a member of the Atypical DUSP Protein Tyrosine Phosphatase family, meaning that it does not contain typical MAP kinase targeting motifs, while being able to dephosphorylate tyrosine and serine/threonine residues. DUSP12 contains, apart from its catalytic domain, a zinc finger domain, making it one of the largest DUSPs, which displays strong nuclear expression in several tissues. In this work we identified nuclear targets of DUSP12 in two different cancer cell lines (A549 and MCF-7), challenging them with genotoxic stimuli to observe the effect on the networks and to link existing information about DUSP12 functions to the data obtained though mass spectrometry. We found network connections to the cytoskeleton (e.g. IQGAP1), to the chromatin (e.g. HP1BP3), to the splicing machinery and to the previously known pathway of ribosome maturation (e.g. TCOF1), which draw insight into many of the functions of this phosphatase, much likely connecting it to distinct, previously unknown genomic stability mechanisms.
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Affiliation(s)
- Lucas Falcão Monteiro
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Fábio Luís Forti
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
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7
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The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules. Int J Mol Sci 2019; 20:ijms20010140. [PMID: 30609737 PMCID: PMC6337102 DOI: 10.3390/ijms20010140] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/21/2018] [Accepted: 12/23/2018] [Indexed: 12/18/2022] Open
Abstract
We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.
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8
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Moriggi G, Gaspar SG, Nieto B, Bustelo XR, Dosil M. Focal accumulation of preribosomes outside the nucleolus during metaphase-anaphase in budding yeast. RNA (NEW YORK, N.Y.) 2017; 23:1432-1443. [PMID: 28588079 PMCID: PMC5558912 DOI: 10.1261/rna.061259.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
Saccharomyces cerevisiae contains one nucleolus that remains intact in the mother-cell side of the nucleus throughout most of mitosis. Based on this, it is assumed that the bulk of ribosome production during cell division occurs in the mother cell. Here, we show that the ribosome synthesis machinery localizes not only in the nucleolus but also at a center that is present in the bud side of the nucleus after the initiation of mitosis. This center can be visualized by live microscopy as a punctate body located in close proximity to the nuclear envelope and opposite to the nucleolus. It contains ribosomal DNA (rDNA) and precursors of both 40S and 60S ribosomal subunits. Proteins that actively participate in ribosome synthesis, but not functionally defective variants, accumulate in that site. The formation of this body occurs in the metaphase-to-anaphase transition when discrete regions of rDNA occasionally exit the nucleolus and move into the bud. Collectively, our data unveil the existence of a previously unknown mechanism for preribosome accumulation at the nuclear periphery in budding yeast. We propose that this might be a strategy to expedite the delivery of ribosomes to the growing bud.
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Affiliation(s)
- Giulia Moriggi
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - Sonia G Gaspar
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - Blanca Nieto
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Centro de Investigación del Cáncer, 37007 Salamanca, Spain
| | - Mercedes Dosil
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, University of Salamanca, 37007 Salamanca, Spain
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Wu T, Ren MX, Chen GP, Jin ZM, Wang G. Rrp15 affects cell cycle, proliferation, and apoptosis in NIH3T3 cells. FEBS Open Bio 2016; 6:1085-1092. [PMID: 27833849 PMCID: PMC5095146 DOI: 10.1002/2211-5463.12128] [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: 03/29/2016] [Revised: 07/27/2016] [Accepted: 09/08/2016] [Indexed: 11/06/2022] Open
Abstract
Riken 2810430M08 (hereinafter referred to as Rrp15) is a newly identified and reported gene from the mouse genome. In our previous work, we found that the gene had a relationship with the proliferation and activation of T cells. Rrp15 protein is highly homologous with RRP15 (budding yeast), which has an important role in ribosomal RNA processing. We explored the potential function of Rrp15 in apoptosis, cell proliferation, and its involvement with RNA in the nucleus. We constructed a knockdown of the Rrp15 gene in NIH3T3 cells and then performed real-time PCR, western blotting, flow cytometry, and immunofluorescence to determine the function of the Rrp15 gene. Knockdown of the Rrp15 gene suppresses proliferation and induces apoptosis. We also found that the Rrp15 protein was normally distributed in the nucleus and bound to RNA or pre-RNA in the nucleus. Additionally, Rrp15 altered the activity of the 20S proteasome. Rrp15 promotes proliferation and inhibits apoptosis in NIH3T3 cells and may have a relationship with RNA in the nucleus.
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Affiliation(s)
- Tao Wu
- Department of Cardiology The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Mei-Xia Ren
- Department of Cardiology The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Guo-Ping Chen
- Department of Endocrinology The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Zheng-Ming Jin
- Department of Cardiology The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Gang Wang
- Cancer Institute of Integrative Medicine Tongde Hospital of Zhejiang Province Zhejiang Provincial Academy of Traditional Chinese Medicine Hangzhou China
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RRP12 is a crucial nucleolar protein that regulates p53 activity in osteosarcoma cells. Tumour Biol 2015; 37:4351-8. [PMID: 26499779 DOI: 10.1007/s13277-015-4062-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/04/2015] [Indexed: 10/22/2022] Open
Abstract
RRP12 (ribosomal RNA processing 12 homolog), a nucleolar protein, plays important roles in cell cycle progression and the response to deoxyribonucleic acid (DNA) damage in yeast cells. However, its role has not been investigated in mammalian cells that possess p53, which has close functional association to nucleolus. We explored the role of RRP12 in nucleolar stress condition using an osteosarcoma cell line, U2OS. To induce DNA damage and nucleolar disruption, two cytotoxic drugs, doxorubicin and actinomycin D were used. Cytotoxic stress resulted nucleolar disruption induced cell cycle arrest and apoptosis in U2OS cells. However, RRP12 overexpression promoted resistance to cytotoxic stress. In contrast, RRP12 silencing enhanced susceptibility to cytotoxic stress. During drug treatment, p53 activity and cell death were suppressed by RRP12 overexpression but promoted by RRP12 silencing. This study demonstrated that RRP12 was crucial for cell survival during cytotoxic stress via the repression of p53 stability. Thus, targeting RRP12 may enhance chemotherapeutic effect in cancers.
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11
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Moriggi G, Nieto B, Dosil M. Rrp12 and the Exportin Crm1 participate in late assembly events in the nucleolus during 40S ribosomal subunit biogenesis. PLoS Genet 2014; 10:e1004836. [PMID: 25474739 PMCID: PMC4256259 DOI: 10.1371/journal.pgen.1004836] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/17/2014] [Indexed: 11/20/2022] Open
Abstract
During the biogenesis of small ribosomal subunits in eukaryotes, the pre-40S particles formed in the nucleolus are rapidly transported to the cytoplasm. The mechanisms underlying the nuclear export of these particles and its coordination with other biogenesis steps are mostly unknown. Here we show that yeast Rrp12 is required for the exit of pre-40S particles to the cytoplasm and for proper maturation dynamics of upstream 90S pre-ribosomes. Due to this, in vivo elimination of Rrp12 leads to an accumulation of nucleoplasmic 90S to pre-40S transitional particles, abnormal 35S pre-rRNA processing, delayed elimination of processing byproducts, and no export of intermediate pre-40S complexes. The exportin Crm1 is also required for the same pre-ribosome maturation events that involve Rrp12. Thus, in addition to their implication in nuclear export, Rrp12 and Crm1 participate in earlier biosynthetic steps that take place in the nucleolus. Our results indicate that, in the 40S subunit synthesis pathway, the completion of early pre-40S particle assembly, the initiation of byproduct degradation and the priming for nuclear export occur in an integrated manner in late 90S pre-ribosomes.
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Affiliation(s)
- Giulia Moriggi
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (IBMCC), CSIC-University of Salamanca, Salamanca, Spain
| | - Blanca Nieto
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (IBMCC), CSIC-University of Salamanca, Salamanca, Spain
| | - Mercedes Dosil
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (IBMCC), CSIC-University of Salamanca, Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, University of Salamanca, Salamanca, Spain
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