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Bourgeois G, Ney M, Gaspar I, Aigueperse C, Schaefer M, Kellner S, Helm M, Motorin Y. Eukaryotic rRNA Modification by Yeast 5-Methylcytosine-Methyltransferases and Human Proliferation-Associated Antigen p120. PLoS One 2015. [PMID: 26196125 PMCID: PMC4510066 DOI: 10.1371/journal.pone.0133321] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Modified nucleotide 5-methylcytosine (m5C) is frequently present in various eukaryotic RNAs, including tRNAs, rRNAs and in other non-coding RNAs, as well as in mRNAs. RNA:m5C-methyltranferases (MTases) Nop2 from S. cerevisiae and human proliferation-associated nucleolar antigen p120 are both members of a protein family called Nop2/NSUN/NOL1. Protein p120 is well-known as a tumor marker which is over-expressed in various cancer tissues. Using a combination of RNA bisulfite sequencing and HPLC-MS/MS analysis, we demonstrated here that p120 displays an RNA:m5C- MTase activity, which restores m5C formation at position 2870 in domain V of 25S rRNA in a nop2Δ yeast strain. We also confirm that yeast proteins Nop2p and Rcm1p catalyze the formation of m5C in domains V and IV, respectively. In addition, we do not find any evidence of m5C residues in yeast 18S rRNA. We also performed functional complementation of Nop2-deficient yeasts by human p120 and studied the importance of different sequence and structural domains of Nop2 and p120 for yeast growth and m5C-MTase activity. Chimeric protein formed by Nop2 and p120 fragments revealed the importance of Nop2 N-terminal domain for correct protein localization and its cellular function. We also validated that the presence of Nop2, rather than the m5C modification in rRNA itself, is required for pre-rRNA processing. Our results corroborate that Nop2 belongs to the large family of pre-ribosomal proteins and possesses two related functions in pre-rRNA processing: as an essential factor for cleavages and m5C:RNA:modification. These results support the notion of quality control during ribosome synthesis by such modification enzymes.
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Affiliation(s)
- Gabrielle Bourgeois
- Laboratoire IMoPA, UMR 7365 UL-CNRS, BioPole de UL, Vandoeuvre-les-Nancy, France
| | - Michel Ney
- Laboratoire IMoPA, UMR 7365 UL-CNRS, BioPole de UL, Vandoeuvre-les-Nancy, France
| | - Imre Gaspar
- EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | | | - Matthias Schaefer
- Division of Epigenetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefanie Kellner
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Yuri Motorin
- Laboratoire IMoPA, UMR 7365 UL-CNRS, BioPole de UL, Vandoeuvre-les-Nancy, France
- * E-mail:
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52
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Khoddami V, Yerra A, Cairns BR. Experimental Approaches for Target Profiling of RNA Cytosine Methyltransferases. Methods Enzymol 2015; 560:273-96. [PMID: 26253975 DOI: 10.1016/bs.mie.2015.03.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA cytosine methyltransferases (m(5)C-RMTs) constitute an important class of RNA-modifying enzymes, methylating specific cytosines within particular RNA targets in both coding and noncoding RNAs. Almost all organisms express at least one m(5)C-RMT, and vertebrates often express different types or variants of m(5)C-RMTs in different cell types. Deletion or mutation of particular m(5)C-RMTs is connected to severe pathological manifestations ranging from developmental defects to infertility and mental retardation. Some m(5)C-RMTs show spatiotemporal patterns of expression and activity requiring careful experimental design for their analysis in order to capture their context-dependent targets. An essential step for understanding the functions of both the enzymes and the modified cytosines is defining the one-to-one connection between particular m(5)C-RMTs and their target cytosines. Recent technological and methodological advances have provided researchers with new tools to comprehensively explore RNA cytosine methylation and methyltransferases. Here, we describe three complementary approaches applicable for both discovery and validation of candidate target sites of specific m(5)C-RMTs.
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Affiliation(s)
- Vahid Khoddami
- HHMI, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA; Current address: Department of Cell Biology, Howard Hughes Medical Institute, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Archana Yerra
- HHMI, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Bradley R Cairns
- HHMI, Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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53
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Abstract
Modified RNA molecules have recently been shown to regulate nervous system functions. This mini-review and associated mini-symposium provide an overview of the types and known functions of novel modified RNAs in the nervous system, including covalently modified RNAs, edited RNAs, and circular RNAs. We discuss basic molecular mechanisms involving RNA modifications as well as the impact of modified RNAs and their regulation on neuronal processes and disorders, including neural fate specification, intellectual disability, neurodegeneration, dopamine neuron function, and substance use disorders.
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54
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Blanco S, Frye M. Role of RNA methyltransferases in tissue renewal and pathology. Curr Opin Cell Biol 2014; 31:1-7. [PMID: 25014650 PMCID: PMC4238901 DOI: 10.1016/j.ceb.2014.06.006] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 06/13/2014] [Indexed: 12/13/2022]
Abstract
Over the last five decades more than 100 types of RNA modifications have been identified in organism of all kingdoms of life, yet their function and biological relevance remain largely elusive. The recent development of transcriptome-wide techniques to detect RNA modifications such as N(6)-methyladenosine (m(6)A) and 5-methylcytidine (m(5)C) has not only created a new field of research 'the epitranscriptome' but also featured essential regulatory roles of RNA methylation in a wide range of fundamental cellular processes. Here, we discuss the current knowledge of m(6)A and m(5)C RNA methylation pathways and summarize how they impact normal tissues and contribute to human disease.
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Affiliation(s)
- Sandra Blanco
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom
| | - Michaela Frye
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, United Kingdom.
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55
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Okamoto M, Fujiwara M, Hori M, Okada K, Yazama F, Konishi H, Xiao Y, Qi G, Shimamoto F, Ota T, Temme A, Tatsuka M. tRNA modifying enzymes, NSUN2 and METTL1, determine sensitivity to 5-fluorouracil in HeLa cells. PLoS Genet 2014; 10:e1004639. [PMID: 25233213 PMCID: PMC4169382 DOI: 10.1371/journal.pgen.1004639] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Accepted: 07/30/2014] [Indexed: 11/18/2022] Open
Abstract
Nonessential tRNA modifications by methyltransferases are evolutionarily conserved and have been reported to stabilize mature tRNA molecules and prevent rapid tRNA decay (RTD). The tRNA modifying enzymes, NSUN2 and METTL1, are mammalian orthologs of yeast Trm4 and Trm8, which are required for protecting tRNA against RTD. A simultaneous overexpression of NSUN2 and METTL1 is widely observed among human cancers suggesting that targeting of both proteins provides a novel powerful strategy for cancer chemotherapy. Here, we show that combined knockdown of NSUN2 and METTL1 in HeLa cells drastically potentiate sensitivity of cells to 5-fluorouracil (5-FU) whereas heat stress of cells revealed no effects. Since NSUN2 and METTL1 are phosphorylated by Aurora-B and Akt, respectively, and their tRNA modifying activities are suppressed by phosphorylation, overexpression of constitutively dephosphorylated forms of both methyltransferases is able to suppress 5-FU sensitivity. Thus, NSUN2 and METTL1 are implicated in 5-FU sensitivity in HeLa cells. Interfering with methylation of tRNAs might provide a promising rationale to improve 5-FU chemotherapy of cancer. The cellular mechanisms for sensing and responding to stress on nucleic acid metabolism or to genotoxic stress are the fundamental and ancient evolutionary biological activities with conserved and diverse biological functions. In yeast, hypomodified mature tRNA species are rapidly decayed under heat stress by the RTD pathway. Yet, it has been shown that tRNA-specific methyltransferases Trm4 and Trm8 protect from tRNA decay. 5-FU, a pyrimidine analog used for cancer treatment, is generally known to act as a thymidylate synthase inhibitor although other ways for the mechanisms of action are suggested. We studied NSUN2 and METTL1, the human orthologs of Trm4 and Trm8 in yeast, and demonstrated that these RTD-related tRNA modifying enzymes are involved in 5-FU sensitivity in cervical cancer HeLa cells. We conclude that the evolutionarily conserved regulation of tRNA modifications is a potential mechanism of chemotherapy resistance in cancer cells.
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Affiliation(s)
- Mayumi Okamoto
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shoubara, Hiroshima, Japan
| | - Mamoru Fujiwara
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shoubara, Hiroshima, Japan
| | - Masato Hori
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shoubara, Hiroshima, Japan
| | - Kaoru Okada
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shoubara, Hiroshima, Japan
| | - Futoshi Yazama
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shoubara, Hiroshima, Japan
| | - Hiroaki Konishi
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shoubara, Hiroshima, Japan
| | - Yegui Xiao
- Department of Management Information Systems, Faculty of Management and Information System, Prefectural University of Hiroshima, Minami-ku, Hiroshima, Japan
| | - Guangying Qi
- Department of Health Sciences, Faculty of Human Culture and Science, Prefectural University of Hiroshima, Minami-ku, Hiroshima, Japan
| | - Fumio Shimamoto
- Department of Health Sciences, Faculty of Human Culture and Science, Prefectural University of Hiroshima, Minami-ku, Hiroshima, Japan
| | - Takahide Ota
- Department of Life Science, Medical Research Institute, Kanazawa Medical University, Uchinada, Ishikawa, Japan
| | - Achim Temme
- Department of Neurosurgery, University Hospital Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Masaaki Tatsuka
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shoubara, Hiroshima, Japan
- * E-mail:
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56
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Torres AG, Batlle E, Ribas de Pouplana L. Role of tRNA modifications in human diseases. Trends Mol Med 2014; 20:306-14. [PMID: 24581449 DOI: 10.1016/j.molmed.2014.01.008] [Citation(s) in RCA: 298] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/17/2014] [Accepted: 01/23/2014] [Indexed: 12/22/2022]
Abstract
Transfer RNAs (tRNAs) are key for efficient and accurate protein translation. To be fully active, tRNAs need to be heavily modified post-transcriptionally. Growing evidence indicates that tRNA modifications and the enzymes catalyzing such modifications may play important roles in complex human pathologies. Here, we have compiled current knowledge that directly link tRNA modifications to human diseases such as cancer, type 2 diabetes (T2D), neurological disorders, and mitochondrial-linked disorders. The molecular mechanisms behind these connections remain, for the most part, unknown. As we progress towards the understanding of the roles played by hypomodified tRNAs in human disease, novel areas of therapeutic intervention may be discovered.
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Affiliation(s)
- Adrian Gabriel Torres
- Institute for Research in Biomedicine (IRB), Parc Cientific de Barcelona, 08028 Catalunya, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB), Parc Cientific de Barcelona, 08028 Catalunya, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010 Catalunya, Spain
| | - Lluis Ribas de Pouplana
- Institute for Research in Biomedicine (IRB), Parc Cientific de Barcelona, 08028 Catalunya, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010 Catalunya, Spain.
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57
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Khoddami V, Cairns BR. Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP. Nat Protoc 2014; 9:337-61. [PMID: 24434802 DOI: 10.1038/nprot.2014.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Cytosine methylation within RNA is common, but its full scope and functions are poorly understood, as the RNA targets of most mammalian cytosine RNA methyltransferases (m(5)C-RMTs) remain uncharacterized. To enable their characterization, we developed a mechanism-based method for transcriptome-wide m(5)C-RMT target profiling. All characterized mammalian m(5)C-RMTs form a reversible covalent intermediate with their cytosine substrate-a covalent linkage that is trapped when conducted on the cytosine analog 5-azacytidine (5-aza-C). We used this property to develop Aza-immunoprecipitation (Aza-IP), a methodology to form stable m(5)C-RMT-RNA linkages in cell culture, followed by IP and high-throughput sequencing, to identify direct RNA substrates of m(5)C-RMTs. Remarkably, a cytosine-to-guanine (C→G) transversion occurs specifically at target cytosines, allowing the simultaneous identification of the precise target cytosine within each RNA. Thus, Aza-IP reports only direct RNA substrates and the C→G transversion provides an important criterion for target cytosine identification, which is not available in alternative approaches. Here we present a step-by-step protocol for Aza-IP and downstream analysis, designed to reveal identification of substrate RNAs and precise cytosine targets of m(5)C-RMTs. The entire protocol takes 40-50 d to complete.
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Affiliation(s)
- Vahid Khoddami
- Howard Hughes Medical Institute (HHMI), Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute (HHMI), Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah, USA
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58
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Hussain S, Aleksic J, Blanco S, Dietmann S, Frye M. Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biol 2013; 14:215. [PMID: 24286375 PMCID: PMC4053770 DOI: 10.1186/gb4143] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The post-transcriptional modification 5-methylcytosine (m5C) occurs in a wide range of coding and non-coding RNAs. We describe transcriptome-wide approaches to capture the global m5C RNA methylome. We also discuss the potential functions of m5C in RNA and compare them to 6-methyladenosine modifications.
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Affiliation(s)
- Shobbir Hussain
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Jelena Aleksic
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Sandra Blanco
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Sabine Dietmann
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Michaela Frye
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
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59
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Xhemalce B. From histones to RNA: role of methylation in cancer. Brief Funct Genomics 2013; 12:244-53. [DOI: 10.1093/bfgp/els064] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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60
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Grigoriadis A, Mackay A, Noel E, Wu PJ, Natrajan R, Frankum J, Reis-Filho JS, Tutt A. Molecular characterisation of cell line models for triple-negative breast cancers. BMC Genomics 2012; 13:619. [PMID: 23151021 PMCID: PMC3546428 DOI: 10.1186/1471-2164-13-619] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 10/31/2012] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Triple-negative breast cancers (BC) represent a heterogeneous subtype of BCs, generally associated with an aggressive clinical course and where targeted therapies are currently limited. Target validation studies for all BC subtypes have largely employed established BC cell lines, which have proven to be effective tools for drug discovery. RESULTS Given the lines of evidence suggesting that BC cell lines are effective tools for drug discovery, we assessed the similarities between triple-negative BCs and cell lines, to identify in vitro representatives, modelling the diversity within this BC subtype. 25 BC cell lines, enriched for those lacking ER, PR and HER2 expression, were subjected to transcriptomic, genomic and epigenomic profiling analyses and comparisons were made to existing knowledge of corresponding perturbations in triple-negative BCs. Transcriptional analysis segregated ER-negative BC cell lines into three groups, displaying distinctive abundances for genes involved in epithelial-mesenchymal transition, apocrine and high-grade carcinomas. DNA copy number aberrations of triple-negative BCs were well represented in cell lines and genes with coordinately altered gene expression showed similar patterns in tumours and cell lines. Methylation events in triple-negative BCs were mostly retained in epigenomes of cell lines. Combined methylation and gene expression analyses revealed a subset of genes characteristic of the Claudin-low BC subtype, exhibiting epigenetic-regulated gene expression in BC cell lines and tumours, suggesting that methylation patterns are likely to underpin subtype-specificity. CONCLUSION Here, we provide a comprehensive analysis of triple-negative BC features on several molecular levels in BC cell lines, thereby creating an in-depth resource to access the suitability of individual lines as experimental models for studying BC tumour biology, biomarkers and possible therapeutic targets in the context of preclinical target validation.
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Affiliation(s)
- Anita Grigoriadis
- Breakthrough Breast Cancer Research Unit, Guy's Hospital, King's Health Partners AHSC, King's College London School of Medicine, London SE1 9RT, UK.
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61
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Agboola AJ, Musa AA, Wanangwa N, Abdel-Fatah T, Nolan CC, Ayoade BA, Oyebadejo TY, Banjo AA, Deji-Agboola AM, Rakha EA, Green AR, Ellis IO. Molecular characteristics and prognostic features of breast cancer in Nigerian compared with UK women. Breast Cancer Res Treat 2012; 135:555-69. [PMID: 22842985 DOI: 10.1007/s10549-012-2173-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 07/16/2012] [Indexed: 01/19/2023]
Abstract
Although breast cancer (BC) incidence is lower in African-American women compared with White-American, in African countries such as Nigeria, BC is a common disease. Nigerian women have a higher risk for early-onset, with a high mortality rate from BC, prompting speculation that risk factors could be genetic and the molecular portrait of these tumours are different to those of western women. In this study, 308 BC samples from Nigerian women with complete clinical history and tumour characteristics were included and compared with a large series of BC from the UK as a control group. Immunoprofile of these tumours was characterised using a panel of 11 biomarkers of known relevance to BC. The immunoprofile and patients' outcome were compared with tumour grade-matched UK control group. Nigerian women presenting with BC were more frequently premenopausal, and their tumours were characterised by large primary tumour size, high tumour grade, advanced lymph node stage, and a higher rate of vascular invasion compared with UK women. In the grade-matched groups, Nigerian BC showed over representation of triple-negative and basal phenotypes and BRCA1 deficiency BC compared with UK women, but no difference was found regarding HER2 expression between the two series. Nigerian women showed significantly poorer outcome after development of BC compared with UK women. This study demonstrates that there are possible genetic and molecular differences between an indigenous Black population and a UK-based series. The basal-like, triple negative and BRCA1 dysfunction groups of tumours identified in this study may have implications in the development of screening programs and therapies for African patients and families that are likely to have a BRCA1 dysfunction, basal like and triple negative.
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Affiliation(s)
- A J Agboola
- Division of Pathology, School of Molecular Medical Sciences, University Hospitals and University of Nottingham, Nottingham, UK.
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62
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Towns WL, Begley TJ. Transfer RNA methytransferases and their corresponding modifications in budding yeast and humans: activities, predications, and potential roles in human health. DNA Cell Biol 2012; 31:434-54. [PMID: 22191691 PMCID: PMC3322404 DOI: 10.1089/dna.2011.1437] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 11/07/2011] [Accepted: 11/11/2011] [Indexed: 12/13/2022] Open
Abstract
Throughout the kingdoms of life, transfer RNA (tRNA) undergoes over 100 enzyme-catalyzed, methyl-based modifications. Although a majority of the methylations are conserved from bacteria to mammals, the functions of a number of these modifications are unknown. Many of the proteins responsible for tRNA methylation, named tRNA methyltransferases (Trms), have been characterized in Saccharomyces cerevisiae. In contrast, only a few human Trms have been characterized. A BLAST search for human homologs of each S. cerevisiae Trm revealed a total of 34 human proteins matching our search criteria for an S. cerevisiae Trm homolog candidate. We have compiled a database cataloging basic information about each human and yeast Trm. Every S. cerevisiae Trm has at least one human homolog, while several Trms have multiple candidates. A search of cancer cell versus normal cell mRNA expression studies submitted to Oncomine found that 30 of the homolog genes display a significant change in mRNA expression levels in at least one data set. While 6 of the 34 human homolog candidates have confirmed tRNA methylation activity, the other candidates remain uncharacterized. We believe that our database will serve as a resource for investigating the role of human Trms in cellular stress signaling.
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Affiliation(s)
- William L. Towns
- College of Nanoscale Science and Engineering, University at Albany, Albany, New York
| | - Thomas J. Begley
- College of Nanoscale Science and Engineering, University at Albany, Albany, New York
- RNA Institute, University at Albany, Rensselaer, New York
- Cancer Research Center, University at Albany, Rensselaer, New York
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63
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Okamoto M, Hirata S, Sato S, Koga S, Fujii M, Qi G, Ogawa I, Takata T, Shimamoto F, Tatsuka M. Frequent increased gene copy number and high protein expression of tRNA (cytosine-5-)-methyltransferase (NSUN2) in human cancers. DNA Cell Biol 2011; 31:660-71. [PMID: 22136356 DOI: 10.1089/dna.2011.1446] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
NSUN2, also known as SAKI or MISU, is a methyltransferase which catalyses (cytosine-5-)-methylation of tRNA. The human NSUN2 gene is located on chromosome 5p15.31-33. We show that NSUN2 gene copy number is increased in oral and colorectal cancers. Protein expression levels of NSUN2 were determined by immunoblot using novel polyclonal antibodies raised against a synthetic peptide corresponding to the C-terminal region of the protein. In most normal tissues, NSUN2 expression levels were extremely low. On the other hand, oral and colorectal cancers typically expressed high levels of NSUN2. The level of NSUN2 was similar in interphase and mitotic cells, and immunohistochemical analysis demonstrated strong staining for NSUN2 in oral and colon cancer tissues when compared with normal tissues, providing a distinct diagnostic significance for NSUN2 in comparison with Ki-67, a widely used marker of actively proliferating cells. In addition, elevated protein expression of NSUN2 was confirmed by immunohistochemical analysis of various cancers including esophageal, stomach, liver, pancreas, uterine cervix, prostate, kidney, bladder, thyroid, and breast cancers. NSUN2 is regulated by Aurora-B, a newly developed molecular target for cancer therapy, leading us to propose that NSUN2 might become a valuable target for cancer therapy and a cancer diagnostic marker.
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Affiliation(s)
- Mayumi Okamoto
- Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shoubara, Japan
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64
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Kuratani M, Hirano M, Goto-Ito S, Itoh Y, Hikida Y, Nishimoto M, Sekine SI, Bessho Y, Ito T, Grosjean H, Yokoyama S. Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin. J Mol Biol 2010; 401:323-33. [PMID: 20600111 DOI: 10.1016/j.jmb.2010.06.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Revised: 06/17/2010] [Accepted: 06/19/2010] [Indexed: 12/19/2022]
Abstract
tRNA:m(5)C methyltransferase Trm4 generates the modified nucleotide 5-methylcytidine in archaeal and eukaryotic tRNA molecules, using S-adenosyl-l-methionine (AdoMet) as methyl donor. Most archaea and eukaryotes possess several Trm4 homologs, including those related to diseases, while the archaeon Methanocaldococcus jannaschii has only one gene encoding a Trm4 homolog, MJ0026. The recombinant MJ0026 protein catalyzed AdoMet-dependent methyltransferase activity on tRNA in vitro and was shown to be the M. jannaschii Trm4. We determined the crystal structures of the substrate-free M. jannaschii Trm4 and its complex with sinefungin at 1.27 A and 2.3 A resolutions, respectively. This AdoMet analog is bound in a negatively charged pocket near helix alpha8. This helix can adopt two different conformations, thereby controlling the entry of AdoMet into the active site. Adjacent to the sinefungin-bound pocket, highly conserved residues form a large, positively charged surface, which seems to be suitable for tRNA binding. The structure explains the roles of several conserved residues that were reportedly involved in the enzymatic activity or stability of Trm4p from the yeast Saccharomyces cerevisiae. We also discuss previous genetic and biochemical data on human NSUN2/hTrm4/Misu and archaeal PAB1947 methyltransferase, based on the structure of M. jannaschii Trm4.
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Affiliation(s)
- Mitsuo Kuratani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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65
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Perrera C, Colombo R, Valsasina B, Carpinelli P, Troiani S, Modugno M, Gianellini L, Cappella P, Isacchi A, Moll J, Rusconi L. Identification of Myb-binding protein 1A (MYBBP1A) as a novel substrate for aurora B kinase. J Biol Chem 2010; 285:11775-85. [PMID: 20177074 DOI: 10.1074/jbc.m109.068312] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aurora kinases are mitotic enzymes involved in centrosome maturation and separation, spindle assembly and stability, and chromosome condensation, segregation, and cytokinesis and represent well known targets for cancer therapy because their deregulation has been linked to tumorigenesis. The availability of suitable markers is of crucial importance to investigate the functions of Auroras and monitor kinase inhibition in in vivo models and in clinical trials. Extending the knowledge on Aurora substrates could help to better understand their biology and could be a source for clinical biomarkers. Using biochemical, mass spectrometric, and cellular approaches, we identified MYBBP1A as a novel Aurora B substrate and serine 1303 as the major phosphorylation site. MYBBP1A is phosphorylated in nocodazole-arrested cells and is dephosphorylated upon Aurora B silencing or by treatment with Danusertib, a small molecule inhibitor of Aurora kinases. Furthermore, we show that MYBBP1A depletion by RNA interference causes mitotic progression delay and spindle assembly defects. MYBBP1A has until now been described as a nucleolar protein, mainly involved in transcriptional regulation. The results presented herein show MYBBP1A as a novel Aurora B kinase substrate and reveal a not yet recognized link of this nucleolar protein to mitosis.
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