DOCSLIB.ORG

An International Database and Integrated Analysis Tools for the Study of Cancer Gene Expression

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
An International Database and Integrated Analysis Tools for the Study of Cancer Gene Expression The Pharmacogenomics Journal (2002) 2, 156–164 2002 Nature Publishing Group All rights reserved 1470-269X/02 $25.00 www.nature.com/tpj REVIEW An international database and integrated analysis tools for the study of cancer gene expression RL Strausberg1 ABSTRACT AA Camargo2 Researchers working collaboratively in Brazil and the United States have 3 assembled an International Database of Cancer Gene Expression. Several stra- GJ Riggins tegies have been employed to generate gene expression data including CF Schaefer1 expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), SJ de Souza2 and open reading-frame expressed sequence tags (ORESTES). The database LH Grouse1 contains six million gene tags that reflect the gene expression profiles in a 3 wide variety of cancerous tissues and their normal counterparts. All A Lal sequences are deposited in the public databases, GenBank and SAGEmap. A 1 KH Buetow suite of informatics tools was designed to facilitate in silico analysis of the K Boon3 gene expression datasets and are available through the NCI Cancer Genome SF Greenhut1 Anatomy Project web site (http://cgap.nci.nih.gov). 2 The Pharmacogenomics Journal (2002) 2, 156–164. doi: 10.1038/ AJG Simpson sj.tpj.6500103 1National Cancer Institute, Bethesda, MD, USA; 2Ludwig Institute for Cancer Research, Keywords: cancer; genomics; ORESTES; SAGE; CGAP; gene expression Sa˜o Paulo, Brazil; 3Duke University Medical Center, Durham, NC, USA Cancer is fundamentally a disease of the genome. The genomic changes associa- Correspondence: ted with cancer appear in many shapes and forms, from point mutations and RL Strausberg, National Cancer Institute, 31 Center Drive, Room 10A07, MSC 2580, deletions of single nucleotides to the translocation of large chromosomal seg- Bethesda, MD 20892, USA ments. Moreover, alterations within the genome, in concert with changes in the Tel: 301 451–8027 environment, modulate patterns of gene expression, at both the transcript and Fax: 301 480–4368 protein levels. The challenge to cancer research is to relate the variations in gene E-mail: RLSȰnih.gov expression with specific types of cancer. Indeed, over the past few years, impress- ive efforts have been made to read these molecular signatures of cancer, toward the goal of gaining a more comprehensive understanding of the basic mech- anisms of cancers, which will lead to improved detection, diagnosis, inter- vention, and ultimately prevention.1–9 The platform vital to support these studies is a complete catalog of human and mouse genes, with a specific focus on those genes expressed in cancer cells and their normal counterparts. In 1997, the National Cancer Institute initiated the Cancer Genome Anatomy Project (CGAP)10–13 with the aim of facilitating the interface of genomics and cancer research. The first initiative developed within CGAP was the Tumor Gene Index. The Index was focused to develop a catalog of the genes expressed in a variety of normal and cancerous tissues. Subsequently, additional components evolved within CGAP to further annotate these genes, integrate the gene data- base with the human genome sequence, and correlate these genes with chromo- somal aberrations observed in cancers. For example, the Genetic Annotation Initiative (GAI)14–15 has assembled a database of gene-based single nucleotide polymorphisms (SNPs). These SNPs were identified through analysis of the exten- sive CGAP sequence database, which represents cancerous tissues obtained from Received 18 January 2002 many different individuals. The Cancer Chromosomal Aberration Project Revised 21 February 2002 (cCAP),16,17 another CGAP program, has advanced the convergence of the human Accepted 27 February 2002 physical map and DNA sequence with the cytogenetic map through precise International database of cancer gene expression RL Strausberg et al. 157 mapping of bacterial artificial chromosomes (BACs) clones METHODS APPLIED TO CATALOG GENE EXPRESSION along all human chromosomes using fluorescent in situ The CGAP and HGCP programs have both used approaches hybridization (FISH). Many of the BACs used in this initiat- to build gene catalogs based on cDNAs derived from human ive were substrates also utilized by the public Human Gen- and mouse tumors, as well as normal tissues. The CGAP pro- ome Project. The cCAP is a component of the International ject has utilized two gene-tagging strategies to build a gene BAC Mapping Consortium Project.16 CGAP also displays the expression catalog, the expressed sequence tag (EST) wealth of information about chromosome abnormalities approach,22 and serial analysis of gene expression (SAGE).23 that occur in cancers that is cataloged in the Mitelman Data- In the traditional EST approach, clones from cDNA libraries base of Chromosome Aberrations.18 An electronic and freely are subjected to single-pass sequencing from the 5Ј and/or 3Ј accessible version of this database is available for viewing on end of the cDNAs, producing sequences of several hundred the CGAP web site (http://cgap.nci.nih.gov/). nucleotides, such that a unique identifier is assigned to each In 1998 the Ludwig Institute for Cancer Research (LICR) cDNA. The cDNA libraries are constructed using primers for in Sa˜o Paulo, Brazil, sought to catalog gene expression in first-strand synthesis that are anchored at the 3Ј transcript cancer cells through the application of a novel gene tagging end (the poly(A) sequence). The resulting cDNA molecules approach, open reading frame ESTs (ORESTES). This led to may represent the entire transcript, but are more often a partnership between the LICR and the State of Sa˜o Paulo incomplete, either because of mRNA degradation or incom- Research Foundation (FAPESP) to launch the FAPESP/LICR plete enzymatic processivity during conversion of mRNA to Human Cancer Genome Project (HGCP).19–21 cDNA. Thus, for a specific transcript, there may be multiple In 1998, when discussions between the leaders of the forms of cDNA within a library. To facilitate gene cat- CGAP and HGCP projects were initiated, the synergy aloging, CGAP has focused its sequencing effort on the 3Ј between the programs was immediately apparent and an cDNA end, starting from the poly(A) sequence. Using this informal collaboration quickly formed. The notion for the approach, it is more likely that sequences from transcripts collaboration was that the gene tagging technologies being derived from the same gene will be recognized as such employed in both projects were complementary, as were the (although alternative polyadenylation sites add compli- specific types of cancer that were being targeted. All mem- cation to cataloging gene transcripts). bers of each group were committed to contributing the gene The serial analysis of gene expression (SAGE) approach tag data to public databases maintained by the National produces very short sequence tags (usually 10 nucleotides in Center for Biotechnology Information (NCBI). This would length) located adjacent to defined restriction sites near the ensure that the worldwide community of academic and 3Ј end of the cDNA. In this approach, cDNAs are digested industrial researchers would have access to the data for with a frequently cutting restriction enzyme (often NlaIII) application to both basic and applied cancer research. to which adapters are added that encode the sequence of a Recently, a formal relationship between the Brazilian and type IIs restriction enzyme (BsmF1), such that the 10 nucleo- United States scientists resulted in the creation of an inter- tides adjacent to the NlaIII site are isolated. The individual national database of cancer gene expression. In this report, tags are concatenated to form a single DNA molecule, which the content of this cancer gene expression database, as well is then subjected to DNA sequence analysis. The power of as informatics tools for utilizing the database, are described. SAGE is two-fold. First, unlike EST sequences, which can The web sites for each of these projects, as well as the vary in both location within the transcript and sequence informatics tools, are described in Table 1. length, the SAGE tags are precisely anchored at a defined Table 1 The URLs for the CGAP and HGCP projects and descriptions of the analysis tools available on the CGAP web site Name Purpose Web site CGAP Determines the genomic and gene expression profiles of http://cgap.nci.nih.gov/ normal, precancer and cancer cells. FAPESP/LICR HGCP Supports discovery of new human genes and is pursuing http://www.ludwig.org.br/ORESTES completion of all gene coding regions. Library Finder Searches for one or more tissue-specific libraries from the http://cgap.nci.nih.gov/Tissues/LibraryFinder CGAP, MGC, SAGE, or dbEST collections. Gene Library Finds all the genes in a specific cDNA library or group of http://cgap.nci.nih.gov/Tissues/LibrarySummarizer Summarizer (GLS) libraries. cDNA xProfiler Compares gene expression between two pools of libraries. http://cgap.nci.nih.gov/Tissues/xProfiler Differential Gene Distinguishes the statistical differences in gene expression http://cgap.nci.nih.gov/Tissues/GXS Expression Displayer between two pools of libraries. (DGED) Gene Finder Finds one gene or list of genes, based on selected search http://cgap.nci.nih.gov/Genes/GeneFinder criteria. Links to a Gene Info page, including Virtual Northern, and various NCBI and NCI databases are provided. www.nature.com/tpj International database of cancer gene expression RL Strausberg et al. 158 restriction site within the transcript and are the same length. Therefore, in
Load more

Recommended publications
  • Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers
    Identification and Characterization of TPRKB Dependency in TP53 Deficient Cancers. by Kelly Kennaley A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Molecular and Cellular Pathology) in the University of Michigan 2019 Doctoral Committee: Associate Professor Zaneta Nikolovska-Coleska, Co-Chair Adjunct Associate Professor Scott A. Tomlins, Co-Chair Associate Professor Eric R. Fearon Associate Professor Alexey I. Nesvizhskii Kelly R. Kennaley [email protected] ORCID iD: 0000-0003-2439-9020 © Kelly R. Kennaley 2019 Acknowledgements I have immeasurable gratitude for the unwavering support and guidance I received throughout my dissertation. First and foremost, I would like to thank my thesis advisor and mentor Dr. Scott Tomlins for entrusting me with a challenging, interesting, and impactful project. He taught me how to drive a project forward through set-backs, ask the important questions, and always consider the impact of my work. I’m truly appreciative for his commitment to ensuring that I would get the most from my graduate education. I am also grateful to the many members of the Tomlins lab that made it the supportive, collaborative, and educational environment that it was. I would like to give special thanks to those I’ve worked closely with on this project, particularly Dr. Moloy Goswami for his mentorship, Lei Lucy Wang, Dr. Sumin Han, and undergraduate students Bhavneet Singh, Travis Weiss, and Myles Barlow. I am also grateful for the support of my thesis committee, Dr. Eric Fearon, Dr. Alexey Nesvizhskii, and my co-mentor Dr. Zaneta Nikolovska-Coleska, who have offered guidance and critical evaluation since project inception.
    [Show full text]
  • Genbank Dennis A
    D48–D53 Nucleic Acids Research, 2012, Vol. 40, Database issue Published online 5 December 2011 doi:10.1093/nar/gkr1202 GenBank Dennis A. Benson, Ilene Karsch-Mizrachi, Karen Clark, David J. Lipman, James Ostell and Eric W. Sayers* National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA Received September 30, 2011; Revised November 14, 2011; Accepted November 17, 2011 ABSTRACT sequence (GSS), whole-genome shotgun (WGS) and Õ other high-throughput data from sequencing centers. GenBank is a comprehensive database that The US Office of Patents and Trademarks also contributes contains publicly available nucleotide sequences sequences from issued patents. GenBank participates with for more than 250 000 formally described species. the EMBL Nucleotide Sequence Database (EMBL-Bank), Downloaded from These sequences are obtained primarily through part of the European Nucleotide Archive (ENA) (2), and submissions from individual laboratories and batch the DNA Data Bank of Japan (DDBJ) (3) as a partner submissions from large-scale sequencing projects, in the International Nucleotide Sequence Database including whole-genome shotgun (WGS) and envir- Collaboration (INSDC). The INSDC partners exchange onmental sampling projects. Most submissions data daily to ensure that a uniform and comprehensive http://nar.oxfordjournals.org/ are made using the web-based BankIt or standalone collection of sequence information is available worldwide. Sequin programs, and accession numbers are NCBI makes the GenBank data available at no cost over the Internet, through FTP and a wide range of web-based assigned by GenBank staff upon receipt. Daily data retrieval and analysis services (4).
    [Show full text]
  • Rapid Evolution and Selection Inferred from the Transcriptomes of Sympatric Crater Lake Cichlid Fishes
    Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes K. R. ELMER, S. FAN, H. M. GUNTER, J. C. JONES, S. BOEKHOFF, S. KURAKU and A. MEYER Lehrstuhl fUr Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitiitstrasse 10, 78457 Konstanz, Germany Abstract Crater lakes provide a natural laboratory to study speciation of cichlid fishes by ecological divergence. Up to now, there has been a dearth of transcriptomic and genomic information that would aid in understanding the molecular basis of the phenotypic differentiation between young species. We used next-generation sequencing (Roche 454 massively parallel pyrosequencing) to characterize the diversity of expressed sequence tags between ecologically divergent, endemic and sympatric species of cichlid fishes from crater lake Apoyo, Nicaragua: benthic Amphilophus astorquii and limnetic Amphilophus zaliosus. We obtained 24174 A. astorquii and 21382 A. zaliosus high­ quality expressed sequence tag contigs, of which 13 106 pairs are orthologous between species. Based on the ratio of non synonymous to synonymous substitutions, we identified six sequences exhibiting signals of strong diversifying selection (KalKs > 1). These included genes involved in biosynthesis, metabolic processes and development. This transcriptome sequence variation may be reflective of natural selection acting on the genomes of these young, sympatric sister species. Based on Ks ratios and p-distances between 3'-untranslated regions (UTRs) calibrated to previously published species divergence times, we estimated a neutral transcriptome-wide substitutional mutation rate of ~1.25 x 10-6 per site per year. We conclude that next-generation sequencing technologies allow us to infer natural selection acting to diversify the genomes of young species, such as crater lake cichlids, with much greater scope than previously possible.
    [Show full text]
  • BRE Facilitates Skeletal Muscle Regeneration by Promoting Satellite Cell Motility and Differentiation Lihai Xiao and Kenneth Ka Ho Lee*
    © 2016. Published by The Company of Biologists Ltd | Biology Open (2016) 5, 100-111 doi:10.1242/bio.012450 RESEARCH ARTICLE BRE facilitates skeletal muscle regeneration by promoting satellite cell motility and differentiation Lihai Xiao and Kenneth Ka Ho Lee* ABSTRACT formed myofibers will further fuse with existing intact myofibers The function of the Bre gene in satellite cells was investigated during to repair the damaged muscle. The extent of this bioactivity is skeletal muscle regeneration. The tibialis anterior leg muscle depending on the severity of injury. In vitro, it is possible to follow was experimentally injured in Bre knockout mutant (BRE-KO) mice. the chronological and dynamic process of satellite cell migration, ’ It was established that the accompanying muscle regeneration was differentiation and fusion (O Connor et al., 2007; Bae et al., 2008). impaired as compared with their normal wild-type counterparts (BRE- Many proteins have been now identified to be important in the WT). There were significantly fewer pax7+ satellite cells and smaller regulation of satellite cell migration which includes: fibroblast newly formed myofibers present in the injury sites of BRE-KO mice. growth factor (FGF), hepatocyte growth factor (HGF) and IL-4 Bre was required for satellite cell fusion and myofiber formation. The (Lluri and Jaworski, 2005; Lafreniere et al., 2006). Components of cell fusion index and average length of newly-formed BRE-KO the extracellular matrix (such as fibronectin and laminin) and α myofibers were found to be significantly reduced as compared with chemokines (such as SDF-1 ) also play important roles in BRE-WT myofibers.
    [Show full text]
  • A Computational Model for Classification of BRCA2 Variants Using Mouse Embryonic Stem Cell-Based Functional Assays
    www.nature.com/npjgenmed ARTICLE OPEN A computational model for classification of BRCA2 variants using mouse embryonic stem cell-based functional assays Kajal Biswas1,5, Gary B. Lipton2,5, Stacey Stauffer1, Teresa Sullivan1, Linda Cleveland1, Eileen Southon1,3, Susan Reid1, ✉ ✉ Valentin Magidson4, Edwin S. Iversen Jr. 2 and Shyam K. Sharan 1 Sequencing-based genetic tests to identify individuals at increased risk of hereditary breast and ovarian cancers have resulted in the identification of more than 40,000 sequence variants of BRCA1 and BRCA2. A majority of these variants are considered to be variants of uncertain significance (VUS) because their impact on disease risk remains unknown, largely due to lack of sufficient familial linkage and epidemiological data. Several assays have been developed to examine the effect of VUS on protein function, which can be used to assess their impact on cancer susceptibility. In this study, we report the functional characterization of 88 BRCA2 variants, including several previously uncharacterized variants, using a well-established mouse embryonic stem cell (mESC)- based assay. We have examined their ability to rescue the lethality of Brca2 null mESC as well as sensitivity to six DNA damaging agents including ionizing radiation and a PARP inhibitor. We have also examined the impact of BRCA2 variants on splicing. In addition, we have developed a computational model to determine the probability of impact on function of the variants that can be used for risk assessment. In contrast to the previous VarCall models that are based on a single functional assay, we have developed a new platform to analyze the data from multiple functional assays separately and in combination.
    [Show full text]
  • Genomic Approaches to Research in Lung Cancer Edward Gabrielson the Johns Hopkins University School of Medicine, Baltimore, USA
    http://respiratory-research.com/content/1/1/036 Review Genomic approaches to research in lung cancer Edward Gabrielson The Johns Hopkins University School of Medicine, Baltimore, USA Received: 21 April 2000 Respir Res 2000, 1:36–39 Revisions requested: 11 May 2000 The electronic version of this article can be found online at Revisions received: 1 June 2000 http://respiratory-research.com/content/1/1/036 Accepted: 1 June 2000 Published: 23 June 2000 © Current Science Ltd (Print ISSN 1465-9921; Online ISSN 1465-993X) Abstract The medical research community is experiencing a marked increase in the amount of information available on genomic sequences and genes expressed by humans and other organisms. This information offers great opportunities for improving our understanding of complex diseases such as lung cancer. In particular, we should expect to witness a rapid increase in the rate of discovery of genes involved in lung cancer pathogenesis and we should be able to develop reliable molecular criteria for classifying lung cancers and predicting biological properties of individual tumors. Achieving these goals will require collaboration by scientists with specialized expertise in medicine, molecular biology, and decision-based statistical analysis. Keywords: cDNA arrays, genomics, lung cancer Introduction those diseases. Knowing the polymorphisms that make Genomics – the discipline that characterizes the struc- each of us unique individuals could be the key in the future tural and functional anatomy of the genome – has to predicting individual risks for developing disease and attracted continuously increased interest and invest- individual responses to pharmacological agents. However, ment over the past decade. The complete sequencing the full impact of genomics on medical research is still of the human genome is expected within a few years; unknown.
    [Show full text]
  • BRCC3 Acts As a Prognostic Marker in Nasopharyngeal
    Tu et al. Radiation Oncology (2015) 10:123 DOI 10.1186/s13014-015-0427-3 RESEARCH Open Access BRCC3 acts as a prognostic marker in nasopharyngeal carcinoma patients treated with radiotherapy and mediates radiation resistance in vitro Ziwei Tu1,2, Bingqing Xu1,2, Chen Qu1,2, Yalan Tao1,2, Chen Chen1,2, Wenfeng Hua2, Guokai Feng2, Hui Chang1, Zhigang Liu3, Guo Li4, Changbin Jiang5, Wei Yi5, Musheng Zeng2 and Yunfei Xia1,2* Abstract Background: BRCC3 has been found to be aberrantly expressed in breast tumors and involved in DNA damage response. The contribution of BRCC3 to nasopharyngeal carcinoma prognosis and radiosensitivity is still unclear. Methods: Immunohistochemical analysis of BRCC3 was carried out in 100 nasopharyngeal carcinoma tissues, and the protein level was correlated to patient survival. BRCC3 expression of nasopharyngeal carcinoma cell lines was determined by Western-blotting and real-time PCR. Additionally, the effects of BRCC3 knockdown on nasopharyngeal carcinoma cell clongenic survival, DNA damage repair, and cell cycle distribution after irradiation was assessed. Results: The BRCC3 protein level was inversely correlated with nasopharyngeal carcinoma patient overall survival (P < 0.001) and 3-year loco-regional relapse-free survival (P = 0.034). Multivariate analysis demonstrated that BRCC3 expression was an independent prognostic factor (P = 0.010). The expression of BRCC3 was much higher in radioresistant nasopharyngeal carcinoma cells than in radiosensitive cells. Knockdown of BRCC3 increased the cell survival fraction, attenuated DNA damage repair and resulted in G2/M cell cycle arrest in radioresistant NPC cells. Conclusions: High BRCC3 expression in nasopharyngeal carcinoma patients is associated with poor survival.
    [Show full text]
  • Novel BRCA1 Mutations and More Frequent Intron-20 Alteration Found Among 236 Women from Western Poland
    Oncogene (1997) 15, 1773 ± 1779 1997 Stockton Press All rights reserved 0950 ± 9232/97 $12.00 Novel BRCA1 mutations and more frequent intron-20 alteration found among 236 women from Western Poland Krzysztof Sobczak1, Piotr Kozl owski1, Marek Napieral a1, Jakub Czarny1, Marcin WozÂniak1, Mal gorzata Kapus cin ska1,2, Mal gorzataL os ko1, Magdalena Koziczak1, Anna Jasin ska1, Jolanta Powierska1, Ryszard Braczkowski3, Jan Br borowicz4, Dariusz Godlewski2, . e˛ Andrzej Mackiewicz5 and Wl odzimierz Krzyzosiak1 1Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61 ± 704 PoznanÂ; 2Cancer Epidemiology and Prevention Union, Wielkopolska Cancer Center, Garbary 15, 61 ± 866 PoznanÂ; 35-th Department of Internal Medicine, Silesian University School of Medicine, Bytom; 4Chair of Oncology, University School of Medical Sciences, La˛kowa 1/2 61-878 PoznanÂ; 5Department of Cancer Immunology, University School of Medical Sciences at Wielkopolska Cancer Center, Garbary 15, 61-866 PoznanÂ, Poland Three dierent novel BRCA1 mutations, ®ve independent most frequently form a favorable genetic background cases of the same 12 bp insertion-duplication in intron-20 for the disease. Also at increased risk are the carriers of and two novel rare BRCA1 sequence variants were one abnormal allele of the ataxia telangiectasia gene identi®ed among 122 Polish women with positive, in most (Swift et al., 1991), the carriers of rare minisatelite cases moderate family history of breast and/or ovarian allele at the HRAS1 locus (Krontiris et al., 1993) and cancer, 80 controls and 34 unselected breast cancer the members of Li Fraumeni families with germline tissue specimens.
    [Show full text]
  • Comparative Transcriptomes and Development of Expressed Sequence Tag-Simple Sequence Repeat Markers for Two Closely Related Oak Species
    Journal of Systematics JSE and Evolution doi: 10.1111/jse.12469 Research Article Comparative transcriptomes and development of expressed sequence tag-simple sequence repeat markers for two closely related oak species Jing-Jing Sun1, Tao Zhou2, Rui-Ting Zhang1, Yun Jia1, Yue-Mei Zhao3, Jia Yang1, and Gui-Fang Zhao1* 1Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China 2School of Pharmary, Xi’an Jiaotong University, Xi’an 710061, China 3College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo 726000, Shaanxi, China *Author for correspondence. E-mail: [email protected]. Tel.: 86-29-88305264. Fax: 86-29-88303572. Received 1 December 2017; Accepted 7 October 2018; Article first published online11 xx November Month 2018 2018 Abstract Quercus species comprise the major genera in the family Fagaceae and they are widely distributed in the Northern Hemisphere. Many Quercus species, including several endemics, are distributed in China. Genetic resources have been established for the important genera but few transcriptomes are available for Quercus species in China. In this study, we used Illumina paired-end sequencing to obtain the transcriptomes of two oak species, Q. liaotungensis Koidz. and Q. mongolica Fisch. ex Turcz. Approximately 24 million reads were generated and then a total of 103 618 unigenes were obtained after assembly for both species. Comparative transcriptome analyses of both species identified a total of 12 981 orthologous contigs. The Ka/Ks estimation and enrichment analysis indicated that 1179 (9.08%) orthologs showed rapid evolution, and most of these orthologs were related to functions comprising “DNA repair”, “response to cold”, and “response to drought”.
    [Show full text]
  • BRE Plays an Essential Role in Preventing Replicative and DNA
    www.nature.com/scientificreports OPEN BRE plays an essential role in preventing replicative and DNA damage-induced premature Received: 08 December 2015 Accepted: 08 March 2016 senescence Published: 22 March 2016 Wenting Shi1, Mei Kuen Tang1, Yao Yao1, Chengcheng Tang1, Yiu Loon Chui2 & Kenneth Ka Ho Lee1 The BRE gene, alias BRCC45, produces a 44 kDa protein that is normally distributed in both cytoplasm and nucleus. In this study, we used adult fibroblasts isolated from wild-type (WT) and BRE knockout (BRE−/−) mice to investigate the functional role of BRE in DNA repair and cellular senescence. We compared WT with BRE−/− fibroblasts at different cell passages and observed that the mutant fibroblasts entered replicative senescence earlier than the WT fibroblasts. With the use of gamma irradiation to induce DNA damage in fibroblasts, the percentage of SA-β-Gal+ cells was significantly higher in BRE−/− fibroblasts compared with WT cells, suggesting that BRE is also associated with DNA damage-induced premature senescence. We also demonstrated that the gamma irradiation induced γ-H2AX foci, a DNA damage marker, persisted significantly longer in BRE−/− fibroblasts than in WT fibroblasts, confirming that the DNA repair process is impaired in the absence of BRE. In addition, the BRCA1-A complex recruitment and homologous recombination (HR)-dependent DNA repair process upon DNA damage were impaired in BRE−/− fibroblasts. Taken together, our results demonstrate a role for BRE in both replicative senescence and DNA damage-induced premature senescence. This can be attributed to BRE being required for BRCA1-A complex-driven HR DNA repair. Cellular senescence is an irreversible physiological process that accompanies abnormal and reduced metabolic activities.
    [Show full text]
  • The Atypical Cyclin-Like Protein Spy1 Overrides P53-Mediated Tumour
    Fifield et al. Breast Cancer Research (2019) 21:140 https://doi.org/10.1186/s13058-019-1211-3 RESEARCH ARTICLE Open Access The atypical cyclin-like protein Spy1 overrides p53-mediated tumour suppression and promotes susceptibility to breast tumourigenesis Bre-Anne Fifield1, Ingrid Qemo1, Evie Kirou1, Robert D. Cardiff2 and Lisa Ann Porter1* Abstract Background: Breast cancer is the most common cancer to affect women and one of the leading causes of cancer- related deaths. Proper regulation of cell cycle checkpoints plays a critical role in preventing the accumulation of deleterious mutations. Perturbations in the expression or activity of mediators of cell cycle progression or checkpoint activation represent important events that may increase susceptibility to the onset of carcinogenesis. The atypical cyclin-like protein Spy1 was isolated in a screen for novel genes that could bypass the DNA damage response. Clinical data demonstrates that protein levels of Spy1 are significantly elevated in ductal and lobular carcinoma of the breast. We hypothesized that elevated Spy1 would override protective cell cycle checkpoints and support the onset of mammary tumourigenesis. Methods: We generated a transgenic mouse model driving expression of Spy1 in the mammary epithelium. Mammary development, growth characteristics and susceptibility to tumourigenesis were studied. In vitro studies were conducted to investigate the relationship between Spy1 and p53. Results: We found that in the presence of wild-type p53, Spy1 protein is held ‘in check’ via protein degradation, representing a novel endogenous mechanism to ensure protected checkpoint control. Regulation of Spy1 by p53 is at the protein level and is mediated in part by Nedd4.
    [Show full text]
  • Tumour Suppressor OTUD3 Induces Growth Inhibition and Apoptosis by Directly Deubiquitinating and Stabilizing P53 in Invasive Breast Carcinoma
    Tumour suppressor OTUD3 induces growth inhibition and apoptosis by directly deubiquitinating and stabilizing p53 in invasive breast carcinoma Qian Pu Shandong University Qilu Hospital Yan-rong Lv Shandong University Qilu Hospital Ke Dong Shandong University Qilu Hospital Wen-wen Geng Shandong University Qilu Hospital Hai-dong Gao ( [email protected] ) Shandong University Qilu Hospital Research article Keywords: OTUD3, p53, deubiquitinating enzymes, invasive breast carcinoma Posted Date: November 4th, 2019 DOI: https://doi.org/10.21203/rs.2.16872/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Version of Record: A version of this preprint was published on June 22nd, 2020. See the published version at https://doi.org/10.1186/s12885-020-07069-9. Page 1/21 Abstract Background P53 pathway inactivation plays an important role in the process of breast cancer tumourigenesis. Post-translational protein modication abnormalities have been conrmed to be an important mechanism underlying the inactivation of p53. Numerous deubiquitinating enzymes are aberrantly expressed in breast cancer, and a few deubiquitination enzymes are capable of deubiquitinating and stabilizing p53. Here, we report that OTUD3 is a deubiquitylase of p53 in breast carcinoma.Methods The correlation between the mRNA expression of OTUD3, TP53 and PTEN and the prognosis of BC was assessed with the Kaplan-Meier Plotter tool. OTUD3 protein expression in breast carcinoma was examined by immunohistochemistry and western blotting. The relationship among OTUD3, p53, and p21 proteins was analysed. Half-life analysis and ubiquitylation assay were performed to elucidate the molecular mechanism by which OTUD3 stabilizes p53.
    [Show full text]