Di€Erential Patterns of Cell Cycle Regulatory Proteins Expression in Transgenic Models of Thyroid Tumours

Total Page:16

File Type:pdf, Size:1020Kb

Di€Erential Patterns of Cell Cycle Regulatory Proteins Expression in Transgenic Models of Thyroid Tumours Oncogene (1998) 17, 631 ± 641 1998 Stockton Press All rights reserved 0950 ± 9232/98 $12.00 http://www.stockton-press.co.uk/onc Dierential patterns of cell cycle regulatory proteins expression in transgenic models of thyroid tumours Fre de rique Coppe e1, Fabienne Depoortere1, Jiri Bartek2, Catherine Ledent1, Marc Parmentier1 and Jacques E Dumont1 1IRIBHN, Universite Libre de Bruxelles, Campus Erasme, 808 route de Lennik, B-1070 Bruxelles, Belgium; 2Danish Cancer Society, Division of Cancer Biology, 49 Strand boulevarden, DK-2100 Copenhagen, Denmark Cell cycle proteins regulate the transitions from G1 to S result of the continuous release of adenosine by most and G2 to M phases. In higher eukaryotes, their function cell types (Maenhaut et al., 1990). The Tg-A2aR is controlled by intracellular cascades regulated by transgene promotes in mice, as the cyclic AMP extracellular growth factors. We have studied in (cAMP) cascade in dog thyroid epithelial cells in previously described transgenic mouse models for thyroid primary culture, both cell proliferation and function proliferative diseases the expression of the key proteins (Roger et al., 1982; Roger and Dumont, 1984; Dumont regulating the cell cycle by Western blotting and et al., 1992), resulting in the appearance of a immunohistochemistry, and have correlated the observa- dierentiated goiter and severe hyperthyroidism tions with the known actions of the transgenes on the (Ledent et al., 1992). This model, as the model of signal transduction cascades. In the adenosine A2a mice expressing in the thyroid a Gsa mutant (Michiels receptor model, the cyclic AMP pathway, upstream of et al., 1994), mimics the human autonomous hyper- the Rb family cell division block, is constitutively functional adenomas and non-autoimmune familial activated. In the model expressing HPV 16 E7 protein, hyperthyroidism due to mutations activating the the Rb-like proteins are inhibited. Cyclin-dependent cAMP pathway, such as the constitutive activation of kinases cdk4, cdk2 and cdc2, and the associated cyclins the thyrotropin receptor (Parma et al., 1996; Vassart et D, E and A have been studied. Cyclin D3 appears as the al., 1996), or of the Gsa protein (Lyons et al., 1990; major cyclin D subtype expressed in mouse thyroid Suarez et al., 1991). The major function attributed to epithelial cells in normal and transgenic mice. In the the E7 oncoprotein of the human papillomavirus type adenosine A2aR model, all cell cycle proteins tested were 16 (HPV 16) is to bind and inactivate various proteins accumulated. In the E7 model, all cell cycle proteins of the Rb family (p105-Rb, p107 and p130) (reviewed except for D-type cyclins and cdk4 were also accumu- in Zacksenhaus et al., 1993), allowing the release of lated. A similar pattern was observed in thyroids transcriptional factors of the E2F family that promote coexpressing both transgenes, suggesting a dominant entry into the S phase of the cell cycle (reviewed in eect of E7 over the consequences of the cAMP cascade Nevins 1992; Farnham et al., 1993). The Tg-E7 activation. The cyclin-dependent kinase inhibitors transgenic mice develop a large dierentiated goiter p21cip1/waf1 and p27kip1 were not downregulated in these constituted of functionally active thyrocytes (Ledent et proliferating thyroids which suggest other roles than the al., 1995). In both models, malignant tumours only inhibition of the cell cycle progression. appear in some very old animals. By interbreeding the Tg-A2aR and Tg-E7 transgenic lines, a model of highly Keywords: cyclins; cdk(s); CKI; thyroid; HPV 16 E7; proliferative and hyperfunctional goiter was obtained, cAMP a model of dierentiated thyroid carcinomas character- ized by a high incidence and early occurrence of lung metastases (Coppe e et al., 1996). Both transgenes thus clearly cooperated in promoting proliferation and the Introduction development of early malignant tumours. Although growth factors and oncogenes activate cell Thyroid tumours result from the accumulation of proliferation through various pathways, their action genetic events that activate proliferation pathways in generally converges on the activation of the cyclin the normally `quiescent' thyrocytes (Wynford-Thomas, dependent kinases (cdk). The activity of cdk(s) is 1997). In order to develop models for thyroid tumours, regulated by association with cyclins, by stimulatory or transgenic mouse lines have been generated in our inhibitory phosphorylation events, and by association laboratory, by directing speci®cally the expression of with speci®c inhibitory proteins (reviewed in GraÄ na viral oncogenes or signalling proteins to thyroid and Reddy, 1995; Palmero and Peters, 1996). The epithelial cells (thyrocytes), under the control of the activated cdk(s) catalyze the phosphorylation and the bovine thyroglobulin gene promoter (Tg-) (Christophe inactivation of the Rb family proteins which are a key and Vassart, 1990; Ledent et al., 1990). element in the control of cell proliferation, including in Ectopic expression of the adenosine A2a receptor thyrocytes (Coulonval et al., 1997). Dierent cyclin-cdk leads to permanent stimulation of adenylyl cyclase, as a complexes are sequentially formed and activated during the cell cycle, allowing progression through the dierent checkpoints of this cycle: cyclin D-cdk4 or Correspondence: F Coppe e -cdk6 controls progression through late G1, cyclin E- Received 13 August 1997; revised 11 March 1998; accepted 11 March cdk2 acts at the initiation of S phase, cyclin A-cdk2 1998 and then cdc2 act in S and G2 phases and the cyclin Cell cycle proteins in thyroid transgenic mice F CoppeÂe et al 632 B1-cdc2 at M phase (GraÄ na and Reddy, 1995; Palmero morphology in Tg-A2aR/Tg-E7 animals expressing and Peters, 1996). There are three subtypes of D both transgenes remains homogeneous with age and cyclins (D1, D2 and D3), encoded by dierent genes, is characterized by a high cellular density and narrow but sharing sequence homology (Inaba et al., 1992). colloid lumina. The variable contribution of thyroglo- They are dierentially expressed during G1, depending bulin into the thyroid total protein content of the on the cell types considered (Inaba et al., 1992; dierent models could in¯uence markedly the quantita- Palmero et al., 1993; Ando et al., 1993; Sherr, 1993; tion of cell cycle proteins. To reduce this source of Bartkova et al., 1994; Sweeney et al., 1997). Promoter error, we have separated the cellular fraction from analysis of cyclins D2 and D3 revealed marked colloid by gentle homogenization of thyroid tissue in a dierences in the control of gene expression following non denaturating buer disrupting follicles without the stimulation by growth factors (Brooks et al., 1996). substantial cell damage, followed by low speed Moreover, various observations suggest that individual centrifugation (`cellular' extracts, see Materials and D-type cyclins have distinct functions in dierent cell methods). Equal amounts of the various protein types in addition to activating cdk4/6 (Ewen et al., extracts were run on SDS-polyacrylamide gels, and 1993; Kato and Sherr, 1993; Lucibello et al., 1993; silver staining did not show signi®cant dierences in Sherr, 1993; Han et al., 1996; Kranenburg et al., 1996; the protein pattern among the various transgenic and Sofer-Levi and Resnitzki, 1996). control groups (data not shown). Immunodetection of The activity of the dierent cyclin-cdk complexes is thyroglobulin on Western blots from 1 month-old repressed by two families of Cyclin-dependent Kinase animals showed that most thyroglobulin was eciently Inhibitors (CKI): 1/p21cip1/waf1, p27kip1 and p57kip2 which removed from `cellular' extracts in the various models. negatively regulate the activity of all cyclin-cdk In older animals (5 months), large amounts of complexes in vitro, and probably in vivo, 2/ speci®c thyroglobulin were found in the supernatants, espe- inhibitors of cdk4/6 such as p15INK4b, p16INK4a, p18INK4c cially in the Tg-E7 thyroid extracts (Figure 1). and p19INK4d (reviewed in Sherr and Roberts, 1995). Paradoxically, the cAMP cascade induces the expres- Expression of cyclins and cdks sion of p27 CKI in cells in which it inhibits cell proliferation (Kato et al., 1994; Ward et al., 1996) as The proteins analysed could be expressed in other cell well as in our dog thyrocytes in vitro in which it types than the epithelial cells and contaminate the stimulates it (Roger and Dumont, 1984; Depoortere et protein extracts. However, the epithelial cells represent al., 1996). the majority cells of thyroid cells. Moreover, other cells As most of the work concerning the expression of cell cycle proteins has been carried out in unphysiolo- gical cell system cultures, we have analysed by Western blotting and immunohistochemistry the expression of cdk(s), cyclins and p27 proteins as p21 messenger in the in vivo Tg-A2aR, Tg-E7 and Tg-A2aR/Tg-E7 transgenic models of thyroid proliferation and tumor- igenesis. Results Normalization of thyroglobulin content in protein extracts The functional unit of thyroid tissue is the follicle, a single cuboidal epithelium lining a lumen ®lled with colloid, which normally is the major constituent of the total thyroid mass. Colloid is made essentially of the thyroid hormone precursor thyroglobulin. In our transgenic models, the follicular structure is pre- served, but the ratio between cells and colloid varies according to the model and the age of the animals (Coppe e et al., 1996). The Tg-A2aR mice develop thyroid hyperfunction,
Recommended publications
  • Screening and Identification of Key Biomarkers in Clear Cell Renal Cell Carcinoma Based on Bioinformatics Analysis
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Screening and identification of key biomarkers in clear cell renal cell carcinoma based on bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.21.423889; this version posted December 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignancy of the urinary system. The pathogenesis and effective diagnosis of ccRCC have become popular topics for research in the previous decade. In the current study, an integrated bioinformatics analysis was performed to identify core genes associated in ccRCC. An expression dataset (GSE105261) was downloaded from the Gene Expression Omnibus database, and included 26 ccRCC and 9 normal kideny samples. Assessment of the microarray dataset led to the recognition of differentially expressed genes (DEGs), which was subsequently used for pathway and gene ontology (GO) enrichment analysis.
    [Show full text]
  • G2 Phase Cell Cycle Regulation by E2F4 Following Genotoxic Stress
    G2 Phase Cell Cycle Regulation by E2F4 Following Genotoxic Stress by MEREDITH ELLEN CROSBY Submitted in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Thesis Advisor: Dr. Alex Almasan Department of Environmental Health Sciences CASE WESTERN RESERVE UNIVERSITY May, 2006 CASE WESTERN RESERVE UNIVERSITY SCHOOL OF GRADUATE STUDIES We hereby approve the dissertation of ______________________________________________________ candidate for the Ph.D. degree *. (signed)_______________________________________________ (chair of the committee) ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ ________________________________________________ (date) _______________________ *We also certify that written approval has been obtained for any proprietary material contained therein. TABLE OF CONTENTS TABLE OF CONTENTS………………………………………………………………….1 LIST OF FIGURES……………………………………………………………………….5 LIST OF TABLES………………………………………………………………………...7 ACKNOWLEDGEMENTS……………………………………………………………….8 LIST OF ABBREVIATIONS……………………………………………………………10 ABSTRACT……………………………………………………………………………...15 CHAPTER 1. INTRODUCTION 1.1. CELL CYCLE REGULATION: HISTORICAL OVERVIEW………………...17 1.2. THE E2F FAMILY OF TRANSCRIPTION FACTORS……………………….22 1.3. E2F AND CELL CYCLE CONTROL 1.3.1. G0/G1 Phase Transition………………………………………………….28 1.3.2. S Phase…………………………………………………………………...28 1.3.3. G2/M Phase Transition…………………………………………………..30 1.4.
    [Show full text]
  • Investigation of the Underlying Hub Genes and Molexular Pathogensis in Gastric Cancer by Integrated Bioinformatic Analyses
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Investigation of the underlying hub genes and molexular pathogensis in gastric cancer by integrated bioinformatic analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2020.12.20.423656; this version posted December 22, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract The high mortality rate of gastric cancer (GC) is in part due to the absence of initial disclosure of its biomarkers. The recognition of important genes associated in GC is therefore recommended to advance clinical prognosis, diagnosis and and treatment outcomes. The current investigation used the microarray dataset GSE113255 RNA seq data from the Gene Expression Omnibus database to diagnose differentially expressed genes (DEGs). Pathway and gene ontology enrichment analyses were performed, and a proteinprotein interaction network, modules, target genes - miRNA regulatory network and target genes - TF regulatory network were constructed and analyzed. Finally, validation of hub genes was performed. The 1008 DEGs identified consisted of 505 up regulated genes and 503 down regulated genes.
    [Show full text]
  • Supplementary Data
    SUPPLEMENTARY DATA A cyclin D1-dependent transcriptional program predicts clinical outcome in mantle cell lymphoma Santiago Demajo et al. 1 SUPPLEMENTARY DATA INDEX Supplementary Methods p. 3 Supplementary References p. 8 Supplementary Tables (S1 to S5) p. 9 Supplementary Figures (S1 to S15) p. 17 2 SUPPLEMENTARY METHODS Western blot, immunoprecipitation, and qRT-PCR Western blot (WB) analysis was performed as previously described (1), using cyclin D1 (Santa Cruz Biotechnology, sc-753, RRID:AB_2070433) and tubulin (Sigma-Aldrich, T5168, RRID:AB_477579) antibodies. Co-immunoprecipitation assays were performed as described before (2), using cyclin D1 antibody (Santa Cruz Biotechnology, sc-8396, RRID:AB_627344) or control IgG (Santa Cruz Biotechnology, sc-2025, RRID:AB_737182) followed by protein G- magnetic beads (Invitrogen) incubation and elution with Glycine 100mM pH=2.5. Co-IP experiments were performed within five weeks after cell thawing. Cyclin D1 (Santa Cruz Biotechnology, sc-753), E2F4 (Bethyl, A302-134A, RRID:AB_1720353), FOXM1 (Santa Cruz Biotechnology, sc-502, RRID:AB_631523), and CBP (Santa Cruz Biotechnology, sc-7300, RRID:AB_626817) antibodies were used for WB detection. In figure 1A and supplementary figure S2A, the same blot was probed with cyclin D1 and tubulin antibodies by cutting the membrane. In figure 2H, cyclin D1 and CBP blots correspond to the same membrane while E2F4 and FOXM1 blots correspond to an independent membrane. Image acquisition was performed with ImageQuant LAS 4000 mini (GE Healthcare). Image processing and quantification were performed with Multi Gauge software (Fujifilm). For qRT-PCR analysis, cDNA was generated from 1 µg RNA with qScript cDNA Synthesis kit (Quantabio). qRT–PCR reaction was performed using SYBR green (Roche).
    [Show full text]
  • Proteogenomic Analysis of Inhibitor of Differentiation 4 (ID4) in Basal-Like Breast Cancer Laura A
    Baker et al. Breast Cancer Research (2020) 22:63 https://doi.org/10.1186/s13058-020-01306-6 RESEARCH ARTICLE Open Access Proteogenomic analysis of Inhibitor of Differentiation 4 (ID4) in basal-like breast cancer Laura A. Baker1,2, Holly Holliday1,2†, Daniel Roden1,2†, Christoph Krisp3,4†, Sunny Z. Wu1,2, Simon Junankar1,2, Aurelien A. Serandour5, Hisham Mohammed5, Radhika Nair6, Geetha Sankaranarayanan5, Andrew M. K. Law1,2, Andrea McFarland1, Peter T. Simpson7, Sunil Lakhani7,8, Eoin Dodson1,2, Christina Selinger9, Lyndal Anderson9,10, Goli Samimi11, Neville F. Hacker12, Elgene Lim1,2, Christopher J. Ormandy1,2, Matthew J. Naylor13, Kaylene Simpson14,15, Iva Nikolic14, Sandra O’Toole1,2,9,10, Warren Kaplan1, Mark J. Cowley1,2, Jason S. Carroll5, Mark Molloy3 and Alexander Swarbrick1,2* Abstract Background: Basal-like breast cancer (BLBC) is a poorly characterised, heterogeneous disease. Patients are diagnosed with aggressive, high-grade tumours and often relapse with chemotherapy resistance. Detailed understanding of the molecular underpinnings of this disease is essential to the development of personalised therapeutic strategies. Inhibitor of differentiation 4 (ID4) is a helix-loop-helix transcriptional regulator required for mammary gland development. ID4 is overexpressed in a subset of BLBC patients, associating with a stem-like poor prognosis phenotype, and is necessary for the growth of cell line models of BLBC through unknown mechanisms. Methods: Here, we have defined unique molecular insights into the function of ID4 in BLBC and the related disease high-grade serous ovarian cancer (HGSOC), by combining RIME proteomic analysis, ChIP-seq mapping of genomic binding sites and RNA-seq.
    [Show full text]
  • Cytoplasmic E2f4 Forms Organizing Centres for Initiation of Centriole Amplification During Multiciliogenesis
    ARTICLE Received 13 Feb 2017 | Accepted 8 May 2017 | Published 4 Jul 2017 DOI: 10.1038/ncomms15857 OPEN Cytoplasmic E2f4 forms organizing centres for initiation of centriole amplification during multiciliogenesis Munemasa Mori1, Renin Hazan2, Paul S. Danielian2, John E. Mahoney1,w, Huijun Li1, Jining Lu1, Emily S. Miller2, Xueliang Zhu3, Jacqueline A. Lees2 & Wellington V. Cardoso1 Abnormal development of multiciliated cells is a hallmark of a variety of human conditions associated with chronic airway diseases, hydrocephalus and infertility. Multiciliogenesis requires both activation of a specialized transcriptional program and assembly of cytoplasmic structures for large-scale centriole amplification that generates basal bodies. It remains unclear, however, what mechanism initiates formation of these multiprotein complexes in epithelial progenitors. Here we show that this is triggered by nucleocytoplasmic translocation of the transcription factor E2f4. After inducing a transcriptional program of centriole biogenesis, E2f4 forms apical cytoplasmic organizing centres for assembly and nucleation of deuterosomes. Using genetically altered mice and E2F4 mutant proteins we demonstrate that centriole amplification is crucially dependent on these organizing centres and that, without cytoplasmic E2f4, deuterosomes are not assembled, halting multiciliogenesis. Thus, E2f4 integrates nuclear and previously unsuspected cytoplasmic events of centriole amplification, providing new perspectives for the understanding of normal ciliogenesis, ciliopathies and cancer. 1 Columbia Center for Human Development, Department of Medicine, Pulmonary Allergy Critical Care, Columbia University Medical Center, New York City, New York 10032, USA. 2 David H. Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts 02139, USA. 3 State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.
    [Show full text]
  • Table of Contents Methods
    SUPPLEMENTARY MATERIAL FOR: Intrinsic specificity differences between transcription factor paralogs partly explain their differential in vivo binding Ning Shen1,2,3, Jingkang Zhao1,3,4, Joshua Schipper1,3, Yuning Zhang1,4,Tristan Bepler1, Dan Leehr1, John Bradley1, John Horton1,3, Hilmar Lapp1, Raluca Gordan1,3,5* 1Center for Genomic and Computational Biology, 2Department of Pharmacology and Cancer Biology, 3Department of Biostatistics and Bioinformatics, 4Program in Computational Biology and Bioinformatics, 5Department of Computer Science, Duke University, Durham, NC 27708 * Corresponding author. E-mail: [email protected] Table of Contents Methods ................................................................................................................................................... 1 1. ChIP-seq and DNase-seq data ................................................................................................................. 1 2. Design of DNA libraries for gcPBM assays .......................................................................................... 1 3. Protein expression and purification .................................................................................................... 3 4. Universal and genomic-context PBM assays ..................................................................................... 4 5. gcPBM data processing. Identifying core motifs .............................................................................. 4 6. Building core-stratified SVR models of TF-DNA binding specificity
    [Show full text]
  • Transcriptional and Post-Transcriptional Regulation of ATP-Binding Cassette Transporter Expression
    Transcriptional and Post-transcriptional Regulation of ATP-binding Cassette Transporter Expression by Aparna Chhibber DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Pharmaceutical Sciences and Pbarmacogenomies in the Copyright 2014 by Aparna Chhibber ii Acknowledgements First and foremost, I would like to thank my advisor, Dr. Deanna Kroetz. More than just a research advisor, Deanna has clearly made it a priority to guide her students to become better scientists, and I am grateful for the countless hours she has spent editing papers, developing presentations, discussing research, and so much more. I would not have made it this far without her support and guidance. My thesis committee has provided valuable advice through the years. Dr. Nadav Ahituv in particular has been a source of support from my first year in the graduate program as my academic advisor, qualifying exam committee chair, and finally thesis committee member. Dr. Kathy Giacomini graciously stepped in as a member of my thesis committee in my 3rd year, and Dr. Steven Brenner provided valuable input as thesis committee member in my 2nd year. My labmates over the past five years have been incredible colleagues and friends. Dr. Svetlana Markova first welcomed me into the lab and taught me numerous laboratory techniques, and has always been willing to act as a sounding board. Michael Martin has been my partner-in-crime in the lab from the beginning, and has made my days in lab fly by. Dr. Yingmei Lui has made the lab run smoothly, and has always been willing to jump in to help me at a moment’s notice.
    [Show full text]
  • Mammalian Atypical E2fs Link Endocycle Control to Cancer
    Mammalian Atypical E2Fs Link Endocycle Control to Cancer DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Hui-Zi Chen Graduate Program in Integrated Biomedical Science Program The Ohio State University 2011 Dissertation Committee: Gustavo Leone, PhD, Advisor Michael Ostrowski, PhD Clay Marsh, MD Tsonwin Hai, PhD Kathryn Wikenheiser-Brokamp, MD PhD Copyright by Hui-Zi Chen 2011 Abstract The endocycle is a developmentally programmed variant cell cycle consisting of successive S (DNA synthesis) and G (Gap) phases without an intervening M phase or cytokinesis. As a consequence of the regulated “decoupling” of DNA replication and mitosis, which are two central processes of the traditional cell division program, endocycling cells acquire highly polyploid genomes after having undergone multiple rounds of whole genome reduplication. Although essential for metazoan development, relatively little is known about the regulation of endocycle or its physiologic role in higher vertebrates such as the mammal. A substantial body of work in the model organism Drosophila melanogaster has demonstrated an important function for dE2Fs in the control of endocycle. Genetic studies showed that both endocycle initiation and progression is severely disrupted by altering the expression of the fly E2F activator (dE2F1) or repressor (dE2F2). In mammals, the E2F family is comprised of nine structurally related proteins, encoded by eight distinct genes, that can be classified into transcriptional activators (E2f1, E2f2, E2f3a and E2f3b) or repressors (E2f4, E2f5, E2f6, E2f7 and E2f8). The repressor subclass may then be further divided into canonical (E2f4, E2f5 and E2f6) or atypical E2fs (E2f7 and E2f8).
    [Show full text]
  • A Scalable Disease Module Identification Algorithm with Application to Glioma Progression
    DiME: A Scalable Disease Module Identification Algorithm with Application to Glioma Progression Yunpeng Liu1, Daniel A. Tennant2, Zexuan Zhu4, John K. Heath3, Xin Yao1, Shan He1,3* 1 School of Computer Science, University of Birmingham, Birmingham, United Kingdom, 2 School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom, 3 Centre for Systems Biology, School of Biological Sciences, University of Birmingham, Birmingham, United Kingdom, 4 College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, China Abstract Disease module is a group of molecular components that interact intensively in the disease specific biological network. Since the connectivity and activity of disease modules may shed light on the molecular mechanisms of pathogenesis and disease progression, their identification becomes one of the most important challenges in network medicine, an emerging paradigm to study complex human disease. This paper proposes a novel algorithm, DiME (Disease Module Extraction), to identify putative disease modules from biological networks. We have developed novel heuristics to optimise Community Extraction, a module criterion originally proposed for social network analysis, to extract topological core modules from biological networks as putative disease modules. In addition, we have incorporated a statistical significance measure, B- score, to evaluate the quality of extracted modules. As an application to complex diseases, we have employed DiME to investigate the molecular mechanisms that underpin the progression of glioma, the most common type of brain tumour. We have built low (grade II) - and high (GBM) - grade glioma co-expression networks from three independent datasets and then applied DiME to extract potential disease modules from both networks for comparison.
    [Show full text]
  • A Comprehensive Chip–Chip Analysis of E2F1, E2F4, and E2F6 in Normal and Tumor Cells Reveals Interchangeable Roles of E2F Family Members
    Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Research A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members Xiaoqin Xu,1 Mark Bieda,1 Victor X. Jin,1 Alina Rabinovich,1 Mathew J. Oberley,2 Roland Green,3 and Peggy J. Farnham1,4 1Department of Pharmacology and the Genome Center, University of California-Davis, Davis, California 95616, USA; 2University of Wisconsin Medical School, Madison, Wisconsin, 53705 USA; 3NimbleGen Systems Inc., Madison, Wisconsin, 53711 USA Using ChIP–chip assays (employing ENCODE arrays and core promoter arrays), we examined the binding patterns of three members of the E2F family in five cell types. We determined that most E2F1, E2F4, and E2F6 binding sites are located within 2 kb of a transcription start site, in both normal and tumor cells. In fact, the majority of promoters that are active (as defined by TAF1 or POLR2A binding) in GM06990 B lymphocytes and Ntera2 carcinoma cells were also bound by an E2F. This very close relationship between E2F binding sites and binding sites for general transcription factors in both normal and tumor cells suggests that a chromatin-bound E2F may be a signpost for active transcription initiation complexes. In general, we found that several E2Fs bind to a given promoter and that there is only modest cell type specificity of the E2F family. Thus, it is difficult to assess the role of any particular E2F in transcriptional regulation, due to extreme redundancy of target promoters.
    [Show full text]
  • Differential Pax5 Levels Promote Mcl Dispersal and Progression and Predict a Poor Prognosis in Advanced Mcl Patients
    The Texas Medical Center Library DigitalCommons@TMC The University of Texas MD Anderson Cancer Center UTHealth Graduate School of The University of Texas MD Anderson Cancer Biomedical Sciences Dissertations and Theses Center UTHealth Graduate School of (Open Access) Biomedical Sciences 12-2014 DIFFERENTIAL PAX5 LEVELS PROMOTE MCL DISPERSAL AND PROGRESSION AND PREDICT A POOR PROGNOSIS IN ADVANCED MCL PATIENTS Albert Teo Follow this and additional works at: https://digitalcommons.library.tmc.edu/utgsbs_dissertations Part of the Medicine and Health Sciences Commons Recommended Citation Teo, Albert, "DIFFERENTIAL PAX5 LEVELS PROMOTE MCL DISPERSAL AND PROGRESSION AND PREDICT A POOR PROGNOSIS IN ADVANCED MCL PATIENTS" (2014). The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access). 533. https://digitalcommons.library.tmc.edu/utgsbs_dissertations/533 This Dissertation (PhD) is brought to you for free and open access by the The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at DigitalCommons@TMC. It has been accepted for inclusion in The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access) by an authorized administrator of DigitalCommons@TMC. For more information, please contact [email protected]. DIFFERENTIAL PAX5 LEVELS PROMOTE MCL DISPERSAL AND PROGRESSION AND PREDICT A POOR PROGNOSIS IN ADVANCED MCL PATIENTS by Albert Eng Keong Teo, B.S. APPROVED: ______________________________ Advisory Professor Nami McCarty, Ph.D. ______________________________ Zhiqiang An, Ph.D. ______________________________ R. Eric Davis, M.D. ______________________________ Shiaw-Yih Lin, Ph.D. ______________________________ Timothy J. McDonnell, M.D., Ph.D.
    [Show full text]