DOCSLIB.ORG

Epigenetic, Metabolic and Signal Transduction Pathways Involved in Radiation Response of Normal and Transformed Thyrocytes

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Epigenetic, Metabolic and Signal Transduction Pathways Involved in Radiation Response of Normal and Transformed Thyrocytes ei involved in radiation response of normal and transformed response in radiation involved transduction and signal pathways metabolic, Epigenetic, Epigenetic, metabolic and signal transduction pathways involved in radiation response of normal and transformed thyrocytes Khalil Abouelaradat Khalil Abouelaradat ISBN 978-90-5989-484-6 2011 9 789059 894846 "Once something actually happens somewhere as wildly complicated as the Universe, Kevin knows where it will all end up – where 'Kevin' is any random entity that doesn't know nothin' about nothin'" Douglas Adams, 'Mostly Harmless' Book 5 of the Trilogy of Five ii Promoters: Prof. Dr. Ir. Wim VAN CRIEKINGE Department of Mathematical Modeling, Statistics and Bioinformatics Faculty of Bioscience Engineering Ghent University Prof. Dr. Sarah BAATOUT Radiobiology Unit Belgian Nuclear Research Center (SCK•CEN) & Department of Molecular Biotechnology Faculty of Bioscience Engineering Ghent University Prof. Dr. Ir. Tim DE MEYER Department of Mathematical Modeling, Statistics and Bio-informatics /Department of Molecular Biotechnology Faculty of Bioscience Engineering Ghent University Dr. Ir. Sofie BEKAERT Clinical Research Center Faculty for Medicine and Health Sciences Ghent University Dean: Prof. Dr. Ir. Guido VAN HUYLENBROECK Rector: Prof. Dr. Paul VAN CAUWENBERGE iii Epigenetic, metabolic, and signal transduction pathways involved in radiation response of normal and transformed thyrocytes Khalil Abouelaradat Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences iv "Epigenetische, metabole en signaaloverdrachtmechanismen betrokken bij de stralingsrespons van normale en getransformeerde schildkliercellen" Cover Illustration: Colored gamma scan (scintigram) of a healthy human thyroid gland, in front view (Centre Jean Perrin/Science Photo Library). A radioactive tracer (Tc-99m) highlights areas of activity in the thyroid where blue represents areas of low activity and green/red areas of high activity. Gamma scans involve injecting a radioactive tracer and then measuring the gamma rays emitted using a gamma camera. Picture was converted to ASCII art using Ascgen2 (http://sourceforge.net/projects/ascgen2). The ASCII picture is made out of repeats of the word RET/PTC. The gamma scan picture is overlayed with an image of a monarch butterfly (Danaus plexippus) (© 2009, Encyclopaedia Britannica). Cover art design by Khalil Abouelaradat Abouelaradat Khalil (2011). Epigenetic, metabolic, and signal transduction pathways involved in radiation response of normal and transformed thyrocytes. PhD Thesis. Ghent University. ISBN: 978-90-5989-484-6 The author and the promoters give the authorization to consult and to copy parts of this work for personal use only. Any other use is limited by the Laws of Copyright. Permission to reproduce any material contained in this work should be obtained from the author. v Members of the Examination Committee Prof. Dr. Ir. Wim Van Criekinge (Promoter) Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University Prof. Dr. Sarah Baatout (Co-promoter) Radiobiology Unit, Belgian Nuclear Research Center (SCK•CEN) Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University Prof. Dr. Ir. Sofie Bekaert (Co-promoter) Clinical Research Center, Faculty of Medicine and Health Sciences, Ghent University Prof. Dr. Ir. Tim De Meyer (Co-promoter) Department of Molecular Biotechnology/Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University Prof. Dr. Ir. Dirk Reheul (Chairman) Department of Plant Production, Faculty of Bioscience Engineering, Ghent University Prof. Dr. Ir. Guy Smagghe (Secretary) Department of Crop Production, Faculty of Bioscience Engineering , Ghent University Dr. Anne-Catherine Gérard Morphology Group, Institute of Fundamental and Clinical Research, Catholic University of Louvain (UCL) Prof. Dr. Hubert Thierens Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Ghent University Em. Prof. Dr. Patrick Van Oostveldt Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University Prof. Dr. Jan Philippé Department of Clinical Chemistry, Microbiology and Immunology, Faculty of Medicine and Health Sciences, Ghent University vi vii Table of Contents List of Figures ......................................................................................................................................... xiv List of Tables .......................................................................................................................................... xvi List of Abbreviations ............................................................................................................................ xviii Chapter 1: General Introduction 1. The Nuclear Conundrum ..................................................................................................................... 3 1.1 TMI and Chernobyl: Compare and Contrast .................................................................................. 3 1.2 Nuclear Weapons Testing .............................................................................................................. 5 1.3 Fukushima: Lessons from the Past ................................................................................................ 6 1.4 External Irradiation ........................................................................................................................ 7 2. The Thyroid .......................................................................................................................................... 9 2.1 Iodine Metabolism and Hormone Synthesis ................................................................................. 9 2.2 Thyroid Homeostasis ................................................................................................................... 13 3. Thyroid Cancer................................................................................................................................... 15 3.1 Thyroid Cancer Types .................................................................................................................. 15 3.2 Mutations in PTC ......................................................................................................................... 17 3.2.1 RAF ........................................................................................................................................ 17 3.2.2 RET/PTC ................................................................................................................................ 17 3.2.2.1 Prominance of RET/PTC Translocations in Radiation-induced PTCs .................................. 19 3.2.3 NTRK Rearrangments ........................................................................................................... 21 3.2.4 Ras ........................................................................................................................................ 21 4. Low Dose Radiation Introduction ...................................................................................................... 23 4.1 The Linear Non-Threshold Model (LNT) ...................................................................................... 23 4.2 The LNT: Pros and Cons, Epidemiology ....................................................................................... 25 4.3 Health Risk Estimates: Molecular ................................................................................................ 26 4.3.1 γH2AX ................................................................................................................................... 26 4.3.2 Cell Survival .......................................................................................................................... 27 4.4 Deviations from the LNT .............................................................................................................. 28 4.4.1 HRS/IRR ................................................................................................................................. 28 4.4.2 The Bystander Effect ............................................................................................................ 29 4.4.3 Adaptive Response ............................................................................................................... 30 viii 4.4.4 Hormesis ............................................................................................................................... 30 4.5 Interindividual Sensitivity ............................................................................................................ 31 4.6 Risk to the Thyroid ....................................................................................................................... 31 4.7 Conclusion ................................................................................................................................... 32 5. Senescence Introduction: To Divide or Not To Divide....................................................................... 33 5.1 The Hayflick Mosaic ..................................................................................................................... 34 5.2 Hitting the Breaks: Premature Senescence ................................................................................. 36
Load more

Recommended publications
  • Reversible Human Immunodeficiency Virus Type-1 Latency in Primary Human Monocyte-Derived Macrophages Induced by Sustained M1
    www.nature.com/scientificreports OPEN Reversible Human Immunodefciency Virus Type-1 Latency in Primary Human Received: 11 January 2018 Accepted: 13 August 2018 Monocyte-Derived Macrophages Published: xx xx xxxx Induced by Sustained M1 Polarization Francesca Graziano1,4, Giulia Aimola1, Greta Forlani 2, Filippo Turrini 1, Roberto S. Accolla2, Elisa Vicenzi1 & Guido Poli1,3 We have reported that short-term stimulation of primary human monocyte-derived macrophages (MDM) with interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α), i.e. M1 polarization, leads to a signifcant containment of virus replication. Here we show that M1-MDM restimulation with these cytokines 7 days after infection (M12 MDM) promoted an increased restriction of HIV-1 replication characterized by very low levels of virus production near to undetectable levels. In comparison to control and M1-MDM that were not restimulated, M12 MDM showed a stronger reduction of both total and integrated HIV DNA as well as of viral mRNA expression. M12 MDM were characterized by an upregulated expression of restriction factors acting at the level of reverse transcription (RT), including apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A (APOBEC3A) and APOBEC3G, but not SAM domain and HD domain-containing protein 1 (SAMHD1). M12 MDM also showed an increased expression of Class II Transactivator (CIITA) and Tripartite Motif22 (TRIM22), two negative regulators of proviral transcription, whereas expression and phosphorylation of transcriptional inducers of HIV-1, such as nuclear factor kB (NF-kB) and signal transducer and activator of transcription 1 (STAT1), were not impaired in these cells. The almost quiescent state of the infection in M12 MDM was promptly reversed by coculture with mitogen-stimulated leukocytes or cell incubation with their fltered culture supernatant.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Identification of C3 As a Therapeutic Target for Diabetic Nephropathy By
    www.nature.com/scientificreports OPEN Identifcation of C3 as a therapeutic target for diabetic nephropathy by bioinformatics analysis ShuMei Tang, XiuFen Wang, TianCi Deng, HuiPeng Ge & XiangCheng Xiao* The pathogenesis of diabetic nephropathy is not completely understood, and the efects of existing treatments are not satisfactory. Various public platforms already contain extensive data for deeper bioinformatics analysis. From the GSE30529 dataset based on diabetic nephropathy tubular samples, we identifed 345 genes through diferential expression analysis and weighted gene coexpression correlation network analysis. GO annotations mainly included neutrophil activation, regulation of immune efector process, positive regulation of cytokine production and neutrophil-mediated immunity. KEGG pathways mostly included phagosome, complement and coagulation cascades, cell adhesion molecules and the AGE-RAGE signalling pathway in diabetic complications. Additional datasets were analysed to understand the mechanisms of diferential gene expression from an epigenetic perspective. Diferentially expressed miRNAs were obtained to construct a miRNA-mRNA network from the miRNA profles in the GSE57674 dataset. The miR-1237-3p/SH2B3, miR-1238-5p/ ZNF652 and miR-766-3p/TGFBI axes may be involved in diabetic nephropathy. The methylation levels of the 345 genes were also tested based on the gene methylation profles of the GSE121820 dataset. The top 20 hub genes in the PPI network were discerned using the CytoHubba tool. Correlation analysis with GFR showed that SYK, CXCL1, LYN, VWF, ANXA1, C3, HLA-E, RHOA, SERPING1, EGF and KNG1 may be involved in diabetic nephropathy. Eight small molecule compounds were identifed as potential therapeutic drugs using Connectivity Map. It is estimated that a total of 451 million people sufered from diabetes by 2017, and the number is speculated to be 693 million by 2045 1.
    [Show full text]
  • Epigenetic Regulation of Intestinal Peptide Transporter PEPT1
    Wang et al. Cell Death and Disease (2021) 12:532 https://doi.org/10.1038/s41419-021-03814-5 Cell Death & Disease ARTICLE Open Access Epigenetic regulation of intestinal peptide transporter PEPT1 as a potential strategy for colorectal cancer sensitization Yanhong Wang1,JiaqiWang1, Lingrong Yang2, Liqing Qiu2,YuhuiHua2,ShixiuWu3,SuZeng1,LushanYu1 and Xiaoli Zheng3 Abstract Human intestinal peptide transporter PEPT1 is commonly repressed in human colorectal cancer (CRC), yet its relationship with sensitivity to the common CRC treatment ubenimex has not previously been elucidated. In this study, we confirmed PEPT1 suppression in CRC using real-time quantitative polymerase chain reaction and western blotting and then investigated the underlying epigenetic pathways involved using bisulfite sequencing, chromatin immunoprecipitation, siRNA knockdown, and reporter gene assays. We found that PEPT1 transcriptional repression was due to both DNMT1-mediated DNA methylation of the proximal promoter region and HDAC1-mediated histone deacetylation, which blocked P300-mediated H3K18/27Ac at the PEPT1 distal promoter. Finally, the effects of the epigenetic activation of PEPT1 on the CRC response to ubenimex were evaluated using sequential combination therapy of decitabine and ubenimex both in vitro and in xenografts. In conclusion, epigenetic silencing of PEPT1 due to increased DNMT1 and HDAC1 expression plays a vital role in the poor response of CRC to ubenimex. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Introduction advanced or metastatic CRC2. The resistance of malignant Colorectal cancer (CRC) is the third most commonly tumor cells to chemotherapy is a crucial reason for poor diagnosed cancer and the second most deadly cancer survival among CRC patients. One explanation for this worldwide, with an estimated over 1.9 million new cases multidrug resistance (MDR) to cancer chemotherapy is and 935,000 deaths recorded in 20201.
    [Show full text]
  • WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT (51) International Patent Classification: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, C12Q 1/68 (2018.01) A61P 31/18 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/70 (2006.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2018/056167 OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (22) International Filing Date: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 16 October 2018 (16. 10.2018) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/573,025 16 October 2017 (16. 10.2017) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, ΓΕ , IS, IT, LT, LU, LV, (71) Applicant: MASSACHUSETTS INSTITUTE OF MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TECHNOLOGY [US/US]; 77 Massachusetts Avenue, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Cambridge, Massachusetts 02139 (US).
    [Show full text]
  • UNIVERSITY of CALIFORNIA RIVERSIDE Investigations Into The
    UNIVERSITY OF CALIFORNIA RIVERSIDE Investigations into the Role of TAF1-mediated Phosphorylation in Gene Regulation A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Cell, Molecular and Developmental Biology by Brian James Gadd December 2012 Dissertation Committee: Dr. Xuan Liu, Chairperson Dr. Frank Sauer Dr. Frances M. Sladek Copyright by Brian James Gadd 2012 The Dissertation of Brian James Gadd is approved Committee Chairperson University of California, Riverside Acknowledgments I am thankful to Dr. Liu for her patience and support over the last eight years. I am deeply indebted to my committee members, Dr. Frank Sauer and Dr. Frances Sladek for the insightful comments on my research and this dissertation. Thanks goes out to CMDB, especially Dr. Bachant, Dr. Springer and Kathy Redd for their support. Thanks to all the members of the Liu lab both past and present. A very special thanks to the members of the Sauer lab, including Silvia, Stephane, David, Matt, Stephen, Ninuo, Toby, Josh, Alice, Alex and Flora. You have made all the years here fly by and made them so enjoyable. From the Sladek lab I want to thank Eugene, John, Linh and Karthi. Special thanks go out to all the friends I’ve made over the years here. Chris, Amber, Stephane and David, thank you so much for feeding me, encouraging me and keeping me sane. Thanks to the brothers for all your encouragement and prayers. To any I haven’t mentioned by name, I promise I haven’t forgotten all you’ve done for me during my graduate years.
    [Show full text]
  • Variants in TRIM22 That Affect NOD2 Signaling Are Associated with Very Early Onset Inflammatory Bowel Disease
    Accepted Manuscript Variants in TRIM22 that Affect NOD2 Signaling Are Associated With Very Early Onset Inflammatory Bowel Disease Qi Li, Cheng Hiang Lee, Lauren A. Peters, Lucas A. Mastropaolo, Cornelia Thoeni, Abdul Elkadri, Tobias Schwerd, Jun Zhu, Bin Zhang, Yongzhong Zhao, Ke Hao, Antonio Dinarzo, Gabriel Hoffman, Brian A. Kidd, Ryan Murchie, Ziad Al Adham, Conghui Guo, Daniel Kotlarz, Ernest Cutz, Thomas D. Walters, Dror S. Shouval, Mark Curran, Radu Dobrin, Carrie Brodmerkel, Scott B. Snapper, Christoph Klein, John H. Brumell, Mingjing Hu, Ralph Nanan, Brigitte Snanter-Nanan, Melanie Wong, Francoise Le Deist, Elie Haddad, Chaim M. Roifman, Colette Deslandres, Anne M. Griffiths, Kevin J. Gaskin, Holm H. Uhlig, Eric E. Schadt, Aleixo M. Muise PII: S0016-5085(16)00123-2 DOI: 10.1053/j.gastro.2016.01.031 Reference: YGAST 60258 To appear in: Gastroenterology Accepted Date: 22 January 2016 Please cite this article as: Li Q, Lee CH, Peters LA, Mastropaolo LA, Thoeni C, Elkadri A, Schwerd T, Zhu J, Zhang B, Zhao Y, Hao K, Dinarzo A, Hoffman G, Kidd BA, Murchie R, Al Adham Z, Guo C, Kotlarz D, Cutz E, Walters TD, Shouval DS, Curran M, Dobrin R, Brodmerkel C, Snapper SB, Klein C, Brumell JH, Hu M, Nanan R, Snanter-Nanan B, Wong M, Le Deist F, Haddad E, Roifman CM, Deslandres C, Griffiths AM, Gaskin KJ, Uhlig HH, Schadt EE, Muise AM, Variants in TRIM22 that Affect NOD2 Signaling Are Associated With Very Early Onset Inflammatory Bowel Disease, Gastroenterology (2016), doi: 10.1053/j.gastro.2016.01.031. This is a PDF file of an unedited manuscript that has been accepted for publication.
    [Show full text]
  • The Viral Oncoproteins Tax and HBZ Reprogram the Cellular Mrna Splicing Landscape
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021. 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. The viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape Charlotte Vandermeulen1,2,3, Tina O’Grady3, Bartimee Galvan3, Majid Cherkaoui1, Alice Desbuleux1,2,4,5, Georges Coppin1,2,4,5, Julien Olivet1,2,4,5, Lamya Ben Ameur6, Keisuke Kataoka7, Seishi Ogawa7, Marc Thiry8, Franck Mortreux6, Michael A. Calderwood2,4,5, David E. Hill2,4,5, Johan Van Weyenbergh9, Benoit Charloteaux2,4,5,10, Marc Vidal2,4*, Franck Dequiedt3*, and Jean-Claude Twizere1,2,11* 1Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium.2Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.3Laboratory of Gene Expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium.4Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. 5Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.6Laboratory of Biology and Modeling of the Cell, CNRS UMR 5239, INSERM U1210, University of Lyon, Lyon, France.7Department of Pathology and Tumor Biology, Kyoto University, Japan.8Unit of Cell and Tissue Biology, GIGA Institute, University of Liege, Liege, Belgium.9Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven, Leuven, Belgium.10Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium.11Lead Contact. *Correspondence: [email protected]; [email protected]; [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021.
    [Show full text]
  • Virtual Chip-Seq: Predicting Transcription Factor Binding
    bioRxiv preprint doi: https://doi.org/10.1101/168419; this version posted March 12, 2019. 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. 1 Virtual ChIP-seq: predicting transcription factor binding 2 by learning from the transcriptome 1,2,3 1,2,3,4,5 3 Mehran Karimzadeh and Michael M. Hoffman 1 4 Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada 2 5 Princess Margaret Cancer Centre, Toronto, ON, Canada 3 6 Vector Institute, Toronto, ON, Canada 4 7 Department of Computer Science, University of Toronto, Toronto, ON, Canada 5 8 Lead contact: michael.hoff[email protected] 9 March 8, 2019 10 Abstract 11 Motivation: 12 Identifying transcription factor binding sites is the first step in pinpointing non-coding mutations 13 that disrupt the regulatory function of transcription factors and promote disease. ChIP-seq is 14 the most common method for identifying binding sites, but performing it on patient samples is 15 hampered by the amount of available biological material and the cost of the experiment. Existing 16 methods for computational prediction of regulatory elements primarily predict binding in genomic 17 regions with sequence similarity to known transcription factor sequence preferences. This has limited 18 efficacy since most binding sites do not resemble known transcription factor sequence motifs, and 19 many transcription factors are not even sequence-specific. 20 Results: 21 We developed Virtual ChIP-seq, which predicts binding of individual transcription factors in new 22 cell types using an artificial neural network that integrates ChIP-seq results from other cell types 23 and chromatin accessibility data in the new cell type.
    [Show full text]
  • Zenglv Fumai Granule Protects Cardiomyocytes Against Hypoxia/Reoxygenation-Induced Apoptosis Via Inhibiting TRIM28 Expression
    MOLECULAR MEDICINE REPORTS 23: 171, 2021 Zenglv Fumai Granule protects cardiomyocytes against hypoxia/reoxygenation-induced apoptosis via inhibiting TRIM28 expression XIAO-HUA ZHANG1, HONG-YU ZHAO2, YU WANG2, LIN DI2, XIN-YU LIU2, FENG QIAN1 and SHU-RONG LIU1 1Department of Cardiovascular Diseases, The First Clinical Hospital of Jilin Academy of Chinese Medicine Sciences; 2Drug Pharmacology and Toxicology Evaluation Center, Jilin Academy of Chinese Medicine Sciences, Changchun, Jilin 130021, P.R. China Received April 14, 2020; Accepted November 23, 2020 DOI: 10.3892/mmr.2020.11810 Abstract. Myocardial ischemia/reperfusion (MIR) injury, limited by the action of ROS inhibitor N-acetyl-L-cysteine. In which occurs following acute myocardial infarction, can addition, the mRNA and protein levels of antioxidant enzyme cause secondary damage to the heart. Tripartite interaction glutathione peroxidase (GPX)1 were significantly downregu- motif (TRIM) proteins, a class of E3 ubiquitin ligases, have lated in H/R-injured cardiomyocytes. TRIM28 knockdown been recognized as critical regulators in MIR injury. Zenglv restored GPX1 protein levels but had no effect on mRNA Fumai Granule (ZFG) is a clinical prescription for the treat- expression levels. Co-immunoprecipitation and ubiquitination ment of sick sinus syndrome, a disease that is associated assays demonstrated that TRIM28 negatively regulated GPX1 with MIR injury. The present study aimed to investigate the via ubiquitination. In sum, the present study revealed that ZFG effect of ZFG on MIR injury and to determine whether ZFG attenuated H/R-induced cardiomyocyte apoptosis by regu- exerts its effects via regulation of TRIM proteins. In order lating the TRIM28/GPX1/ROS pathway.
    [Show full text]
  • An Influenza Virus-Triggered SUMO Switch Orchestrates Co-Opted Endogenous Retroviruses to Stimulate Host Antiviral Immunity
    An influenza virus-triggered SUMO switch orchestrates co-opted endogenous retroviruses to stimulate host antiviral immunity Nora Schmidta, Patricia Dominguesa,1,2, Filip Golebiowskia,1, Corinna Patzinaa,3, Michael H. Tathamb, Ronald T. Hayb, and Benjamin G. Halea,4 aInstitute of Medical Virology, University of Zurich, 8057 Zurich, Switzerland; and bCentre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, DD1 5EH Dundee, United Kingdom Edited by Stephen P. Goff, Columbia University Medical Center, New York, NY, and approved July 15, 2019 (received for review April 24, 2019) Dynamic small ubiquitin-like modifier (SUMO) linkages to diverse hypothesis that stress-induced host-derived self elements may have cellular protein groups are critical to orchestrate resolution of stresses been co-opted to promote antiviral IFN-mediated defenses. such as genome damage, hypoxia, or proteotoxicity. Defense against SUMOylation is a dynamic posttranslational modification of pathogen insult (often reliant upon host recognition of “non-self” protein lysine residues that is crucial for regulating many cellular nucleic acids) is also modulated by SUMO, but the underlying mech- processes, including transcription, mRNA processing, chromatin anisms are incompletely understood. Here, we used quantitative remodeling, DNA replication, and DNA damage responses (14). SILAC-based proteomics to survey pan-viral host SUMOylation re- Importantly, SUMOylation is highly stress-responsive, and is a sponses, creating a resource of almost 600 common and unique critical mediator in the resolution of cellular insults, including SUMO remodeling events that are mounted during influenza A and hypoxia, heat shock, and genotoxic stresses (15). The small B virus infections, as well as during viral innate immune stimulation.
    [Show full text]
  • Identification of a Potential Tumor Suppressor Gene, UBL3, in Non-Small Cell Lung Cancer
    Cancer Biol Med 2020. doi: 10.20892/j.issn.2095-3941.2019.0279 ORIGINAL ARTICLE Identification of a potential tumor suppressor gene, UBL3, in non-small cell lung cancer Xinchun Zhao1,2,3, Yongchun Zhou4, Qian Hu2,5, Sanhui Gao2,3, Jie Liu2,3, Hong Yu2,5, Yanfei Zhang2,3, Guizhen Wang2,3, Yunchao Huang4, Guangbiao Zhou2,3 1School of Life Sciences, University of Science and Technology of China, Hefei 230026, China; 2State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; 3State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; 4Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University, Kunming 650106, China;5 School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100029, China ABSTRACT Objective: Oncogenes have been shown to be drivers of non-small cell lung cancer (NSCLC), yet the tumor suppressing genes involved in lung carcinogenesis remain to be systematically investigated. This study aimed to identify tumor suppressing ubiquitin pathway genes (UPGs) that were critical to lung tumorigenesis. Methods: The 696 UPGs were silenced by an siRNA screening in NSCLC cells; the potential tumor suppressing UPGs were analyzed, and their clinical significance was investigated. Results: We reported that silencing of 11 UPGs resulted in enhanced proliferation of NSCLC cells, and four UPGs (UBL3, TRIM22, UBE2G2, and MARCH1) were significantly downregulated in tumor samples compared to that in normal lung tissues and their expression levels were positively associated with overall survival (OS) of NSCLC patients.
    [Show full text]