Investigation of Chd7 Function in Developmental Models Of

Total Page:16

File Type:pdf, Size:1020Kb

Investigation of Chd7 Function in Developmental Models Of INVESTIGATION OF CHD7 FUNCTION IN DEVELOPMENTAL MODELS OF CHARGE SYNDROME by STEPHANIE ANN BALOW Submitted in partial fulfillment of the requirements For the degree of Doctor of Philosophy Dissertation advisor: Peter C. Scacheri, Ph.D. Department of Genetics and Genome Sciences CASE WESTERN RESERVE UNIVERSITY May 2014 To my parents, for their constant love and support ! "! Table of Contents List of tables!!!!!!!!!!!!!!!!!!!!!!!!!!!.... 4 List of figures!!!!!!!!!!!!!!!!!!!!!!!!!!!.. 5 Acknowledgements!!!!!!!!!!!!!!!!!!!!!!!!... 7 Abstract!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 9 Chapter 1: Introduction and Background!!!!!!!!!!!!!!.. 11 Overview of chromatin remodeling and development!!!!!!!!12 Chromodomain helicase DNA-binding (CHD) protein family!!!!!13 Subfamily I: CHD1 and CHD2!!!!!!!!!!!!!!...13 Subfamily II: CHD3, CHD4, and CHD5!!!!!!!!!!!15 Subfamily III: CHD6, CHD7, CHD8, and CHD9!!!!!!!. 17 CHD7!!!!!!!!!!!!!!!!!!!!!!!!!!!! 18 Molecular function of the CHD7 protein!!!!!!!!!!...18 Expression of CHD7 during development!!!!!!!!!. 22 CHARGE syndrome!!!!!!!!!!!!!!!!!!!!!!23 Overview!!!!!!!!!!!!!!!!!!!!!!!.. 23 Expansion of the CHARGE syndrome clinical presentation!! 23 Ocular coloboma!!!!!!!!!!!!!!!!!.24 Heart defects!!!!!!!!!!!!!!!!!!.. 24 Choanal atresia!!!!!!!!!!!!!!!!!.. 24 Growth retardation!!!!!!!!!!!!!!!!. 25 Genital abnormalities!!!!!!!!!!!!!!!. 25 Ear anomalies!!!!!!!!!!!!!!!!!!. 26 Other common phenotypes!!!!!!!!!!!!.. 26 Mutation spectrum!!!!!!!!!!!!!!!!!!!. 27 Clinical overlap with other syndromes!!!!!!!!!!! 28 Animal models of CHARGE syndrome!!!!!!!!!!...29 Regulation of rDNA expression!!!!!!!!!!!!!!!!....31 The nucleolus and building a ribosome!!!!!!!!!!...32 Structure and transcriptional regulation of rDNA!!!!!!!32 Epigenetic regulation of rDNA repeats!!!!!!!!!!....35 FBXL10 is an epigenetic modifier of rDNA expression!!!.....36 Dysregulation of ribosome biogenesis!!!!!!!!!!!!!.!39 The nucleolar stress response!!!!!!!!!!!!!!..39 Ribosomopathies!!!!!!!!!!!!!!!!!!!.!43 Summary and Research Aims!!!!!!!!!!!!!!!!!...46 Chapter 2: Knockdown of fbxl10/kdm2bb rescues chd7 morphant phenotype in a zebrafish model of CHARGE syndrome!!!!!!...!..49 Abstract!!!!!!!!!!!!!!!!!!!!!!!!!...!...50 Introduction!!!!!!!!!!!!!!!!!!!!!!!!...!.52 Results!!!!!!!!!!!!!!!!!!!!!!!!!!...!.55 Organization of the zebrafish chd7 gene!!!!!!!!!......55 chd7-morpholino gene targeting recapitulates major features of CHARGE syndrome!!!!!!!!!!!!!!!!!!.55 ! #! chd7 morphants develop defects in neural crest-derived craniofacial cartilage!!!!!!!!!!!!!!!!!!..63 Chd7 is required for normal cellular proliferation during zebrafish development!!!!!!!!!!!!!!!!!..68 Fbxl10 regulates rRNA levels during zebrafish embryogenesis!!!!!!!!!!!!!!!!!!!!...72 Rescue of chd7 morphant phenotype upon knockdown of fbxl10!!!!!!!!!!!!!!!!!!!!!!!!...76 Analysis of rRNA and cell cycle genes in fbxl10/chd7 double morphants!!!!!!!!!!!!!!!!!!!!!!...84 Discussion!!!!!!!!!!!!!!!!!!!!!!!!!...87 Materials and methods!!!!!!!!!!!!!!!!!!!!..91 Chapter 3: Dissecting CHD7 functions in a human iPS cell model of CHARGE syndrome..!!!!!!!!!!!!!!!!!!!!!!!..98 Introduction!!!!!!!!!!!!!!!!!!!!!!!!!.99 Results!!!!!!!!!!!!!!!!!!!!!!!!!!...102 Early characterization and preliminary data in CHARGE syndrome patient-derived iPS cells!!!!!!!.102 Discussion!!!!!!!!!!!!!!!!!!!!!!!!!..111 Materials and methods!!!!!!!!!!!!!!!!!!!!.114 Chapter 4: Discussion and future directions!!!!!!!!!!!!..117 Summary!!!!!!!!!!!!!!!!!!!!!!!!!!118 Discussion and future directions!!!!!!!!!!!!!!!!120 Implications of zebrafish chd7 morphant model studies!!!120 Does chd7 regulate cellular proliferation in specific tissues?..........................................................................120 What is the molecular mechanism of chd7 morphant rescue by fbxl10 knockdown!!!!!!!!!!!...121 Are these findings applicable to mammalian development?.................................................................125 Future experiments investigating the nucleolar and nuclear functions of CHD7 using iPS cells as a developmental model of CHARGE syndrome!!!!!!!..126 Summary remarks!!!!!!!!!!!!!!!!!!!!!....132 Bibliography!!!!!!!!!!!!!!!!!!!!!!!!!!....134 ! $! List of tables Chapter 2 Table 2-1. CHD7 mutant phenotypes comparison across multiple species!!!!!!!!!!!!!!!!!!!!!!!.62 Table 2-2. PCR primers designed to measure gene expression!!!!!97 ! %! List of figures Chapter 1 Figure 1-1. Members of the CHD family!!!!!!!!!!!!!!!..14 Figure 1-2. Simple schematic of a single mouse rDNA gene!!!!!!..34 Figure 1-3. Schematic of FBXL10 protein domain composition!!!!!..37 Figure 1-4. Overview of the nucleolar stress response!!!!!!!!!40 Figure 1-5. Disruption of ribosomal biogenesis alters nucleolar structure resulting in the stabilization of p53!!!!!!!!!!!..42 Chapter 2 Figure 2-1. Morpholino targeting of the zebrafish chd7 RNA induces an aberrant transcript!!!!!!!!!!!!!!!!!!..56 Figure 2-2. Zebrafish chd7 targeting results in CHARGE-like phenotypes!!!!!!!!!!!!!!!!!!!!!..60 Figure 2-3. chd7 morphants display variable defects in craniofacial cartilage!!!!!!!!!!!!!!!!!!!!!!...64 Figure 2-4. Sectioning of chd7 morphants reveals moderate to severe craniofacial cartilage abnormalities!!!!!!!!!!!.66 Figure 2-5. chd7 targeting impairs cellular proliferation!!!!!!!!...69 Figure 2-6. Targeting of zebrafish fbxl10 transcript modulates pre-rRNA expression!!!!!!!!!!!!!!!!!!!!!...73 Figure 2-7. Modulation of fbxl10 expression results in normal development of gross anatomical and craniofacial structures!!!!!!..........................................................75 Figure 2-8. Modulation of fbxl10 expression rescues CHARGE-like phenotypes and improves cellular proliferation defects.!!.77 Figure 2-9. Changes in cellular proliferation correlate with embryonic head size!!!!!!!!!!!!!!!!!!!!!!79 Figure 2-10. Sagittal sectioning of 4 dpf chd7/fbxl10 double morphants indicates variable restoration of ceratobranchial cartilage development!!!!!!!!!!!!!!!!!!!!..82 ! &! Figure 2-11. Gene expression changes in cell-cycle regulators in chd7/fbxl10 double morphants!!!!!!!!!!!!!85 Chapter 3 Figure 3-1. The locations of CHD7 mutations in CHARGE syndrome patient-derived iPS cell lines!!!!!!!!!!!!!..103 Figure 3-2. Reprogrammed CHARGE syndrome patient cells express multiple markers of pluripotency!!!!!!!!!!!....105 Figure 3-3. CHD7 expression is significantly reduced in CHARGE syndrome patient-derived iPS cells!!!!!!!!!.!..106 Figure 3-4. CHD7 protein localizes to different cell sub-compartments in different cell types!!!!!!!!!!!!!!!!....109 Figure 3-5. Decreases in CHD7 expression do not affect 45S pre-rRNA expression in iPS cells!!!!!!!!!!!!!!!....110 Chapter 4 Figure 4-1. Model of interactions potentially involved in molecular mechanism of rescue in chd7/fbxl10 double morphants!....123 Figure 4-2. Multiple histone tail modifications demarcate enhancer activity and expression of target genes!!!!...................130 ! '! Acknowledgments First and foremost, I would like to thank my advisor, Peter Scacheri, for his expertise, guidance, and his commitment to my success. My time in his laboratory has been invaluable and has helped me build strong skill sets both at the bench and in communication. It has been clear over these past 5 years that he has a vested interest in my well-being, and I appreciate this immensely. I am truly grateful for all his help, patience, and encouragement, which have helped mold me into a more confident and independent scientist. I would also like to thank my committee members Ron Conlon, Peter Harte, and Brian McDermott for their support and encouragement throughout my graduate career. They continuously provided vital outside perspective to my project by asking questions and providing suggestions. I am also indebted to our collaborator, Paul Tesar, for his help and advice. I would also like to extend my thank you to the entire departmental faculty and administrative staff. I truly believe that my interactions with the faculty over the years, whether in the classroom or casually in the hallway, have been vital in shaping my progress. I would also like to thank the past and present members of the Scacheri laboratory, as without them, none of this would be possible. Although everyone has been a great source of camaraderie both personally and scientifically, there are three members that I would like to especially thank. I am particularly indebted to Cindy Bartels for her technical support and her overall willingness to drop everything to help me in times of need. I would also like to thank Olivia Corradin, who for the past several years, has not only been my baymate but also a good ! (! friend. She is always a constant source of positivity and has always been willing to listen and discuss. Lastly, I am beyond grateful for my friendship with my previous baymate and “lab brother”, Gabe Zentner. I owe him more than I can say for the scientific discussions that helped shaped the beginnings of this project and also for his mental support along the way. Furthermore, I would like to thank my friends from both here and afar for all their support. I would like to especially thank my best friend, Meghana Gupta. We met during the first week of graduate school orientation and I could not have been luckier to have met such a loyal and caring friend. She has been there for me in the best and worst of times over the years and, without her, I think I would have lost my sanity ages ago. I would also like to thank my dear friends Jason Heaney, Lorrie Rice, Meetha Gould,
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]
  • 422.Full.Pdf
    Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Research Dioxin receptor and SLUG transcription factors regulate the insulator activity of B1 SINE retrotransposons via an RNA polymerase switch Angel Carlos Roma´n,1 Francisco J. Gonza´lez-Rico,1 Eduardo Molto´,2,3 Henar Hernando,4 Ana Neto,5 Cristina Vicente-Garcia,2,3 Esteban Ballestar,4 Jose´ L. Go´mez-Skarmeta,5 Jana Vavrova-Anderson,6 Robert J. White,6,7 Lluı´s Montoliu,2,3 and Pedro M. Ferna´ndez-Salguero1,8 1Departamento de Bioquı´mica y Biologı´a Molecular, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain; 2Centro Nacional de Biotecnologı´a (CNB), Consejo Superior de Investigaciones Cientı´ficas (CSIC), Department of Molecular and Cellular Biology, Campus de Cantoblanco, C/Darwin 3, 28049 Madrid, Spain; 3Centro de Investigacio´n Biome´dica en Red de Enfermedades Raras (CIBERER), ISCIII, Madrid, Spain; 4Chromatin and Disease Group, Cancer Epigenetics and Biology Programme, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08907, Spain; 5Centro Andaluz de Biologı´a del Desarrollo, CSIC-Universidad Pablo de Olavide, 41013 Sevilla, Spain; 6College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom; 7Beatson Institute for Cancer Research, Glasgow, G61 1BD, United Kingdom Complex genomes utilize insulators and boundary elements to help define spatial and temporal gene expression patterns. We report that a genome-wide B1 SINE (Short Interspersed Nuclear Element) retrotransposon (B1-X35S) has potent in- trinsic insulator activity in cultured cells and live animals. This insulation is mediated by binding of the transcription factors dioxin receptor (AHR) and SLUG (SNAI2) to consensus elements present in the SINE.
    [Show full text]
  • Fish Mutant, Where Is Thy Phenotype?
    PERSPECTIVE Fish mutant, where is thy phenotype? Darius Balciunas* Department of Biology, Temple University, Philadelphia, Pennsylvania, United States of America * [email protected] The field of genetics emerged as a study of the inheritance of desirable or otherwise interesting traits. Mutations were characterized as recessive or dominant, assigned to complementation groups, mapped, and finally, the affected genes were identified. By default, recessive mutations could only be isolated in genes that played an important role in the biological process of inter- est, be it pea color or segmentation pattern of the fruit fly embryo. As methodologies to mutate specific genes in various model systems were developed, scien- tists began to employ reverse genetics, whereby a gene of interest is selected and a mutant is generated. Ideally, the mutant displays a phenotype that can be studied (green panels in Fig 1). Such best-case scenarios pose the danger of confirmation bias ([1] and references therein). It may therefore be prudent to validate the phenotype by engineering an independent mutant allele. This is especially straightforward in zebrafish, given that targeted mutagenesis using CRISPR/Cas9 requires relatively little effort [2±4]. In zebrafish, the phenotype may also be confirmed by performing knockdown using morpholino oligonucleotides [5±6]. a1111111111 Real experiments rarely follow best-case scenarios, and very frequently, mutants generated a1111111111 by reverse genetics fail to display overt phenotypes. Are the majority of protein-coding genes a1111111111 indeed not required, often despite a very high degree of evolutionary conservation? Genetic a1111111111 redundancy, most obviously in the form of homologous or duplicated genes, certainly contrib- a1111111111 utes to a lack of mutant phenotypes.
    [Show full text]
  • Transcriptome-Wide Profiling of Cerebral Cavernous Malformations
    www.nature.com/scientificreports OPEN Transcriptome-wide Profling of Cerebral Cavernous Malformations Patients Reveal Important Long noncoding RNA molecular signatures Santhilal Subhash 2,8, Norman Kalmbach3, Florian Wegner4, Susanne Petri4, Torsten Glomb5, Oliver Dittrich-Breiholz5, Caiquan Huang1, Kiran Kumar Bali6, Wolfram S. Kunz7, Amir Samii1, Helmut Bertalanfy1, Chandrasekhar Kanduri2* & Souvik Kar1,8* Cerebral cavernous malformations (CCMs) are low-fow vascular malformations in the brain associated with recurrent hemorrhage and seizures. The current treatment of CCMs relies solely on surgical intervention. Henceforth, alternative non-invasive therapies are urgently needed to help prevent subsequent hemorrhagic episodes. Long non-coding RNAs (lncRNAs) belong to the class of non-coding RNAs and are known to regulate gene transcription and involved in chromatin remodeling via various mechanism. Despite accumulating evidence demonstrating the role of lncRNAs in cerebrovascular disorders, their identifcation in CCMs pathology remains unknown. The objective of the current study was to identify lncRNAs associated with CCMs pathogenesis using patient cohorts having 10 CCM patients and 4 controls from brain. Executing next generation sequencing, we performed whole transcriptome sequencing (RNA-seq) analysis and identifed 1,967 lncRNAs and 4,928 protein coding genes (PCGs) to be diferentially expressed in CCMs patients. Among these, we selected top 6 diferentially expressed lncRNAs each having signifcant correlative expression with more than 100 diferentially expressed PCGs. The diferential expression status of the top lncRNAs, SMIM25 and LBX2-AS1 in CCMs was further confrmed by qRT-PCR analysis. Additionally, gene set enrichment analysis of correlated PCGs revealed critical pathways related to vascular signaling and important biological processes relevant to CCMs pathophysiology.
    [Show full text]
  • Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture
    Genes 2015, 6, 790-811; doi:10.3390/genes6030790 OPEN ACCESS genes ISSN 2073-4425 www.mdpi.com/journal/genes Review Chromatin Insulators and Topological Domains: Adding New Dimensions to 3D Genome Architecture Navneet K. Matharu 1,* and Sajad H. Ahanger 2,* 1 Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143, USA 2 Department of Ophthalmology, Lab for Retinal Cell Biology, University of Zurich, Wagistrasse 14, Zurich 8952, Switzerland * Authors to whom correspondence should be addressed; E-Mails: [email protected] (N.K.M.); [email protected] (S.H.A.). Academic Editor: Jessica Tyler Received: 8 June 2015 / Accepted: 20 August 2015 / Published: 1 September 2015 Abstract: The spatial organization of metazoan genomes has a direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. It is imperative to understand the mechanisms that shape the 3D organization of the eukaryotic genomes. Chromatin insulators have emerged as one of the central components of the genome organization tool-kit across species. Recent advancements in chromatin conformation capture technologies have provided important insights into the architectural role of insulators in genomic structuring. Insulators are involved in 3D genome organization at multiple spatial scales and are important for dynamic reorganization of chromatin structure during reprogramming and differentiation. In this review, we will discuss the classical view and our renewed understanding of insulators as global genome organizers. We will also discuss the plasticity of chromatin structure and its re-organization during pluripotency and differentiation and in situations of cellular stress.
    [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]
  • Molecular Basis of the Function of Transcriptional Enhancers
    cells Review Molecular Basis of the Function of Transcriptional Enhancers 1,2, 1, 1,3, Airat N. Ibragimov y, Oleg V. Bylino y and Yulii V. Shidlovskii * 1 Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; [email protected] (A.N.I.); [email protected] (O.V.B.) 2 Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia 3 I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia * Correspondence: [email protected]; Tel.: +7-4991354096 These authors contributed equally to this study. y Received: 30 May 2020; Accepted: 3 July 2020; Published: 5 July 2020 Abstract: Transcriptional enhancers are major genomic elements that control gene activity in eukaryotes. Recent studies provided deeper insight into the temporal and spatial organization of transcription in the nucleus, the role of non-coding RNAs in the process, and the epigenetic control of gene expression. Thus, multiple molecular details of enhancer functioning were revealed. Here, we describe the recent data and models of molecular organization of enhancer-driven transcription. Keywords: enhancer; promoter; chromatin; transcriptional bursting; transcription factories; enhancer RNA; epigenetic marks 1. Introduction Gene transcription is precisely organized in time and space. The process requires the participation of hundreds of molecules, which form an extensive interaction network. Substantial progress was achieved recently in our understanding of the molecular processes that take place in the cell nucleus (e.g., see [1–9]).
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Histone Methylases As Novel Drug Targets. Focus on EZH2 Inhibition. Catherine BAUGE1,2,#, Céline BAZILLE 1,2,3, Nicolas GIRARD1
    Histone methylases as novel drug targets. Focus on EZH2 inhibition. Catherine BAUGE1,2,#, Céline BAZILLE1,2,3, Nicolas GIRARD1,2, Eva LHUISSIER1,2, Karim BOUMEDIENE1,2 1 Normandie Univ, France 2 UNICAEN, EA4652 MILPAT, Caen, France 3 Service d’Anatomie Pathologique, CHU, Caen, France # Correspondence and copy request: Catherine Baugé, [email protected], EA4652 MILPAT, UFR de médecine, Université de Caen Basse-Normandie, CS14032 Caen cedex 5, France; tel: +33 231068218; fax: +33 231068224 1 ABSTRACT Posttranslational modifications of histones (so-called epigenetic modifications) play a major role in transcriptional control and normal development, and are tightly regulated. Disruption of their control is a frequent event in disease. Particularly, the methylation of lysine 27 on histone H3 (H3K27), induced by the methylase Enhancer of Zeste homolog 2 (EZH2), emerges as a key control of gene expression, and a major regulator of cell physiology. The identification of driver mutations in EZH2 has already led to new prognostic and therapeutic advances, and new classes of potent and specific inhibitors for EZH2 show promising results in preclinical trials. This review examines roles of histone lysine methylases and demetylases in cells, and focuses on the recent knowledge and developments about EZH2. Key-terms: epigenetic, histone methylation, EZH2, cancerology, tumors, apoptosis, cell death, inhibitor, stem cells, H3K27 2 Histone modifications and histone code Epigenetic has been defined as inheritable changes in gene expression that occur without a change in DNA sequence. Key components of epigenetic processes are DNA methylation, histone modifications and variants, non-histone chromatin proteins, small interfering RNA (siRNA) and micro RNA (miRNA).
    [Show full text]
  • Molecular Diagnostic Requisition
    BAYLOR MIRACA GENETICS LABORATORIES SHIP TO: Baylor Miraca Genetics Laboratories 2450 Holcombe, Grand Blvd. -Receiving Dock PHONE: 800-411-GENE | FAX: 713-798-2787 | www.bmgl.com Houston, TX 77021-2024 Phone: 713-798-6555 MOLECULAR DIAGNOSTIC REQUISITION PATIENT INFORMATION SAMPLE INFORMATION NAME: DATE OF COLLECTION: / / LAST NAME FIRST NAME MI MM DD YY HOSPITAL#: ACCESSION#: DATE OF BIRTH: / / GENDER (Please select one): FEMALE MALE MM DD YY SAMPLE TYPE (Please select one): ETHNIC BACKGROUND (Select all that apply): UNKNOWN BLOOD AFRICAN AMERICAN CORD BLOOD ASIAN SKELETAL MUSCLE ASHKENAZIC JEWISH MUSCLE EUROPEAN CAUCASIAN -OR- DNA (Specify Source): HISPANIC NATIVE AMERICAN INDIAN PLACE PATIENT STICKER HERE OTHER JEWISH OTHER (Specify): OTHER (Please specify): REPORTING INFORMATION ADDITIONAL PROFESSIONAL REPORT RECIPIENTS PHYSICIAN: NAME: INSTITUTION: PHONE: FAX: PHONE: FAX: NAME: EMAIL (INTERNATIONAL CLIENT REQUIREMENT): PHONE: FAX: INDICATION FOR STUDY SYMPTOMATIC (Summarize below.): *FAMILIAL MUTATION/VARIANT ANALYSIS: COMPLETE ALL FIELDS BELOW AND ATTACH THE PROBAND'S REPORT. GENE NAME: ASYMPTOMATIC/POSITIVE FAMILY HISTORY: (ATTACH FAMILY HISTORY) MUTATION/UNCLASSIFIED VARIANT: RELATIONSHIP TO PROBAND: THIS INDIVIDUAL IS CURRENTLY: SYMPTOMATIC ASYMPTOMATIC *If family mutation is known, complete the FAMILIAL MUTATION/ VARIANT ANALYSIS section. NAME OF PROBAND: ASYMPTOMATIC/POPULATION SCREENING RELATIONSHIP TO PROBAND: OTHER (Specify clinical findings below): BMGL LAB#: A COPY OF ORIGINAL RESULTS ATTACHED IF PROBAND TESTING WAS PERFORMED AT ANOTHER LAB, CALL TO DISCUSS PRIOR TO SENDING SAMPLE. A POSITIVE CONTROL MAY BE REQUIRED IN SOME CASES. REQUIRED: NEW YORK STATE PHYSICIAN SIGNATURE OF CONSENT I certify that the patient specified above and/or their legal guardian has been informed of the benefits, risks, and limitations of the laboratory test(s) requested.
    [Show full text]
  • Table of Contents
    Table of Contents 1. - EXAMINING ATTITUDES AND WILLINGNESS TO PAY FOR AQUACULTURED SEAFOOD ATTRIBUTES I. Ko Britwum * II. Caroline Noblet 2. - Development of a Hybrid Thermoplastic Composite and Concrete Deck System I. Benjamin Smith * II. William Davids 3. - Undergraduate Nursing Students’ Perspectives and Attitudes Caring for Elderly Patients at End of Life I. Karen Chase * II. Patricia Poirier 4. - Backpack Programs: How Maine Elementary Schools Are Tackling Childhood Hunger I. Julianna Acheson * II. Julia Van Steenberge III. Dean Rando IV. Ashlee Atchinson V. Sandra Caron 5. - Using Structure from Motion and 3D Printing as a Method for Preserving the Petroglyphs of Machias Bay, Maine I. Kendra Bird * II. Lisa Neuman 6. - Capacity Assessment of Older T-Beam Bridges Using Field Load Testing and Nonlinear Proxy Finite-Element Analysis I. Andrew Schanck * II. William Davids 7. - Interventions Supporting Social Communication Skills in Preschool-Aged Children with Autism Spectrum Disorder I. Paige Hanson * II. Paige Castonguay III. Heather Lowry IV. Taylor Dupont V. Paige Lane 8. - Attitudes Towards Immigration Following the 2018 Family Separation Crisis: Content Analysis of Tweets in The Washington Post vs Fox News I. Rebecca Blodgett * II. Vincent Eze III. Ariana Cruwys IV. Sandra Caron 9. - Nurses Role in Central Line-Associated Bloodstream Infection Prevention I. Laura Roberts * II. Julia Schnee III. Bronwyn West IV. Alex Roderick V. Valerie Herbert 10. - Overwintering strategies of the salmon louse Lepeophtheirus salmonis I. Emma Taccardi * II. Carrie Byron III. Ian Bricknell 11. - The eects of diverse aged enrollment on community school literacy rates in rural Zambia: Case study on Impact Network International schools, Eastern Province Zambia I.
    [Show full text]
  • Histone Deacetylase Inhibitors Synergizes with Catalytic Inhibitors of EZH2 to Exhibit Anti-Tumor Activity in Small Cell Carcinoma of the Ovary, Hypercalcemic Type
    Author Manuscript Published OnlineFirst on September 19, 2018; DOI: 10.1158/1535-7163.MCT-18-0348 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Histone deacetylase inhibitors synergizes with catalytic inhibitors of EZH2 to exhibit anti- tumor activity in small cell carcinoma of the ovary, hypercalcemic type Yemin Wang1,2,*, Shary Yuting Chen1,2, Shane Colborne3, Galen Lambert2, Chae Young Shin2, Nancy Dos Santos4, Krystal A. Orlando5, Jessica D. Lang6, William P.D. Hendricks6, Marcel B. Bally4, Anthony N. Karnezis1,2, Ralf Hass7, T. Michael Underhill8, Gregg B. Morin3,9, Jeffrey M. Trent6, Bernard E. Weissman5, David G. Huntsman1,2,10,* 1Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada 2Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC, Canada. 3Michael Smith Genome Science Centre, British Columbia Cancer Agency, Vancouver, BC, Canada. 4Department of Experimental Therapeutics, British Columbia Cancer Research Centre, Vancouver, BC, Canada. 5Department of Pathology and Laboratory Medicine and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA. 6Division of Integrated Cancer Genomics, Translational Genomics Research Institute (TGen), Phoenix, AZ, USA. 7Department of Obstetrics and Gynecology, Hannover Medical School, D-30625 Hannover, Germany. 8Department of Cellular and Physiological Sciences and Biomedical Research Centre, University 1 Downloaded from mct.aacrjournals.org on September 26, 2021. © 2018 American Association for Cancer Research. Author Manuscript Published OnlineFirst on September 19, 2018; DOI: 10.1158/1535-7163.MCT-18-0348 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited.
    [Show full text]