DOCSLIB.ORG

Prelamin a Influences a Program of Gene Expression in Regulation of Cell Cycle Control Christina N

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Prelamin a Influences a Program of Gene Expression in Regulation of Cell Cycle Control Christina N East Tennessee State University Digital Commons @ East Tennessee State University Electronic Theses and Dissertations Student Works 5-2012 Prelamin A Influences a Program of Gene Expression In Regulation of Cell Cycle Control Christina N. Bridges East Tennessee State University Follow this and additional works at: https://dc.etsu.edu/etd Part of the Biological Phenomena, Cell Phenomena, and Immunity Commons Recommended Citation Bridges, Christina N., "Prelamin A Influences a Program of Gene Expression In Regulation of Cell Cycle Control" (2012). Electronic Theses and Dissertations. Paper 1213. https://dc.etsu.edu/etd/1213 This Dissertation - Open Access is brought to you for free and open access by the Student Works at Digital Commons @ East Tennessee State University. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of Digital Commons @ East Tennessee State University. For more information, please contact [email protected]. Prelamin A Influences a Program of Gene Expression in the Regulation of Cell Cycle Control _____________________ A dissertation presented to the faculty of the Department of Biochemistry & Molecular Biology East Tennessee State University In partial fulfillment of the requirements for the degree Doctor of Philosopy in Biomedical Sciences _____________________ by Christina Norton Bridges May 2012 _____________________ Antonio E. Rusiñol, Chair Douglas P. Thewke Sharon E. Campbell Deling Yin Robert V. Schoborg Keywords: Prelamin A, Lamin A, Cell Cycle, Quiescence, Senescence, FoxO, p27, Progeria, Pin1 ABSTRACT Prelamin A Influences a Program of Gene Expression In Regulation of Cell Cycle Control by Christina Norton Bridges The A-type lamins are intermediate filament proteins that constitute a major part of the eukaryotic nuclear lamina—a tough, polymerized, mesh lining of the inner nuclear membrane, providing shape and structural integrity to the nucleus. Lamin A (LA) filaments also permeate the nucleoplasm, providing additional structural support, but also scaffolding numerous tethered molecules to stabilize, organize, and facilitate molecular interactions to accomplish critical functions of cellular metabolism. Over the past 2 decades, much attention has been focused on roles of LA in maintenance of nuclear structural integrity. Only since the late 1990s have scientists discovered the devastating effects of LA gene (LMNA) mutations, as they have associated hundreds of LMNA mutations to a large group of diseases, called laminopathies, with a broad spectrum of phenotypes, ranging from skeletal, muscular, and neurological defects, to defective lipid storage, to accelerated aging phenotypes in diseases called progerias. Recent advances demonstrate LA regulatory functions include cell signaling, cell cycle regulation, transcription, chromatin organization, viral egress, and DNA damage repair. Amidst the flurry of fascinating research, only recently have researchers begun to focus attention on the different isoforms that exist for LA, a precursor form among them. LA is initially synthesized as Prelamin A (PreA), and undergoes a series of modifications that 2 truncate the protein to produce “mature” LA. Existence of the precursor form, and its complex maturation pathway, have puzzled researchers since their realization. With a pattern of expression related to cell cycle phase, we hypothesized a role for PreA in cell cycle control. To investigate, we have performed array studies to assess gene expression effects at the levels of transcript expression, protein expression, and phosphorylation modification status. Here, we present evidence for a PreA-mediated program of cell cycle regulatory gene and protein expression modulation. Implicated pathways include RB-E2F, p53, p27Kip1, FoxOs, p300, and the Cyclins, with additional evidence indicating a role for the Pin1 prolyl isomerase in mediating PreA regulation of the cell cycle. 3 Copyright 2012 by Christina N. Bridges, All Rights Reserved 4 DEDICATION Dedicated to Doris Worley Norton and Mary Jane Charlson To my mother Doris and to Mary Jane, both so beloved to me: Being the recipient of the love, support, and guidance of two such strong, nurturing, beautiful, kind, generous women has been a blessing in my life beyond imagination. The two of you have made me the person that I am, each by showing me the person I want to become. Thank you both, so much, for everything. In memoriam: Doris Worley Norton (September 1, 1955 - August 19, 1992) And as I humbly dedicate everything in my life to God, without headlines or banners, this goes, as well, and I give Him thanks for His many blessings upon me, not the least of which is the gift of the love of my soulmate and husband, Andy, who, by some miracle, has managed to stay with me through these years of the insanity that have been graduate school. Here’s to getting on with life and love… 5 ACKNOWLEDGEMENTS This work was supported by grants from the NIH (1R15HL091502-01A1), East Tennessee State University, and the Progeria Foundation to Antonio Rusiñol and Michael Sinensky. I wish to express my gratitude to Dr. Rusiñol and Dr. Sinensky and these organizations for funding of this work. I would also like to thank the ETSU Biomedical Sciences Graduate Program for funding and support to me. I appreciate Dr. Yaping Zong at Fullmoon Biosciences for providing helpful analysis of data from antibody arrays. Also, I would like to thank Dr. Francis Collins, Director, NIH, and Dr. Robert Goldman, Northwestern University, for providing plasmids used in this project. Grateful Acknowledgement Goes to: Michael Stephan Sinensky: For starting this project, for funding, for amazing pioneering work in the field, and finally, for inspiration. Thank you, Dr. Sinensky! For patience and guidance: My Graduate Committee: Antonio E. Rusiñol, Douglas P. Thewke, Sharon E. Campbell, Robert V. Schoborg, and Deling Yin For thoughtful academic discussion, assistance, and expertise: Michael Sinensky, Philip Musich, and Yue Zou For endless moral support along the way: Mitchell Robinson, Beverly Sherwood, Angela Thompson, Karen Ford, Judy Branson, Brian Rowe, Barbara Turner, Scott Champney, David Johnson, and Jack Rary And for technical assistance and discussions, with a big dose of friendship: Lia Lerner,* Jessica Keasler,* Courtney Netherland, Ben Hilton, Rhesa Dykes, Jaime Parman-Ryans, Theresa Pickle, and Hui Tang *Lia & Jessica performed essential laboratory experiments for this project And finally, my thanks to the Fullerton Genetics Laboratory, Asheville, NC, for allowing me to perform a multitude of sequencing experiments there and for providing me with unbelievable flexibility as an employee while I have pursued this degree, not to mention the compassion and moral support of a wonderful group of friends. 6 CONTENTS Page ABSTRACT ............................................................................................................ 2 DEDICATION .......................................................................................................... 5 ACKNOWLEDGEMENTS ....................................................................................... 6 LIST OF TABLES .................................................................................................... 13 LIST OF FIGURES .................................................................................................. 14 LIST OF ABBREVIATIONS ..................................................................................... 17 Chapter 1. INTRODUCTION ................................................................................................. 23 The Nuclear Lamins ..................................................................................... 23 Posttranslational Lamin Processing ....................................................... 24 The Laminopathies .................................................................................. 26 Lamin A Structural Functions .................................................................. 29 Lamin A Nonstructural Functions ............................................................ 31 Lamin A Functions in Cell Cycle Regulation............................................ 31 Aims of this Study ......................................................................................... 34 2. MATERIALS AND METHODS ............................................................................ 36 Materials ....................................................................................................... 36 General Laboratory Chemicals, Buffers, Reagents ................................. 36 Enzymes, Kits ......................................................................................... 37 General Laboratory Supplies and Equipment.......................................... 38 Materials Used in Cloning/Subcloning and Bacterial Cell Culture ........... 39 Plasmids and Oligonucleotides ............................................................... 39 Cloning Vectors 43 Transfection Reagents ............................................................................ 41 Antibodies ............................................................................................... 41 Mammalian Cell Culture .......................................................................... 42 7 Chapter Page Buffers ..................................................................................................... 42 Software .................................................................................................
Load more

Recommended publications
  • EH&S COVID-19 Chemical Disinfectant Safety Information
    COVID-19 CHEMICAL DISINFECTANT SAFETY INFORMATION Updated June 24, 2020 The COVID-19 pandemic has caused an increase in the number of disinfection products used throughout UW departments. This document provides general information about EPA-registered disinfectants, such as potential health hazards and personal protective equipment recommendations, for the commonly used disinfectants at the UW. Chemical Disinfectant Base / Category Products Potential Hazards Controls ● Ethyl alcohol Highly flammable and could form explosive Disposable nitrile gloves Alcohols ● ● vapor/air mixtures. ● Use in well-ventilated areas away from o Clorox 4 in One Disinfecting Spray Ready-to-Use ● May react violently with strong oxidants. ignition sources ● Alcohols may de-fat the skin and cause ● Wear long sleeve shirt and pants ● Isopropyl alcohol dermatitis. ● Closed toe shoes o Isopropyl Alcohol Antiseptic ● Inhalation of concentrated alcohol vapor 75% Topical Solution, MM may cause irritation of the respiratory tract (Ready to Use) and effects on the central nervous system. o Opti-Cide Surface Wipes o Powell PII Disinfectant Wipes o Super Sani Cloth Germicidal Wipe 201 Hall Health Center, Box 354400, Seattle, WA 98195-4400 206.543.7262 ￜ fax 206.543.3351ￜ www.ehs.washington.edu ● Formaldehyde Formaldehyde in gas form is extremely Disposable nitrile gloves for Aldehydes ● ● flammable. It forms explosive mixtures with concentrations 10% or less ● Paraformaldehyde air. ● Medium or heavyweight nitrile, neoprene, ● Glutaraldehyde ● It should only be used in well-ventilated natural rubber, or PVC gloves for ● Ortho-phthalaldehyde (OPA) areas. concentrated solutions ● The chemicals are irritating, toxic to humans ● Protective clothing to minimize skin upon contact or inhalation of high contact concentrations.
    [Show full text]
  • Genetic Variations Associated with Resistance to Doxorubicin and Paclitaxel in Breast Cancer
    GENETIC VARIATIONS ASSOCIATED WITH RESISTANCE TO DOXORUBICIN AND PACLITAXEL IN BREAST CANCER by Irada Ibrahim-zada A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto © Copyright by Irada Ibrahim-zada 2010 ii Genetic variations associated with resistance to doxorubicin and paclitaxel in breast cancer Irada Ibrahim-zada Doctor of Philosophy Department of Laboratory Medicine and Pathobiology University of Toronto 2010 Abstract Anthracycline- and taxane-based regimens have been the mainstay in treating breast cancer patients using chemotherapy. Yet, the genetic make-up of patients and their tumors may have a strong impact on tumor sensitivity to these agents and to treatment outcome. This study represents a new paradigm assimilating bioinformatic tools with in vitro model systems to discover novel genetic variations that may be associated with chemotherapy response in breast cancer. This innovative paradigm integrates drug response data for the NCI60 cell line panel with genome-wide Affymetrix SNP data in order to identify genetic variations associated with drug resistance. This genome wide association study has led to the discovery of 59 candidate loci that may play critical roles in breast tumor sensitivity to doxorubicin and paclitaxel. 16 of them were mapped within well-characterized genes (three related to doxorubicin and 13 to paclitaxel). Further in silico characterization and in vitro functional analysis validated their differential expression in resistant cancer cell lines treated with the drug of interest (over-expression of RORA and DSG1, and under-expression of FRMD6, SGCD, SNTG1, LPHN2 and DCT). iii Interestingly, three and six genes associated with doxorubicin and paclitaxel resistance, respectively, are involved in the apoptotic process in cells.
    [Show full text]
  • Chromosomal Assignment of the Genes for Human Aldehyde Dehydrogenase-1 and Aldehyde Dehydrogenase-2 LILY C
    Am J Hum Genet 38:641-648, 1986 Chromosomal Assignment of the Genes for Human Aldehyde Dehydrogenase-1 and Aldehyde Dehydrogenase-2 LILY C. Hsu,', AKIRA YOSHIDA,' AND T. MOHANDAS2 SUMMARY Chromosomal assignment of the genes for two major human aldehyde dehydrogenase isozymes, that is, cytosolic aldehyde dehydrogenase-1 (ALDH1) and mitochondrial aldehyde dehydrogenase-2 (ALDH2) were determined. Genomic DNA, isolated from a panel of mouse- human and Chinese hamster-human hybrid cell lines, was digested by restriction endonucleases and subjected to Southern blot hybridiza- tion using cDNA probes for ALDH1 and for ALDH2. Based on the distribution pattern of ALDH1 and ALDH2 in cell hybrids, ALDHI was assigned to the long arm of human chromosome 9 and ALDH2 to chromosome 12. INTRODUCTION Two major and at least two minor aldehyde dehydrogenase isozymes exist in human and other mammalian livers. One of the major isozymes, designated as ALDH 1, or E1, is of cytosolic origin, and another major isozyme, designated as ALDH2 or E2, is of mitochondrial origin. The two isozymes are different from each other with respect to their kinetic properties, sensitivity to disulfiram inactivation, and protein structure [1-5]. Remarkable racial differences be- tween Caucasians and Orientals have been found in these isozymes. Approxi- mately 50% of Orientals have a variant form of ALDH2 associated with dimin- ished activity, while virtually all Caucasians have the wild-type active ALDH2 Received July 10, 1985; revised September 23, 1985. This work was supported by grant AA05763 from the National Institutes of Health. ' Department of Biochemical Genetics, Beckman Research Institute of the City of Hope, Duarte, CA 91010.
    [Show full text]
  • The Spectraplakin Dystonin Antagonizes YAP Activity and Suppresses Tumourigenesis Praachi B
    www.nature.com/scientificreports OPEN The spectraplakin Dystonin antagonizes YAP activity and suppresses tumourigenesis Praachi B. Jain1,2,3, Patrícia S. Guerreiro1,2,3, Sara Canato1,2,3 & Florence Janody 1,2,3* Aberrant expression of the Spectraplakin Dystonin (DST) has been observed in various cancers, including those of the breast. However, little is known about its role in carcinogenesis. In this report, we demonstrate that Dystonin is a candidate tumour suppressor in breast cancer and provide an underlying molecular mechanism. We show that in MCF10A cells, Dystonin is necessary to restrain cell growth, anchorage-independent growth, self-renewal properties and resistance to doxorubicin. Strikingly, while Dystonin maintains focal adhesion integrity, promotes cell spreading and cell-substratum adhesion, it prevents Zyxin accumulation, stabilizes LATS and restricts YAP activation. Moreover, treating DST- depleted MCF10A cells with the YAP inhibitor Verteporfn prevents their growth. In vivo, the Drosophila Dystonin Short stop also restricts tissue growth by limiting Yorkie activity. As the two Dystonin isoforms BPAG1eA and BPAG1e are necessary to inhibit the acquisition of transformed features and are both downregulated in breast tumour samples and in MCF10A cells with conditional induction of the Src proto-oncogene, they could function as the predominant Dystonin tumour suppressor variants in breast epithelial cells. Thus, their loss could deem as promising prognostic biomarkers for breast cancer. Breast cancer progression depends on cell autonomous regulatory mechanisms, driven by mutations and epi- genetic changes, and on non-cell autonomous interactions with the surrounding tumour microenvironment1,2. During this multistep process, normal breast epithelial cells acquire various cellular properties arising from dereg- ulated cellular signalling3,4.
    [Show full text]
  • Drp1 Overexpression Induces Desmin Disassembling and Drives Kinesin-1 Activation Promoting Mitochondrial Trafficking in Skeletal Muscle
    Cell Death & Differentiation (2020) 27:2383–2401 https://doi.org/10.1038/s41418-020-0510-7 ARTICLE Drp1 overexpression induces desmin disassembling and drives kinesin-1 activation promoting mitochondrial trafficking in skeletal muscle 1 1 2 2 2 3 Matteo Giovarelli ● Silvia Zecchini ● Emanuele Martini ● Massimiliano Garrè ● Sara Barozzi ● Michela Ripolone ● 3 1 4 1 5 Laura Napoli ● Marco Coazzoli ● Chiara Vantaggiato ● Paulina Roux-Biejat ● Davide Cervia ● 1 1 2 1,4 6 Claudia Moscheni ● Cristiana Perrotta ● Dario Parazzoli ● Emilio Clementi ● Clara De Palma Received: 1 August 2019 / Revised: 13 December 2019 / Accepted: 23 January 2020 / Published online: 10 February 2020 © The Author(s) 2020. This article is published with open access Abstract Mitochondria change distribution across cells following a variety of pathophysiological stimuli. The mechanisms presiding over this redistribution are yet undefined. In a murine model overexpressing Drp1 specifically in skeletal muscle, we find marked mitochondria repositioning in muscle fibres and we demonstrate that Drp1 is involved in this process. Drp1 binds KLC1 and enhances microtubule-dependent transport of mitochondria. Drp1-KLC1 coupling triggers the displacement of KIF5B from 1234567890();,: 1234567890();,: kinesin-1 complex increasing its binding to microtubule tracks and mitochondrial transport. High levels of Drp1 exacerbate this mechanism leading to the repositioning of mitochondria closer to nuclei. The reduction of Drp1 levels decreases kinesin-1 activation and induces the partial recovery of mitochondrial distribution. Drp1 overexpression is also associated with higher cyclin-dependent kinase-1 (Cdk-1) activation that promotes the persistent phosphorylation of desmin at Ser-31 and its disassembling. Fission inhibition has a positive effect on desmin Ser-31 phosphorylation, regardless of Cdk-1 activation, suggesting that induction of both fission and Cdk-1 are required for desmin collapse.
    [Show full text]
  • Comparison of Effectiveness Disinfection of 2%
    ORIGINAL RESEARCH Journal of Dentomaxillofacial Science (J Dentomaxillofac Sci ) December 2018, Volume 3, Number 3: 169-171 P-ISSN.2503-0817, E-ISSN.2503-0825 Comparison of effectiveness disinfection of 2% Original Research glutaraldehyde and 4.8% chloroxylenol on tooth extraction instruments in the Department of Oral CrossMark http://dx.doi.org/10.15562/jdmfs.v3i2.794 Maxillofacial Surgery, Faculty of Dentistry, University of North Sumatera Month: December Ahyar Riza,* Isnandar, Indra B. Siregar, Bernard Volume No.: 3 Abstract Objective: To compare disinfecting effectiveness of 2% glutaraldehyde while the control group was treated with 4.8% chloroxylenol. Each Issue: 2 and 4.8% chloroxylenol on tooth extraction instruments at the instrument was pre-cleaned using a brush, water and soap for both Department of Oral Surgery, Faculty of Dentistry, University of North groups underwent the disinfection process. Sumatera. Results: The results were statistically analyzed using Mann-Whitney Material and Methods: This was an experimental study with post- Test. The comparison between glutaraldehyde and chloroxylenol First page No.: 147 test only control group design approach. Purposive technique is showed a significant difference to the total bacteria count on applied to collect samples which are lower molar extraction forceps. In instrument after disinfection (p=0.014 < 0.05). this study, sample were divided into 2 groups and each consisting of 18 Conclusion: 2% glutaraldehyde was more effective than 4.8% P-ISSN.2503-0817 instruments. The treatment group was treated with 2% glutaraldehyde chloroxylenol at disinfecting lower molar extraction forceps. Keyword: Disinfection, Glutaraldehyde, Chloroxylenol, Forceps E-ISSN.2503-0825 Cite this Article: Riza A, Siregar IB, Isnandar, Bernard.
    [Show full text]
  • The Characterization of Human Adenylate Kinases 7 and 8
    The characterization of human adenylate kinases 7 and 8 demonstrates differences in kinetic parameters and structural organization among the family of adenylate kinase isoenzymes Christakis Panayiotou, Nicola Solaroli, Yunjian Xu, Magnus Johansson, Anna Karlsson To cite this version: Christakis Panayiotou, Nicola Solaroli, Yunjian Xu, Magnus Johansson, Anna Karlsson. The char- acterization of human adenylate kinases 7 and 8 demonstrates differences in kinetic parameters and structural organization among the family of adenylate kinase isoenzymes. Biochemical Journal, Port- land Press, 2011, 433 (3), pp.527-534. 10.1042/BJ20101443. hal-00558097 HAL Id: hal-00558097 https://hal.archives-ouvertes.fr/hal-00558097 Submitted on 21 Jan 2011 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Biochemical Journal Immediate Publication. Published on 16 Nov 2010 as manuscript BJ20101443 The characterization of human adenylate kinases 7 and 8 demonstrates differences in kinetic parameters and structural organization among the family of adenylate kinase isoenzymes
    [Show full text]
  • Molecular Docking Investigation of the Amantadine Binding to the Enzymes Upregulated Or Downregulated in Parkinson's Disease
    ADMET & DMPK 8(2) (2020) 149-175; doi: http://dx.doi.org/10.5599/admet.854 Open Access : ISSN : 1848-7718 http://www.pub.iapchem.org/ojs/index.php/admet/index Original scientific paper Molecular docking investigation of the amantadine binding to the enzymes upregulated or downregulated in Parkinson’s disease 1,2 Mihaela Ileana Ionescu 1Department of Microbiology, Iuliu Hațieganu University of Medicine and Pharmacy, 6 Louis Pasteur, 400349, Cluj- Napoca, Romania, [email protected] 2Department of Microbiology, County Emergency Clinical Hospital, 400006, Cluj-Napoca, Romania E-mail: [email protected]; Received: May 15, 2020; Revised: June 01, 2020; Published: June 15, 2020 Abstract Parkinson’s disease (PD) is a progressive neurodegenerative disease. Levodopa in combination with amantadine has a demonstrated efficacy in motility impairment. An extensive investigation of some enzymes described to be upregulated or downregulated in PD was made – adenylate kinase (AK), adenine phosphoribosyltransferase (APRT), ectonucleoside triphosphate diphosphohydrolase 1 (ENTPD1), nucleoside-diphosphate kinase 3 (NDK3), purine nucleoside phosphorylase 1 (PNP1), and ecto-5’- nucleotidase (NT5E). Also, creatine kinase (CK) was included in the study because it is one of the main enzymes involved in the regulation of the nucleotide ratio in energy metabolism. To date, there is no proven link between amantadine treatment of PD and these enzymes. Because there are many AKs isoforms modified in PD, the AK was the first investigated. The molecular docking experiments allow the analysis of the selective binding of amantadine – unionized (with –NH2 group) and ionized form (with – + NH3 group) – to the AKs’ isoforms implicated in PD. Using available X-ray 3D structures of human AKs in closed-conformation, it was demonstrated that there are notable differences between the interactions of the two forms of amantadine for the zebrafish AK1 (5XZ2), human AK2 (2C9Y), human AK5 (2BWJ), and AK from B.stearothermophilus.
    [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]
  • Supp Material.Pdf
    Simon et al. Supplementary information: Table of contents p.1 Supplementary material and methods p.2-4 • PoIy(I)-poly(C) Treatment • Flow Cytometry and Immunohistochemistry • Western Blotting • Quantitative RT-PCR • Fluorescence In Situ Hybridization • RNA-Seq • Exome capture • Sequencing Supplementary Figures and Tables Suppl. items Description pages Figure 1 Inactivation of Ezh2 affects normal thymocyte development 5 Figure 2 Ezh2 mouse leukemias express cell surface T cell receptor 6 Figure 3 Expression of EZH2 and Hox genes in T-ALL 7 Figure 4 Additional mutation et deletion of chromatin modifiers in T-ALL 8 Figure 5 PRC2 expression and activity in human lymphoproliferative disease 9 Figure 6 PRC2 regulatory network (String analysis) 10 Table 1 Primers and probes for detection of PRC2 genes 11 Table 2 Patient and T-ALL characteristics 12 Table 3 Statistics of RNA and DNA sequencing 13 Table 4 Mutations found in human T-ALLs (see Fig. 3D and Suppl. Fig. 4) 14 Table 5 SNP populations in analyzed human T-ALL samples 15 Table 6 List of altered genes in T-ALL for DAVID analysis 20 Table 7 List of David functional clusters 31 Table 8 List of acquired SNP tested in normal non leukemic DNA 32 1 Simon et al. Supplementary Material and Methods PoIy(I)-poly(C) Treatment. pIpC (GE Healthcare Lifesciences) was dissolved in endotoxin-free D-PBS (Gibco) at a concentration of 2 mg/ml. Mice received four consecutive injections of 150 μg pIpC every other day. The day of the last pIpC injection was designated as day 0 of experiment.
    [Show full text]
  • Supplementary Table S2
    1-high in cerebrotropic Gene P-value patients Definition BCHE 2.00E-04 1 Butyrylcholinesterase PLCB2 2.00E-04 -1 Phospholipase C, beta 2 SF3B1 2.00E-04 -1 Splicing factor 3b, subunit 1 BCHE 0.00022 1 Butyrylcholinesterase ZNF721 0.00028 -1 Zinc finger protein 721 GNAI1 0.00044 1 Guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1 GNAI1 0.00049 1 Guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1 PDE1B 0.00069 -1 Phosphodiesterase 1B, calmodulin-dependent MCOLN2 0.00085 -1 Mucolipin 2 PGCP 0.00116 1 Plasma glutamate carboxypeptidase TMX4 0.00116 1 Thioredoxin-related transmembrane protein 4 C10orf11 0.00142 1 Chromosome 10 open reading frame 11 TRIM14 0.00156 -1 Tripartite motif-containing 14 APOBEC3D 0.00173 -1 Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D ANXA6 0.00185 -1 Annexin A6 NOS3 0.00209 -1 Nitric oxide synthase 3 SELI 0.00209 -1 Selenoprotein I NYNRIN 0.0023 -1 NYN domain and retroviral integrase containing ANKFY1 0.00253 -1 Ankyrin repeat and FYVE domain containing 1 APOBEC3F 0.00278 -1 Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F EBI2 0.00278 -1 Epstein-Barr virus induced gene 2 ETHE1 0.00278 1 Ethylmalonic encephalopathy 1 PDE7A 0.00278 -1 Phosphodiesterase 7A HLA-DOA 0.00305 -1 Major histocompatibility complex, class II, DO alpha SOX13 0.00305 1 SRY (sex determining region Y)-box 13 ABHD2 3.34E-03 1 Abhydrolase domain containing 2 MOCS2 0.00334 1 Molybdenum cofactor synthesis 2 TTLL6 0.00365 -1 Tubulin tyrosine ligase-like family, member 6 SHANK3 0.00394 -1 SH3 and multiple ankyrin repeat domains 3 ADCY4 0.004 -1 Adenylate cyclase 4 CD3D 0.004 -1 CD3d molecule, delta (CD3-TCR complex) (CD3D), transcript variant 1, mRNA.
    [Show full text]
  • Queryor: a Comprehensive Web Platform for Genetic Variant Analysis
    Bertoldi et al. BMC Bioinformatics (2017) 18:225 DOI 10.1186/s12859-017-1654-4 SOFTWARE Open Access QueryOR: a comprehensive web platform for genetic variant analysis and prioritization Loris Bertoldi1, Claudio Forcato1, Nicola Vitulo1,5, Giovanni Birolo1, Fabio De Pascale1, Erika Feltrin1, Riccardo Schiavon2, Franca Anglani3, Susanna Negrisolo4, Alessandra Zanetti4, Francesca D’Avanzo4, Rosella Tomanin4, Georgine Faulkner2, Alessandro Vezzi2 and Giorgio Valle1,2* Abstract Background: Whole genome and exome sequencing are contributing to the extraordinary progress in the study of human genetic variants. In this fast developing field, appropriate and easily accessible tools are required to facilitate data analysis. Results: Here we describe QueryOR, a web platform suitable for searching among known candidate genes as well as for finding novel gene-disease associations. QueryOR combines several innovative features that make it comprehensive, flexible and easy to use. Instead of being designed on specific datasets, it works on a general XML schema specifying formats and criteria of each data source. Thanks to this flexibility, new criteria can be easily added for future expansion. Currently, up to 70 user-selectable criteria are available, including a wide range of gene and variant features. Moreover, rather than progressively discarding variants taking one criterion at a time, the prioritization is achieved by a global positive selection process that considers all transcript isoforms, thus producing reliable results. QueryOR is easy to use and its intuitive interface allows to handle different kinds of inheritance as well as features related to sharing variants in different patients. QueryOR is suitable for investigating single patients, families or cohorts. Conclusions: QueryOR is a comprehensive and flexible web platform eligible for an easy user-driven variant prioritization.
    [Show full text]