DOCSLIB.ORG

Epidermal Growth Factor Receptor

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Epidermal Growth Factor Receptor Volume 1 - Number 1 May - September 1997 Volume 24 - Number 9 September 2020 Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Scope The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal in open access, devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. It is made for and by: clinicians and researchers in cytogenetics, molecular biology, oncology, haematology, and pathology. One main scope of the Atlas is to conjugate the scientific information provided by cytogenetics/molecular genetics to the clinical setting (diagnostics, prognostics and therapeutic design), another is to provide an encyclopedic knowledge in cancer genetics. The Atlas deals with cancer research and genomics. It is at the crossroads of research, virtual medical university (university and post-university e-learning), and telemedicine. It contributes to "meta-medicine", this mediation, using information technology, between the increasing amount of knowledge and the individual, having to use the information. Towards a personalized medicine of cancer. It presents structured review articles ("cards") on: 1- Genes, 2- Leukemias, 3- Solid tumors, 4- Cancer-prone diseases, and also 5- "Deep insights": more traditional review articles on the above subjects and on surrounding topics. It also present 6- Case reports in hematology and 7- Educational items in the various related topics for students in Medicine and in Sciences. The Atlas of Genetics and Cytogenetics in Oncology and Haematology does not publish research articles. See also: http://documents.irevues.inist.fr/bitstream/handle/2042/56067/Scope.pdf Editorial correspondance Jean-Loup Huret, MD, PhD, [email protected] Editor, Editorial Board and Publisher See:http://documents.irevues.inist.fr/bitstream/handle/2042/48485/Editor-editorial-board-and-publisher.pdf The Atlas of Genetics and Cytogenetics in Oncology and Haematology is published 12 times a year by ARMGHM, a non profit organisation, and by the INstitute for Scientific and Technical Information of the French National Center for Scientific Research (INIST-CNRS) since 2008. The Atlas is hosted by INIST-CNRS (http://www.inist.fr) Staff: Vanessa Le Berre Philippe Dessen is the Database Directorof the on-line version (Gustave Roussy Institute – Villejuif – France). Publisher Contact: INIST-CNRS Mailing Address: Catherine Morel, 2,Allée du Parc de Brabois, CS 10130, 54519 Vandoeuvre-lès-Nancy France. Email Address:[email protected] Articles of the ATLAS are free in PDF format, and metadata are available on the web in Dublin Core XML format and freely harvestable.A Digital object identifier (DOI®), recorded at the International Agency CrossRefhttp://www.crossref.org/ is assigned to each article. http://AtlasGeneticsOncology.org © ATLAS - ISSN 1768-3262 The PDF version of the Atlas of Genetics and Cytogenetics in Oncology and Haematology is a reissue of the original articles published in collaboration with the Institute for Scientific and Technical Information (INstitut de l’Information Scientifique et Technique - INIST) of the French National Center for Scientific Research (CNRS) on its electronic publishing platform I-Revues. Online and PDF versions of the Atlas of Genetics and Cytogenetics in Oncology and Haematology are hosted by INIST-CNRS. Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Editors-in-Chief Jesús María Hernández Rivas (Salamanca, Spain) Paola Dal Cin (Boston, Massachusetts) Jean-Loup Huret (Poitiers, France) Hematology Section Editor Ana E. Rodríguez, Teresa Gonzalez (Salamanca, Spain) Bone Tumors Section Editor Judith Bovee (Leiden, Netherlands) Head and Neck Tumors Section Editor Cécile Badoual (Paris, France) Urinary Tumors Section Editor Paola Dal Cin (Boston, Massachusetts) Pediatric Tumors Section Editor Frederic G. Barr (Bethesda, Maryland) Cancer Prone Diseases Section Editor Gaia Roversi (Milano, Italy) Cell Cycle Section Editor João Agostinho Machado-Neto (São Paulo, Brazil) DNA Repair Section Editor Godefridus Peters (Amsterdam, Netherlands) Epigenetics Section Editor Roberto Piergentili (Rome, Italy) Hematopoeisis Section Editor Olga Weinberg (Boston, Massachusetts) Hormones and Growth factors Section Editor Gajanan V. Sherbet (Newcastle upon Tyne, UK) Mitosis Section Editor Patrizia Lavia (Rome, Italy) Oxidative stress Section Editor Thierry Soussi (Stockholm, Sweden/Paris, France) WNT pathway Section Editor Alessandro Beghini (Milano, Italy) B-cell activation Section Editors Anette Gjörloff Wingren, Barnabas Nyesiga (Malmö, Sweden) Board Members Sreeparna Banerjee Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; [email protected] Alessandro Beghini Department of Health Sciences, University of Milan, Italy; [email protected] Judith Bovée 2300 RC Leiden, The Netherlands; [email protected] Antonio Cuneo Dipartimento di ScienzeMediche, Sezione di Ematologia e Reumatologia Via Aldo Moro 8, 44124 - Ferrara, Italy; [email protected] Paola Dal Cin Department of Pathology, Brigham, Women's Hospital, 75 Francis Street, Boston, MA 02115, USA; [email protected] IRBA, Departement Effets Biologiques des Rayonnements, Laboratoire de Dosimetrie Biologique des Irradiations, Dewoitine C212, 91223 François Desangles Bretigny-sur-Orge, France; [email protected] Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Roosevelt Dr. Oxford, OX37BN, UK Enric Domingo [email protected] Ayse Elif Erson- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey; [email protected] Bensan Ad Geurts van Department of Human Genetics, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, 6500 HB Nijmegen, Kessel The Netherlands; [email protected] Department of Pediatrics and Adolescent Medicine, St. Anna Children's Hospital, Medical University Vienna, Children's Cancer Research Oskar A. Haas Institute Vienna, Vienna, Austria. [email protected] Anne Hagemeijer Center for Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium; [email protected] Department of Pathology, The Ohio State University, 129 Hamilton Hall, 1645 Neil Ave, Columbus, OH 43210, USA; Nyla Heerema [email protected] Sakari Knuutila Hartmann Institute and HUSLab, University of Helsinki, Department of Pathology, Helsinki, Finland; [email protected] Lidia Larizza Lab Centro di Ricerche e TecnologieBiomedicheIRCCS-IstitutoAuxologico Italiano Milano, Italy; l.larizza@auxologico Department of Human, Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms, Cell Cultures, Braunschweig, Roderick Mc Leod Germany; [email protected] Cristina Mecucci Hematology University of Perugia, University Hospital S.Mariadella Misericordia, Perugia, Italy; [email protected] Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden; Fredrik Mertens [email protected] Konstantin Miller Institute of Human Genetics, Hannover Medical School, 30623 Hannover, Germany; [email protected] Department of Clinical Genetics, University and Regional Laboratories, Lund University, SE-221 85 Lund, Sweden; Felix Mitelman [email protected] Hossain Mossafa Laboratoire CERBA, 95066 Cergy-Pontoise cedex 9, France; [email protected] Department of Human, Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms, Cell Cultures, Braunschweig, Stefan Nagel Germany; [email protected] Florence Pedeutour Laboratory of Solid Tumors Genetics, Nice University Hospital, CNRSUMR 7284/INSERMU1081, France; [email protected] Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 250, Memphis, Tennessee 38105- Susana Raimondi 3678, USA; [email protected] Clelia Tiziana Department of Biology, University of Bari, Bari, Italy; [email protected] Storlazzi Sabine Strehl CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschunge.V., Vienna, Austria; [email protected] Nancy Uhrhammer Laboratoire Diagnostic Génétique et Moléculaire, Centre Jean Perrin, Clermont-Ferrand, France; [email protected] Dan L. Van Dyke Mayo Clinic Cytogenetics Laboratory, 200 First St SW, Rochester MN 55905, USA; [email protected] Roberta Vanni Universita di Cagliari, Dipartimento di ScienzeBiomediche(DiSB), CittadellaUniversitaria, 09042 Monserrato (CA) - Italy; [email protected] Atlas Genet Cytogenet Oncol Haematol. 2020; 24(9) Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Volume 24, Number 9, September 2020 Table of contents Gene Section EGFR (Epidermal Growth Factor Receptor) 325 Ayca Circir Hatil, Esra Cicek, Merve Oyken, A.Elif Erson-Bensan SNX3 (Sorting Nexin 3) 333 Esra Cicek, Ayca Circir Hatil, Merve Oyken, Harun Cingoz, A.Elif Erson-Bensan EEF1B2 (eukaryotic translation elongation factor 1 beta 2) 337 Luigi Cristiano Leukaemia Section t(12;15)(p13;q25) ETV6/NTRK3 in Hematological malignancies 346 Jean Loup Huret Solid Tumour Section t(12;15)(p13;q25) ETV6/NTRK3 in solid tumors 350 Jean Loup Huret Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL INIST-CNRS Gene Section Review EGFR (Epidermal Growth Factor Receptor) Ayca Circir
Load more

Recommended publications
  • FGFR1 Fusion and Amplification in a Solid Variant of Alveolar Rhabdomyosarcoma
    Modern Pathology (2011) 24, 1327–1335 & 2011 USCAP, Inc. All rights reserved 0893-3952/11 $32.00 1327 FOXO1–FGFR1 fusion and amplification in a solid variant of alveolar rhabdomyosarcoma Jinglan Liu1,2, Miguel A Guzman1,2, Donna Pezanowski1, Dilipkumar Patel1, John Hauptman1, Matthew Keisling3, Steve J Hou2,3, Peter R Papenhausen4, Judy M Pascasio1,2, Hope H Punnett1,5, Gregory E Halligan2,6 and Jean-Pierre de Chadare´vian1,2 1Department of Pathology and Laboratory Medicine, St Christopher’s Hospital for Children, Philadelphia, PA, USA; 2Drexel University College of Medicine, Philadelphia, PA, USA; 3Department of Pathology and Laboratory Medicine, Hahnneman University Hospital, Philadelphia, PA, USA; 4Laboratory Corporation of America, The Research Triangle Park, NC, USA; 5Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA, USA and 6Department of Pediatrics, Section of Oncology, St Christopher’s Hospital for Children, Philadelphia, PA, USA Rhabdomyosarcoma is the most common pediatric soft tissue malignancy. Two major subtypes, alveolar rhabdomyosarcoma and embryonal rhabdomyosarcoma, constitute 20 and 60% of all cases, respectively. Approximately 80% of alveolar rhabdomyosarcoma carry two signature chromosomal translocations, t(2;13)(q35;q14) resulting in PAX3–FOXO1 fusion, and t(1;13)(p36;q14) resulting in PAX7–FOXO1 fusion. Whether the remaining cases are truly negative for gene fusion has been questioned. We are reporting the case of a 9-month-old girl with a metastatic neck mass diagnosed histologically as solid variant alveolar rhabdomyosarcoma. Chromosome analysis showed a t(8;13;9)(p11.2;q14;9q32) three-way translocation as the sole clonal aberration. Fluorescent in situ hybridization (FISH) demonstrated a rearrangement at the FOXO1 locus and an amplification of its centromeric region.
    [Show full text]
  • Genome-Wide Screen Identifies Genes Whose Inactivation Confer Resistance to Cisplatin in Saccharomyces Cerevisiae
    Research Article Genome-Wide Screen Identifies Genes Whose Inactivation Confer Resistance to Cisplatin in Saccharomyces cerevisiae Ruea-Yea Huang, Martha Eddy, Marija Vujcic, and David Kowalski Department of Cancer Genetics, Roswell Park Cancer Institute, Buffalo, New York Abstract therapy (1). This may be due to the genomic instability of tumors, To identify novel genes that mediate cellular resistance to which gives rise to mutations or defects in multiple molecular cisplatin, we have screened the collection of Saccharomyces pathways. Both gain-of-function and loss-of-function mutations cerevisiae deletion strains. We have found reproducibly 22 can confer resistance to platinum compounds. The best known genes/open reading frames (ORF), which when deleted, confer examples are the loss of DNA mismatch repair (MMR) genes, resistance to cisplatin at a concentration that is lethal to wild- hMLH1, hMSH2, or hPMS2 (1, 4). MMR proteins function in type cells. Complementation of individual deletion strains recognition of damaged DNA adducts. Previous studies indicate with the corresponding wild-type gene abolished cisplatin that mutation or methylation-mediated silencing of these genes resistance, confirming that specific gene deletions caused the results in failure to recognize the adduct and propagate a signal to resistance. Twenty of the genes/ORFs identified have not been the apoptotic machinery, thereby producing low-level resistance to previously linked to cisplatin resistance and belong to several cisplatin (5). In addition, cisplatin treatment can enrich for malignant populations of cells that have lost DNA mismatch distinct functional groups. Major functional groups encode proteins involved in nucleotide metabolism, mRNA catabo- repair both in vitro and in vivo (4).
    [Show full text]
  • Molecular Mechanism for the Subversion of the Retromer Coat By
    Molecular mechanism for the subversion of the PNAS PLUS retromer coat by the Legionella effector RidL Miguel Romano-Morenoa, Adriana L. Rojasa, Chad D. Williamsonb, David C. Gershlickb, María Lucasa, Michail N. Isupovc, Juan S. Bonifacinob, Matthias P. Machnerd,1, and Aitor Hierroa,e,1 aStructural Biology Unit, Centro de Investigación Cooperativa en Biociencias, 48160 Derio, Spain; bCell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; cThe Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Exeter EX4 4SB, United Kingdom; dDivision of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892; and eIKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain Edited by Ralph R. Isberg, Howard Hughes Medical Institute and Tufts University School of Medicine, Boston, MA, and approved November 13, 2017 (received for review August 30, 2017) Microbial pathogens employ sophisticated virulence strategies to VAMP7 together with several Rab GTPases that function along cause infections in humans. The intracellular pathogen Legionella distinct trafficking pathways (18), and the Tre-2/Bub2/Cdc16 pneumophila encodes RidL to hijack the host scaffold protein domain family member 5 (TBC1D5), a GTPase-activating pro- VPS29, a component of retromer and retriever complexes critical for tein (GAP) that causes Rab7 inactivation and redistribution to endosomal cargo recycling. Here, we determined the crystal structure the cytosol (14). of L. pneumophila RidL in complex with the human VPS29–VPS35 Recent biochemical and structural characterization of single retromer subcomplex. A hairpin loop protruding from RidL inserts subunits and subcomplexes from retromer have provided insights into a conserved pocket on VPS29 that is also used by cellular ligands, into its modular architecture and mechanisms of action.
    [Show full text]
  • Mouse Vps29 Conditional Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Vps29 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Vps29 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Vps29 gene (NCBI Reference Sequence: NM_019780 ; Ensembl: ENSMUSG00000029462 ) is located on Mouse chromosome 5. 4 exons are identified, with the ATG start codon in exon 1 and the TAA stop codon in exon 4 (Transcript: ENSMUST00000155671). Exon 2~3 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Vps29 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-97B19 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 0.73% of the coding region. The knockout of Exon 2~3 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 5536 bp, and the size of intron 3 for 3'-loxP site insertion: 533 bp. The size of effective cKO region: ~2760 bp. The cKO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 4 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Vps29 Homology arm cKO region loxP site Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Text-Based Analysis of Genes, Proteins, Aging, and Cancer
    Mechanisms of Ageing and Development 126 (2005) 193–208 www.elsevier.com/locate/mechagedev Text-based analysis of genes, proteins, aging, and cancer Jeremy R. Semeiks, L.R. Grate, I.S. Mianà Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Available online 26 October 2004 Abstract The diverse nature of cancer- and aging-related genes presents a challenge for large-scale studies based on molecular sequence and profiling data. An underexplored source of data for modeling and analysis is the textual descriptions and annotations present in curated gene- centered biomedical corpora. Here, 450 genes designated by surveys of the scientific literature as being associated with cancer and aging were analyzed using two complementary approaches. The first, ensemble attribute profile clustering, is a recently formulated, text-based, semi- automated data interpretation strategy that exploits ideas from statistical information retrieval to discover and characterize groups of genes with common structural and functional properties. Groups of genes with shared and unique Gene Ontology terms and protein domains were defined and examined. Human homologs of a group of known Drosphila aging-related genes are candidates for genes that may influence lifespan (hep/MAPK2K7, bsk/MAPK8, puc/LOC285193). These JNK pathway-associated proteins may specify a molecular hub that coordinates and integrates multiple intra- and extracellular processes via space- and time-dependent interactions with proteins in other pathways. The second approach, a qualitative examination of the chromosomal locations of 311 human cancer- and aging-related genes, provides anecdotal evidence for a ‘‘phenotype position effect’’: genes that are proximal in the linear genome often encode proteins involved in the same phenomenon.
    [Show full text]
  • Ectopic Protein Interactions Within BRD4–Chromatin Complexes Drive Oncogenic Megadomain Formation in NUT Midline Carcinoma
    Ectopic protein interactions within BRD4–chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma Artyom A. Alekseyenkoa,b,1, Erica M. Walshc,1, Barry M. Zeea,b, Tibor Pakozdid, Peter Hsic, Madeleine E. Lemieuxe, Paola Dal Cinc, Tan A. Incef,g,h,i, Peter V. Kharchenkod,j, Mitzi I. Kurodaa,b,2, and Christopher A. Frenchc,2 aDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; bDepartment of Genetics, Harvard Medical School, Boston, MA 02115; cDepartment of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115; dDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA 02115; eBioinfo, Plantagenet, ON, Canada K0B 1L0; fDepartment of Pathology, University of Miami Miller School of Medicine, Miami, FL 33136; gBraman Family Breast Cancer Institute, University of Miami Miller School of Medicine, Miami, FL 33136; hInterdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL 33136; iSylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136; and jHarvard Stem Cell Institute, Cambridge, MA 02138 Contributed by Mitzi I. Kuroda, April 6, 2017 (sent for review February 7, 2017; reviewed by Sharon Y. R. Dent and Jerry L. Workman) To investigate the mechanism that drives dramatic mistargeting of and, in the case of MYC, leads to differentiation in culture (2, 3). active chromatin in NUT midline carcinoma (NMC), we have Similarly, small-molecule BET inhibitors such as JQ1, which identified protein interactions unique to the BRD4–NUT fusion disengage BRD4–NUT from chromatin, diminish megadomain- oncoprotein compared with wild-type BRD4.
    [Show full text]
  • VPS29 Exerts Opposing Effects on Endocytic Viral Entry 2 3 4 Daniel Poston1,2*, Yiska Weisblum1*, Alvaro Hobbs1, Paul D
    bioRxiv preprint doi: https://doi.org/10.1101/2021.08.06.455441; this version posted August 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 VPS29 exerts opposing effects on endocytic viral entry 2 3 4 Daniel Poston1,2*, Yiska Weisblum1*, Alvaro Hobbs1, Paul D. Bieniasz1,3 5 6 7 1. Laboratory of Retrovirology, The Rockefeller University, 1230 York Avenue, New York NY 8 10065 9 2. Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program, 1300 York 10 Avenue, New York NY 10021 11 3. Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New 12 York NY 10065 13 14 15 *These authors contributed equally 16 17 18 Correspondence to: Paul D. Bieniasz, Laboratory of Retrovirology, The Rockefeller University, 19 31 1230 York Avenue, New York NY 10065 E.Mail [email protected] 20 21 22 23 SUMMARY 24 Emerging zoonotic viral pathogens threaten global health and there is an urgent need to discover 25 host and viral determinants influencing infection. We performed a loss-of-function genome-wide 26 CRISPR screen in a human lung cell line using HCoV-OC43, a human betacoronavirus. One 27 candidate gene, VPS29, was required for infection by HCoV-OC43, SARS-CoV-2, other 28 endemic and pandemic threat coronaviruses as well as ebolavirus. However, VPS29 deficiency 29 had no effect on certain other viruses that enter cells via endosomes and had an opposing, 30 enhancing effect on influenza A virus infection.
    [Show full text]
  • The P5-Atpase ATP13A1 Modulates MR1-Mediated Antigen Presentation
    bioRxiv preprint doi: https://doi.org/10.1101/2021.05.26.445708; this version posted May 27, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. The P5-ATPase ATP13A1 modulates MR1- mediated antigen presentation Corinna A. Kulicke1, Erica De Zan2, Zeynep Hein3, Claudia Gonzalez-Lopez1, Swapnil Ghanwat3, Natacha Veerapen4, Gurdyal S. Besra4, Paul Klenerman5,6, John C. Christianson7, Sebastian Springer3, Sebastian Nijman2, Vincenzo Cerundolo1, #, § , and Mariolina Salio1, # 1. MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK 2. Ludwig Institute for Cancer Research Ltd. and Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK 3. Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany. 4. School of Biosciences, University of Birmingham, Birmingham B11 2TT, United Kingdom 5. Peter Medawar Building, Nuffield Department of Medicine, University of Oxford 6. Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford 7. Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK # joint senior authors § deceased January 7th 2020 current addresses: C.K. – Pulmonary and Critical Care Medicine, Oregon Health and Science University, Portland, OR, United States; S.N. – Scenic Biotech BV, Amsterdam, The Netherlands correspondence: [email protected]; [email protected] Keywords: MHC I-related protein 1 (MR1), mucosal-associated invariant T cell (MAIT), MR1-restricted T cell (MR1T), antigen presentation, protein trafficking, HAP1, gene trap, ATP13A1, P5-type ATPase bioRxiv preprint doi: https://doi.org/10.1101/2021.05.26.445708; this version posted May 27, 2021.
    [Show full text]
  • Sleeping Beauty Mutagenesis Reveals Cooperating Mutations and Pathways in Pancreatic Adenocarcinoma
    Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma Karen M. Manna,1, Jerrold M. Warda, Christopher Chin Kuan Yewa, Anne Kovochichb, David W. Dawsonb, Michael A. Blackc, Benjamin T. Brettd, Todd E. Sheetzd,e,f, Adam J. Dupuyg, Australian Pancreatic Cancer Genome Initiativeh,2, David K. Changi,j,k, Andrew V. Biankini,j,k, Nicola Waddelll, Karin S. Kassahnl, Sean M. Grimmondl, Alistair G. Rustm, David J. Adamsm, Nancy A. Jenkinsa,1, and Neal G. Copelanda,1,3 aDivision of Genetics and Genomics, Institute of Molecular and Cell Biology, Singapore 138673; bDepartment of Pathology and Laboratory Medicine and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California, Los Angeles, CA 90095; cDepartment of Biochemistry, University of Otago, Dunedin, 9016, New Zealand; dCenter for Bioinformatics and Computational Biology, University of Iowa, Iowa City, IA 52242; eDepartment of Biomedical Engineering, University of Iowa, Iowa City, IA 52242; fDepartment of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA 52242; gDepartment of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242; hAustralian Pancreatic Cancer Genome Initiative; iCancer Research Program, Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia; jDepartment of Surgery, Bankstown Hospital, Bankstown, Sydney, New South Wales 2200, Australia; kSouth Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia; lQueensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia; and mExperimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, United Kingdom This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected in 2009.
    [Show full text]
  • Mathematical Model of Auxin Metabolism in Shoots Of
    RUSSIAN ACADEMY OF SCIENCES SIBERIAN BRANCH INSTITUTE OF CYTOLOGY AND GENETICS THE SIXTH INTERNATIONAL CONFERENCE ON BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE Abstracts BGRS’2008 Novosibirsk, Russia June 22—28, 2008 Novosibirsk 2008 1 INTERNATIONAL PROGRAM COMMITTEE* Nikolay Kolchanov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia (Chairman of the Conference) Ralf Hofestadt University of Bielefeld, Germany (Co-Chairman of the Conference) Dagmara Furman Institute of Cytology and Genetics SB RAS, Novosibirsk, (Conference Scientific Secretary) Dmitry Afonnikov Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Shandar Ahmad National Institute of Biomedical Innovation, Japan Philip Bourne University of California San Diego, San-Diego, USA Samir Brahmachari Institute of Genomics and Integrative Biology, Delhi, India Ming Chen Department of Bioinformatics Zhejiang University, Hangzhou, China А. Fazel Famili University of Ottawa, IIT/ITI - National Research Council Canada, Ottawa, Canada Mikhail Gelfand Institute for Information Transmission Problems RAS, Russia Boris M. Glinsky Institute of Computational Mathematics and Mathematical Geophysics SB RAS, Novosibirsk, Russia Nikolay Goncharov Institute of Cytology and Genetics, Novosibirsk, Russia Charlie Hodgman Multidisciplinary Centre for Integrative Biology, School of Biosciences, University of Nottingham, UK Alexis Ivanov Institute of Biomedical Chemistry RAMS, Moscow, Russia Manfred Kayser Erasmus University Medical Centre Rotterdam, Rotterdam, The Netherlands
    [Show full text]
  • WAPL Maintains Dynamic Cohesin to Preserve Lineage Specific Distal Gene Regulation
    bioRxiv preprint doi: https://doi.org/10.1101/731141; this version posted August 9, 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. WAPL maintains dynamic cohesin to preserve lineage specific distal gene regulation Ning Qing Liu1, Michela Maresca1, Teun van den Brand1, Luca Braccioli1, Marijne M.G.A. Schijns1, Hans Teunissen1, Benoit G. Bruneau2,3,4, Elphѐge P. Nora2,3, Elzo de Wit1,* Affiliations 1 Division Gene Regulation, Oncode Institute, Netherlands Cancer Institute, Amsterdam, The Netherlands; 2 Gladstone Institutes, San Francisco, USA; 3 Cardiovascular Research Institute, University of California, San Francisco; 4 Department of Pediatrics, University of California, San Francisco. *corresponding author: [email protected] bioRxiv preprint doi: https://doi.org/10.1101/731141; this version posted August 9, 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. HIGHLIGHTS 1. The cohesin release factor WAPL is crucial for maintaining a pluripotency-specific phenotype. 2. Dynamic cohesin is enriched at lineage specific loci and overlaps with binding sites of pluripotency transcription factors. 3. Expression of lineage specific genes is maintained by dynamic cohesin binding through the formation of promoter-enhancer associated self-interaction domains. 4. CTCF-independent cohesin binding to chromatin is controlled by the pioneer factor OCT4. bioRxiv preprint doi: https://doi.org/10.1101/731141; this version posted August 9, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder.
    [Show full text]
  • COMMD1 Is Linked to the WASH Complex and Regulates Endosomal Trafficking of the Copper Transporter ATP7A
    M BoC | ARTICLE COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A Christine A. Phillips-Krawczaka,*, Amika Singlab,*, Petro Starokadomskyyb, Zhihui Denga,c, Douglas G. Osbornea, Haiying Lib, Christopher J. Dicka, Timothy S. Gomeza, Megan Koeneckeb, Jin-San Zhanga,d, Haiming Daie, Luis F. Sifuentes-Dominguezb, Linda N. Gengb, Scott H. Kaufmanne, Marco Y. Heinf, Mathew Wallisg, Julie McGaughrang,h, Jozef Geczi,j, Bart van de Sluisk, Daniel D. Billadeaua,l, and Ezra Bursteinb,m aDepartment of Immunology, eDepartment of Molecular Pharmacology and Experimental Therapeutics, and lDepartment of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, MN 55905; bDepartment of Internal Medicine and mDepartment of Molecular Biology, UT Southwestern Medical Center, Dallas, TX 75390-9151; cDepartment of Pathophysiology, Qiqihar Medical University, Qiqihar, Heilongjiang 161006, China; dSchool of Pharmaceutical Sciences and Key Laboratory of Biotechnology and Pharmaceutical Engineering, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; fMax Planck Institute of Biochemistry, 82152 Martinsried, Germany; gGenetic Health Queensland at the Royal Brisbane and Women’s Hospital, Herston, Queensland 4029, Australia; hSchool of Medicine, University of Queensland, Brisbane, Queensland 4072, Australia; iRobinson Institute and jDepartment of Paediatrics, University of Adelaide, Adelaide, South Australia 5005, Australia; kSection of Molecular Genetics at the Department of Pediatrics, University Medical Center Groningen, University of Groningen, 9713 Groningen, Netherlands ABSTRACT COMMD1 deficiency results in defective copper homeostasis, but the mecha- Monitoring Editor nism for this has remained elusive. Here we report that COMMD1 is directly linked to early Jean E. Gruenberg endosomes through its interaction with a protein complex containing CCDC22, CCDC93, and University of Geneva C16orf62.
    [Show full text]