DOCSLIB.ORG

INAUGURAL - DISSERTATION Zur Erlangung Der Doktorw¨Urde Der Naturwissenschaftlich-Mathematischen Gesamtfakult¨At Der Ruprecht - Karls - Universit¨At Heidelberg

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
INAUGURAL - DISSERTATION Zur Erlangung Der Doktorw¨Urde Der Naturwissenschaftlich-Mathematischen Gesamtfakult¨At Der Ruprecht - Karls - Universit¨At Heidelberg INAUGURAL - DISSERTATION zur Erlangung der Doktorw¨urde der Naturwissenschaftlich-Mathematischen Gesamtfakult¨at der Ruprecht - Karls - Universit¨at Heidelberg vorgelegt von Diplom-Biologe Nicolas Delhomme aus Villeneuve sur Lot, Frankreich Tag der m¨undlichen Pr¨ufung: Thema Integrative and Comparative Analysis of Retinoblastoma and Osteosarcoma P.D. Dr. Karsten Rippe Gutachter: Prof. Dr. Peter Lichter Die vorliegende Arbeit wurde am Deutschen Krebsforschungszentrum in der Abteilung von Prof. Dr. Lichter in der Zeit von 01.04.2004 bis 30.11.2008 unter der wissenchaftlichen Anleitung von Prof. Dr. Peter Lichter aus- gef¨uhrt. Eidesstattliche Versicherung Ich erkl¨arehiermit, dass ich diese vorgelegte Dissertation selbst verfasst und mich dabei keiner eanderen als den von mir ausdr¨ucklich bezeichneten Quellen und Hilfen bedient habe. Diese Dissertation wurde in dieser or andere Form weder bereits als Pr¨ufubgsarbeit verwendet, noch einer an- deren Fakult¨atals Dissertation vorgelegt. An keiner anderen Stelle ist ein Pr¨ufungsverfahren beantragt. Heidelberg, den 1. Januar 2013 Nicolas Delhomme Acknowledgments • For the data used in this work, published or not, I want to thank Prof. Dr. Dietmar Lohmann, Dr. Sandrine Gratias, Dr. Boris Zielinski, and Dr. Stephan Wolf. • For offering me the chance to do my PhD and waiting all these years for it to complete, I'm definitely grateful to Prof. Dr. Peter Lichter. • For the nice working atmosphere, the Chistmas parties, the pre-retreat and the retreat, the whole of the B060 division. Thanks for all the memories. • For every day work - and more - Fr´ed´ericBlond, Dr. Grischa T¨odtand of course Dr. Natalia Becker. Natalia, I'm glad you made it in that crowded geek's office! The last member of the SOG, which one can't forget - he will recognize himself - made these days in the office never boring for better or worse. Thanks for that Felix. A special thank to Margit MacLeod and Michael Hain for helping out with the printouts and corrections. Finally, a big thanks to Dr. Felix Kokocinski, who introduced me to the B060s and got me my first publication! • For the submission process, the deanery and the Helmholtz Interna- tional Graduate School for Cancer Research, in particular Heidi Costas and Dr. Lindsay Murrells for their help. I would not have achieved this and be were I'm without an innumerable number of persons, among which I want to thank a few in particular. • Prof. Ladel who transmitted me his passion for both biological and computational science; you started it all! • Prof. Antoine de Daruvar who entrusted me his tool although I was just fresh from school. His continuous mentoring helped me through all these years. Merci Antoine. • Bertrand Fabre for his accessibility when I was still a student and for all the advices he gave me. • A number of other ex-LIONs, Christian Marcazzo, Jean-St´ephane Morin, Niels Bojunga, Bernhard Sultzer, who made me trust my work. • Emilie Fritsch et Sophie Adjaley for their uninterrupted availability to help, even from miles (swedish ones) away. • Michael Knop for the long collaboration on an exciting project and especially for accepting to chair my defense committee. • Charles Girardot and Julien Gagneur for our long Heidelberg common history. We're now dispersed, but I really appreciated working with you. It kept me wanting to get better to reach out to your spheres. Let's the future tells us if I managed. • Hermann Rupp who offered me shelter for a long time. I suppose I was your longest \guest". • My family for everything they did for me. • My other family for their interest, their constant support and their kindness. • And Verena, my half. I cannot be thankful enough for all the efforts she conceded, the patience she showed and the support she gave me while I was working on this thesis. Literally, without her, this document would not be in your hands. This thesis is dedicated to her and to long time friends that probably never believed this chapter of my life will be closing one day. Verena, Marc, Xavier, Martin, this is for you. Zusammenfassung In den letzten eineinhalb Jahrzehnten hat die breite Nutzung der Hochdurch- satzmethoden in der Molekularbiologie zu großen Mengen von Datens¨atzen gefuhrt,¨ die eine unerwartete Komplexit¨at der Zellregulation zeigen. Die kurzlich¨ ver¨offentlichten Ergebnisse des ENCODEProjekts (ENCODE Pro- ject Consortium et al., 2012) haben das Ausmaß dieser Mechanismen im menschlichen Genom gezeigt und sicherlich werden in der Zukunft noch weitere entdeckt. Diese Komplexit¨at innerhalb einer einzelnen Zelle, ganz zu schweigen von Zell-Zell-Wechselwirkungen oder dem Einfluss der Mi- kroumgebung, ist schwer zu erfassen. Dieses Verst¨andnis ist allerdings der Schlussel¨ zur Entwicklung von individuell angepassten Behandlungen gene- tischer Krankheiten oder St¨orungen, darunter auch Krebs. In der Mathematik geht man solche komplexen Probleme mit Methoden an, die die Komplexit¨at reduzieren, so dass man sie in aufl¨osbarer Weise mo- dellieren kann. In der Biologie haben Forscher diese Methode angewandt, um das Systembiologiekonzept zu entwickeln, welches das Verst¨andnis der Zell- regulationsmechanismen vereinfacht. Die meisten ver¨offentlichten Studien, in denen Hochdurchsatz-Technologien verwendet wurden, waren jedoch nur auf eine einzige Art der Zellregulation ausgerichtet und k¨onnen daher nicht als solche verwendet werden, um die Regulationswechselwirkungen zu un- tersuchen. Außerdem ist bei solchen Studien die Unterscheidung zwischen ausl¨osenden Faktoren und St¨orfaktoren schwierig. Diese beiden Punkte waren meine ursprungliche¨ Motivation fur¨ die Ent- wicklung statistischer Methoden, die die integrative und vergleichende Ana- lyse von verschiedenen Arten von Datens¨atzen erm¨oglichen. Es wurden drei verschiedene Softwares entwickelt, um dieses Ziel zu erreichen. Erstens, \cus- tomCDF": dies ist eine Methode, um die Custom Definition File (CDF) des Affymetrix GeneChip R s neu zu definieren; dies dient im Wesentlichen dazu, die st¨andige Aktualisierung der Sequenz des menschlichen Genoms und dessen Annotationen zu erfassen. Zweitens, \aSim": eine Methode, um Microarray-Daten zu simulieren; dies erstellt die notwendigen Daten um die entwickelten Algorithmen auszuwerten. Drittens, eine Reihe von kombinier- ten statistischen Methoden, die integrative Analysen erm¨oglichen und die schließlich durch gezielte Modifikationen auch vergleichende Analysen er- lauben. \CustomCDF" und \aSim" wurden auf unabh¨angigen Datens¨atzen validiert, w¨ahren die entwickelten analytischen Methoden auf \aSim" simu- lierten Dateien und ¨offentlich verfugbaren¨ Datens¨atzen validiert wurden. Die oben beschriebenen Methoden wurden angewandt, um zwei biologi- sche Fragen zu beantworten. Zun¨achst wurden zwei Retinoblastom-Daten- s¨atze benutzt, um die Auswirkung von Genom-Aberrationen auf die Gen- Expressionen zu untersuchen. Dann, motiviert durch die Tatsache, dass Retinoblastom-Patienten im sp¨ateren Leben ein h¨oheres Risiko haben ein Osteosarkom zu entwickeln als der Durchschnitt der Bev¨olkerung, wurden Datens¨atze von beiden Tumoren vergleichend analysiert, um Ahnlichkeiten¨ und Unterschiede zu identifizieren. Trotz der eher begrenzten Anzahl von Datens¨atzen waren beide Ans¨atze dank ihrer hohen Pr¨azision und niedrigen Fehlerrate erfolgreich und haben so die Basis fur¨ gr¨oßere Analysen gebildet. In der Tat hat die hier angewandte integrative Analyse des Retino- blastoms gezeigt, dass dem Zugewinn des Chromosoms 6 eine wichtige Be- deutung in der Progression der Krankheit zukommt, was wiederum darauf hinweist, dass viele Gene auf diesem Chromosom eine Krebsentwicklung f¨ordern. Im Vergleich zu Microarray-Standardanalysen war diese Analyse daruber¨ hinaus in der Lage, die Interaktion von Regulierungsmechanismen zu entdecken: Beispiele von positivem und negativem Ausgleich der Gen- expression in Regionen mit DNA-Zugewinn beziehungsweise -Verlust, sowie Beispiele von Antisense-Transkription, Pseudogen- und snRNA-Regulation wurden in diesem Datensatz identifiziert. Durch die vergleichende Analyse hingegen konnte gezeigt werden, dass Retinoblastome und Osteosarkome große Ahnlichkeit¨ aufweisen und daruber¨ hinaus, dass beide Vorteil aus ihren jeweiligen Mikroumgebungen ziehen und damit verschiedene Signalwege, PKC/Calmodulin in Retinoblastom und GPCR/RAS in Osteosarkom, zu nutzen scheinen. In dieser Arbeit konnte die Bedeutung und der Nutzen der entwickel- ten Softwares und statistischen Methoden demonstriert werden: durch sie konnten pr¨azise Antworten auf die zwei gestellten biologischen Fragen ge- funden werden. Desweiteren konnte dadurch eine Reihe interessanter Hy- pothesen aufgestellt werden, die weitere Untersuchungen erfordern. Diese Softwares sind nicht auf Microarray-Analysen begrenzt, sondern k¨onnen auf alle Hochdurchsatz-Daten appliziert werden: mittels der hier entwickelten Methoden kann das Konzept der Systembiologie auf die Erforschung der Karzinogenese angewandt werden. Abstract In the last one and a half decades, the generalization of high throughput methods in molecular biology has led to the generation of vast amounts of datasets that unraveled the unfathomed complexity of the cell regulatory mechanisms. The recently published results of the ENCODE project (EN- CODE Project Consortium et al., 2012) demonstrated the extend of these in the human genome and certainly more regulation mechanisms will be dis- covered in the future. Already, this complexity within a single cell - without taking into account cell-cell interaction or micro-environment
Load more

Recommended publications
  • Genetic Inhibition of the Ubiquitin Ligase Rnf5 Attenuates Phenotypes
    www.nature.com/scientificreports OPEN Genetic Inhibition Of The Ubiquitin Ligase Rnf5 Attenuates Phenotypes Associated To F508del Received: 02 February 2015 Accepted: 17 June 2015 Cystic Fibrosis Mutation Published: 17 July 2015 Valeria Tomati1, Elvira Sondo1, Andrea Armirotti2, Emanuela Caci1, Emanuela Pesce1, Monica Marini1, Ambra Gianotti1, Young Ju Jeon3, Michele Cilli4, Angela Pistorio1, Luca Mastracci4,5, Roberto Ravazzolo1,6, Bob Scholte7, Ze’ev Ronai3, Luis J. V. Galietta1 & Nicoletta Pedemonte1 Cystic fibrosis (CF) is caused by mutations in the CFTR chloride channel. Deletion of phenylalanine 508 (F508del), the most frequent CF mutation, impairs CFTR trafficking and gating. F508del- CFTR mistrafficking may be corrected by acting directly on mutant CFTR itself or by modulating expression/activity of CFTR-interacting proteins, that may thus represent potential drug targets. To evaluate possible candidates for F508del-CFTR rescue, we screened a siRNA library targeting known CFTR interactors. Our analysis identified RNF5 as a protein whose inhibition promoted significant F508del-CFTR rescue and displayed an additive effect with the investigational drug VX-809. Significantly, RNF5 loss in F508del-CFTR transgenic animals ameliorated intestinal malabsorption and concomitantly led to an increase in CFTR activity in intestinal epithelial cells. In addition, we found that RNF5 is differentially expressed in human bronchial epithelia from CF vs. control patients. Our results identify RNF5 as a target for therapeutic modalities to antagonize mutant CFTR proteins. Cystic Fibrosis (CF), one of the most common inherited diseases (~1/3000 in Caucasian populations), is caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR), a cAMP-regulated chloride channel expressed at the apical membrane of many types of epithelial cells1,2.
    [Show full text]
  • Regulation of Pluripotency by RNA Binding Proteins
    Cell Stem Cell Review Regulation of Pluripotency by RNA Binding Proteins Julia Ye1,2 and Robert Blelloch1,2,* 1The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94143, USA 2Department of Urology, University of California, San Francisco, San Francisco, CA 94143, USA *Correspondence: [email protected] http://dx.doi.org/10.1016/j.stem.2014.08.010 Establishment, maintenance, and exit from pluripotency require precise coordination of a cell’s molecular machinery. Substantial headway has been made in deciphering many aspects of this elaborate system, particularly with respect to epigenetics, transcription, and noncoding RNAs. Less attention has been paid to posttranscriptional regulatory processes such as alternative splicing, RNA processing and modification, nuclear export, regulation of transcript stability, and translation. Here, we introduce the RNA binding proteins that enable the posttranscriptional regulation of gene expression, summarizing current and ongoing research on their roles at different regulatory points and discussing how they help script the fate of pluripotent stem cells. Introduction RBPs are responsible for every event in the life of an RNA Embryonic stem cells (ESCs), which are derived from the inner molecule, including its capping, splicing, cleavage, nontem- cell mass of the mammalian blastocyst, are remarkable because plated nucleotide addition, nucleotide editing, nuclear export, they can propagate in vitro indefinitely while retaining both the cellular localization, stability, and translation (Keene, 2007). molecular identity and the pluripotent properties of the peri-im- Overall, little is known about RBPs: most are classified based plantation epiblast.
    [Show full text]
  • RNF5 Antibody
    RNF5 Antibody CATALOG NUMBER: 27-144 Antibody used in WB on Human HeLa at 0.2-1 ug/ml. Specifications APPLICATIONS: RNF5 antibody can be used for detection of RNF5 by ELISA at 1:12500. RNF5 antibody can be used for detection of RNF5 by western blot at 1 ug/mL, and HRP conjugated secondary antibody should be diluted 1:50,000 - 100,000. USER NOTE: Optimal dilutions for each application to be determined by the researcher. POSITIVE CONTROL: 1) Cat. No. 1201 - HeLa Cell Lysate PREDICTED MOLECULAR 20 kDa WEIGHT: IMMUNOGEN: Antibody produced in rabbits immunized with a synthetic peptide corresponding a region of human RNF5. HOST SPECIES: Rabbit Properties PURIFICATION: Antibody is purified by peptide affinity chromatography method. PHYSICAL STATE: Lyophilized BUFFER: Antibody is lyophilized in PBS buffer with 2% sucrose. Add 50 uL of distilled water. Final antibody concentration is 1 mg/mL. CONCENTRATION: 1 mg/ml STORAGE CONDITIONS: For short periods of storage (days) store at 4˚C. For longer periods of storage, store RNF5 antibody at -20˚C. As with any antibody avoid repeat freeze-thaw cycles. CLONALITY: Polyclonal CONJUGATE: Unconjugated Additional Info ALTERNATE NAMES: RNF5, RING5, RMA1 ACCESSION NO.: NP_008844 PROTEIN GI NO.: 5902054 OFFICIAL SYMBOL: RNF5 GENE ID: 6048 Background BACKGROUND: RNF5 contains a RING finger, which is a motif known to be involved in protein-protein interactions. This protein is a membrane-bound ubiquitin ligase. It can regulate cell motility by targeting paxillin ubiquitination and altering the distribution and localization of paxillin in cytoplasm and cell focal adhesions.The protein encoded by this gene contains a RING finger, which is a motif known to be involved in protein-protein interactions.
    [Show full text]
  • 1 Supporting Information for a Microrna Network Regulates
    Supporting Information for A microRNA Network Regulates Expression and Biosynthesis of CFTR and CFTR-ΔF508 Shyam Ramachandrana,b, Philip H. Karpc, Peng Jiangc, Lynda S. Ostedgaardc, Amy E. Walza, John T. Fishere, Shaf Keshavjeeh, Kim A. Lennoxi, Ashley M. Jacobii, Scott D. Rosei, Mark A. Behlkei, Michael J. Welshb,c,d,g, Yi Xingb,c,f, Paul B. McCray Jr.a,b,c Author Affiliations: Department of Pediatricsa, Interdisciplinary Program in Geneticsb, Departments of Internal Medicinec, Molecular Physiology and Biophysicsd, Anatomy and Cell Biologye, Biomedical Engineeringf, Howard Hughes Medical Instituteg, Carver College of Medicine, University of Iowa, Iowa City, IA-52242 Division of Thoracic Surgeryh, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada-M5G 2C4 Integrated DNA Technologiesi, Coralville, IA-52241 To whom correspondence should be addressed: Email: [email protected] (M.J.W.); yi- [email protected] (Y.X.); Email: [email protected] (P.B.M.) This PDF file includes: Materials and Methods References Fig. S1. miR-138 regulates SIN3A in a dose-dependent and site-specific manner. Fig. S2. miR-138 regulates endogenous SIN3A protein expression. Fig. S3. miR-138 regulates endogenous CFTR protein expression in Calu-3 cells. Fig. S4. miR-138 regulates endogenous CFTR protein expression in primary human airway epithelia. Fig. S5. miR-138 regulates CFTR expression in HeLa cells. Fig. S6. miR-138 regulates CFTR expression in HEK293T cells. Fig. S7. HeLa cells exhibit CFTR channel activity. Fig. S8. miR-138 improves CFTR processing. Fig. S9. miR-138 improves CFTR-ΔF508 processing. Fig. S10. SIN3A inhibition yields partial rescue of Cl- transport in CF epithelia.
    [Show full text]
  • Proquest Dissertations
    INFORMATION TO USERS This manuscript has been reproduced from the microfilm master. UMI films the text directly from the original or copy submitted. Thus, some thesis and dissertation copies are in typewriter face, while others may be from any type of computer printer. The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleedthrough, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send UMI a complete manuscript and there are missing pages, these will be noted. Also, if unauthorized copyright material had to be removed, a note will indicate the deletion. Oversize materials (e.g., maps, drawings, charts) are reproduced by sectioning the original, beginning at the upper left-hand comer and continuing from left to right in equal sections with small overlaps. Each original is also photographed in one exposure and is included in reduced form at the back of the book. Photographs included in the original manuscript have been reproduced xerographically in this copy. Higher quality 6” x 9” black and white photographic prints are available for any photographs or illustrations appearing in this copy for an additional charge. Contact UMI directly to order. UMI Bell & Howell Information and Learning 300 North Zeeb Road, Ann Arbor, Ml 48106-1346 USA 800-521-0600 NOTE TO USERS Page(s) missing in number only; text follows. Microfilmed as received. 222-229 This reproduction is the best copy available. UMI MOLECULAR GENETIC AND BIOCHEMICAL STUDIES OF THE HUMAN AND MOUSE MHC COMPLEMENT GENE CLUSTERS DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Zhenyu Yang, M.S.
    [Show full text]
  • RBM9 Antibody (Monoclonal) (M02) Mouse Monoclonal Antibody Raised Against a Partial Recombinant RBM9
    10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 RBM9 Antibody (monoclonal) (M02) Mouse monoclonal antibody raised against a partial recombinant RBM9. Catalog # AT3594a Specification RBM9 Antibody (monoclonal) (M02) - Product Information Application IF, WB, E Primary Accession O43251 Other Accession BC013115 Reactivity Human, Mouse Host mouse Clonality Monoclonal Isotype IgG2b Kappa Calculated MW 41374 RBM9 Antibody (monoclonal) (M02) - Additional Information Immunofluorescence of monoclonal antibody to RBM9 on A-431 cell. [antibody concentration 10 ug/ml] Gene ID 23543 Other Names RNA binding protein fox-1 homolog 2, Fox-1 homolog B, Hexaribonucleotide-binding protein 2, RNA-binding motif protein 9, RNA-binding protein 9, Repressor of tamoxifen transcriptional activity, RBFOX2, FOX2, HRNBP2, RBM9, RTA Target/Specificity RBM9 (AAH13115, 1 a.a. ~ 100 a.a) partial recombinant protein with GST tag. MW of the GST tag alone is 26 KDa. Dilution Antibody Reactive Against Recombinant WB~~1:500~1000 Protein.Western Blot detection against Immunogen (36.63 KDa) . Format Clear, colorless solution in phosphate buffered saline, pH 7.2 . Storage Store at -20°C or lower. Aliquot to avoid repeated freezing and thawing. Precautions RBM9 Antibody (monoclonal) (M02) is for research use only and not for use in diagnostic or therapeutic procedures. Page 1/3 10320 Camino Santa Fe, Suite G San Diego, CA 92121 Tel: 858.875.1900 Fax: 858.622.0609 RBM9 Antibody (monoclonal) (M02) - Protocols Provided below are standard protocols that you may find useful for product applications. • Western Blot • Blocking Peptides • Dot Blot • Immunohistochemistry • Immunofluorescence • Immunoprecipitation • Flow Cytomety RBM9 monoclonal antibody (M02), clone • Cell Culture 5E11 Western Blot analysis of RBM9 expression in A-431 ( (Cat # AT3594a ) RBM9 monoclonal antibody (M02), clone 5E11.
    [Show full text]
  • Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
    Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement.
    [Show full text]
  • Download Thesis
    This electronic thesis or dissertation has been downloaded from the King’s Research Portal at https://kclpure.kcl.ac.uk/portal/ The Genetics and Spread of Amyotrophic Lateral Sclerosis Jones, Ashley Richard Awarding institution: King's College London The copyright of this thesis rests with the author and no quotation from it or information derived from it may be published without proper acknowledgement. END USER LICENCE AGREEMENT Unless another licence is stated on the immediately following page this work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International licence. https://creativecommons.org/licenses/by-nc-nd/4.0/ You are free to copy, distribute and transmit the work Under the following conditions: Attribution: You must attribute the work in the manner specified by the author (but not in any way that suggests that they endorse you or your use of the work). Non Commercial: You may not use this work for commercial purposes. No Derivative Works - You may not alter, transform, or build upon this work. Any of these conditions can be waived if you receive permission from the author. Your fair dealings and other rights are in no way affected by the above. Take down policy If you believe that this document breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 07. Oct. 2021 THE GENETICS AND SPREAD OF AMYOTROPHIC LATERAL SCLEROSIS Ashley Richard Jones PhD in Clinical Neuroscience - 1 - Abstract Our knowledge of the genetic contribution to Amyotrophic Lateral Sclerosis (ALS) is rapidly growing, and there is increasing research into how ALS spreads through the motor system and beyond.
    [Show full text]
  • Systematic Genetic Analysis of the MHC Region Reveals Mechanistic
    RESEARCH ARTICLE Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease Matteo D’Antonio1,2†, Joaquin Reyna2,3†, David Jakubosky3,4, Margaret KR Donovan4,5, Marc-Jan Bonder6, Hiroko Matsui1, Oliver Stegle6, Naoki Nariai2‡, Agnieszka D’Antonio-Chronowska1,2, Kelly A Frazer1,2* 1Institute for Genomic Medicine, University of California, San Diego, San Diego, United States; 2Department of Pediatrics, Rady Children’s Hospital, University of California, San Diego, San Diego, United States; 3Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, United States; 4Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, San Diego, United States; 5Department of Biomedical Informatics, University of California, San Diego, San Diego, United States; 6European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom Abstract The MHC region is highly associated with autoimmune and infectious diseases. Here we conduct an in-depth interrogation of associations between genetic variation, gene expression and disease. We create a comprehensive map of regulatory variation in the MHC region using WGS from 419 individuals to call eight-digit HLA types and RNA-seq data from matched iPSCs. Building on this regulatory map, we explored GWAS signals for 4083 traits, detecting colocalization for 180 *For correspondence: disease loci with eQTLs. We show that eQTL analyses taking HLA type haplotypes into account [email protected] have substantially greater power compared with only using single variants. We examined the † These authors contributed association between the 8.1 ancestral haplotype and delayed colonization in Cystic Fibrosis, equally to this work postulating that downregulation of RNF5 expression is the likely causal mechanism.
    [Show full text]
  • Genetic Variants and Prostate Cancer Risk: Candidate Replication and Exploration of Viral Restriction Genes
    2137 Genetic Variants and Prostate Cancer Risk: Candidate Replication and Exploration of Viral Restriction Genes Joan P. Breyer,1 Kate M. McReynolds,1 Brian L. Yaspan,2 Kevin M. Bradley,1 William D. Dupont,3 and Jeffrey R. Smith1,2,4 Departments of 1Medicine, 2Cancer Biology, and 3Biostatistics, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine; and 4Medical Research Service, VA Tennessee Valley Healthcare System, Nashville, Tennessee Abstract The genetic variants underlying the strong heritable at genome-wide association study loci 8q24, 11q13, and À À component ofprostate cancer remain largely unknown. 2p15 (P =2.9Â 10 4 to P =4.7Â 10 5), showing study Genome-wide association studies ofprostate cancer population power. We also find evidence to support have yielded several variants that have significantly reported associations at candidate genes RNASEL, replicated across studies, predominantly in cases EZH2, and NKX3-1 (P = 0.031 to P = 0.0085). We unselected for family history of prostate cancer. further explore a set of candidate genes related to Additional candidate gene variants have also been RNASEL and to its role in retroviral restriction, proposed, many evaluated within familial prostate identifying nominal associations at XPR1 and RBM9. cancer study populations. Such variants hold great The effects at 8q24 seem more pronounced for those potential value for risk stratification, particularly for diagnosed at an early age, whereas at 2p15 and early-onset or aggressive prostate cancer, given the RNASEL the effects were more pronounced at a later comorbidities associated with current therapies. Here, age. However, these trends did not reach statistical we investigate a Caucasian study population of523 significance.
    [Show full text]
  • C. Elegans GFP/RFP Alternative Splicing Screen
    ARTICLES Transgenic alternative-splicing reporters reveal tissue-specific expression profiles and regulation s d mechanisms in vivo o h t e 1,2 3,4 3,4 1,2 m Hidehito Kuroyanagi , Tetsuo Kobayashi , Shohei Mitani & Masatoshi Hagiwara e r u t a n / Alternative splicing of pre-mRNAs allows multicellular organisms native exons have been well characterized by analyzing model genes. m o c to create a huge diversity of proteomes from a finite number of Expression cloning strategies have permitted the global collection . e r genes. But extensive studies in vitro or in cultured cells have not of putative sequence elements that function in cultured cells, and u t a fully explained the regulation mechanisms of tissue-specific or bioinformatic analyses have identified putative cis elements within n . developmentally regulated alternative splicing in living exons and introns. Recently, however, conditional knockouts of w w organisms. Here we report a transgenic reporter system that trans-acting SR protein families revealed that alternative splicing of w / / : allows visualization of expression profiles of mutually exclusive only a few target genes are crucially dependent on a specific protein p t t exons in Caenorhabditis elegans. Reporters for egl-15 exons 5A in cardiac muscles, even though many more genes expressed in this h and 5B showed tissue-specific profiles, and we isolated mutants 14 p tissue have typical cis elements . This indicates that we cannot u o defective in the tissue specificity. We identified alternative- precisely predict the alternative splicing patterns in each tissue r G splicing defective-1 (asd-1), encoding a new RNA-binding or cell without the assessment of the regulation mechanisms in g protein of the evolutionarily conserved Fox-1 family, as a living organisms.
    [Show full text]
  • Datasheet Blank Template
    SAN TA C RUZ BI OTEC HNOL OG Y, INC . DOM3Z (B-12): sc-393141 BACKGROUND APPLICATIONS DOM3Z (dom-3 homolog Z), also known as NG6 or DOM3L, is a 396 amino DOM3Z (B-12) is recommended for detection of DOM3Z of mouse, rat and acid ubiquitously expressed protein belonging to the DOM3Z family. The gene human origin by Western Blotting (starting dilution 1:100, dilution range encoding DOM3Z maps to human chromosome 6 in the major histocompati - 1:100-1:1000), immunoprecipitation [1-2 µg per 100-500 µg of total protein bility complex (MHC) class III region. Chromosome 6 contains 170 million base (1 ml of cell lysate)], immunofluorescence (starting dilution 1:50, dilution pairs and comprises nearly 6% of the human genome. Deletion of a portion range 1:50-1:500), immunohistochemistry (including paraffin-embedded of the q arm of chromosome 6 is associated with early onset intestinal can - sections) (starting dilution 1:50, dilution range 1:50-1:500) and solid phase cer, suggesting the presence of a cancer susceptibility locus. Additionally, ELISA (starting dilution 1:30, dilution range 1:30-1:3000). Porphyria cutanea tarda, Parkinson’s disease and Stickler syndrome are all Suitable for use as control antibody for DOM3Z siRNA (h): sc-95321, DOM3Z associated with genes that map to chromosome 6. siRNA (m): sc-143143, DOM3Z shRNA Plasmid (h): sc-95321-SH, DOM3Z shRNA Plasmid (m): sc-143143-SH, DOM3Z shRNA (h) Lentiviral Particles: REFERENCES sc-95321-V and DOM3Z shRNA (m) Lentiviral Particles: sc-143143-V. 1. Brunner, H.G., et al .
    [Show full text]