Changing Nucleotide Specificity of the DEAD-Box Helicase Hera Abrogates Communication Between the Q-Motif and the P-Loop
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Biochemical Characterization of DDX43 (HAGE) Helicase
Biochemical Characterization of DDX43 (HAGE) Helicase A Thesis Submitted to the College of Graduate Studies and Research In Fulfillment of the Requirements For the Degree of Master of Science In the Department of Biochemistry University of Saskatchewan Saskatoon By Tanu Talwar © Copyright Tanu Talwar, March, 2017. All rights reserved PERMISSION OF USE STATEMENT I hereby present this thesis in partial fulfilment of the requirements for a postgraduate degree from the University of Saskatchewan and agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, either in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised this thesis or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts of it for any financial gain will not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Biochemistry University of Saskatchewan 107 Wiggins Road Saskatoon, Saskatchewan, Canada S7N 5E5 i ABSTRACT DDX43, DEAD-box polypeptide 43, also known as HAGE (helicase antigen gene), is a member of the DEAD-box family of RNA helicases. -
Environmental and Genetic Factors in Autism Spectrum Disorders: Special Emphasis on Data from Arabian Studies
International Journal of Environmental Research and Public Health Review Environmental and Genetic Factors in Autism Spectrum Disorders: Special Emphasis on Data from Arabian Studies Noor B. Almandil 1,† , Deem N. Alkuroud 2,†, Sayed AbdulAzeez 2, Abdulla AlSulaiman 3, Abdelhamid Elaissari 4 and J. Francis Borgio 2,* 1 Department of Clinical Pharmacy Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; [email protected] 2 Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; [email protected] (D.N.A.); [email protected] (S.A.) 3 Department of Neurology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; [email protected] or [email protected] 4 Univ Lyon, University Claude Bernard Lyon-1, CNRS, LAGEP-UMR 5007, F-69622 Lyon, France; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +966-13-333-0864 † These authors contributed equally to this work. Received: 26 January 2019; Accepted: 19 February 2019; Published: 23 February 2019 Abstract: One of the most common neurodevelopmental disorders worldwide is autism spectrum disorder (ASD), which is characterized by language delay, impaired communication interactions, and repetitive patterns of behavior caused by environmental and genetic factors. This review aims to provide a comprehensive survey of recently published literature on ASD and especially novel insights into excitatory synaptic transmission. Even though numerous genes have been discovered that play roles in ASD, a good understanding of the pathophysiologic process of ASD is still lacking. -
Hippo and Sonic Hedgehog Signalling Pathway Modulation of Human Urothelial Tissue Homeostasis
Hippo and Sonic Hedgehog signalling pathway modulation of human urothelial tissue homeostasis Thomas Crighton PhD University of York Department of Biology November 2020 Abstract The urinary tract is lined by a barrier-forming, mitotically-quiescent urothelium, which retains the ability to regenerate following injury. Regulation of tissue homeostasis by Hippo and Sonic Hedgehog signalling has previously been implicated in various mammalian epithelia, but limited evidence exists as to their role in adult human urothelial physiology. Focussing on the Hippo pathway, the aims of this thesis were to characterise expression of said pathways in urothelium, determine what role the pathways have in regulating urothelial phenotype, and investigate whether the pathways are implicated in muscle-invasive bladder cancer (MIBC). These aims were assessed using a cell culture paradigm of Normal Human Urothelial (NHU) cells that can be manipulated in vitro to represent different differentiated phenotypes, alongside MIBC cell lines and The Cancer Genome Atlas resource. Transcriptomic analysis of NHU cells identified a significant induction of VGLL1, a poorly understood regulator of Hippo signalling, in differentiated cells. Activation of upstream transcription factors PPARγ and GATA3 and/or blockade of active EGFR/RAS/RAF/MEK/ERK signalling were identified as mechanisms which induce VGLL1 expression in NHU cells. Ectopic overexpression of VGLL1 in undifferentiated NHU cells and MIBC cell line T24 resulted in significantly reduced proliferation. Conversely, knockdown of VGLL1 in differentiated NHU cells significantly reduced barrier tightness in an unwounded state, while inhibiting regeneration and increasing cell cycle activation in scratch-wounded cultures. A signalling pathway previously observed to be inhibited by VGLL1 function, YAP/TAZ, was unaffected by VGLL1 manipulation. -
Gene Ontology Functional Annotations and Pleiotropy
Network based analysis of genetic disease associations Sarah Gilman Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy under the Executive Committee of the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2014 © 2013 Sarah Gilman All Rights Reserved ABSTRACT Network based analysis of genetic disease associations Sarah Gilman Despite extensive efforts and many promising early findings, genome-wide association studies have explained only a small fraction of the genetic factors contributing to common human diseases. There are many theories about where this “missing heritability” might lie, but increasingly the prevailing view is that common variants, the target of GWAS, are not solely responsible for susceptibility to common diseases and a substantial portion of human disease risk will be found among rare variants. Relatively new, such variants have not been subject to purifying selection, and therefore may be particularly pertinent for neuropsychiatric disorders and other diseases with greatly reduced fecundity. Recently, several researchers have made great progress towards uncovering the genetics behind autism and schizophrenia. By sequencing families, they have found hundreds of de novo variants occurring only in affected individuals, both large structural copy number variants and single nucleotide variants. Despite studying large cohorts there has been little recurrence among the genes implicated suggesting that many hundreds of genes may underlie these complex phenotypes. The question -
A Discovery Resource of Rare Copy Number Variations in Individuals with Autism Spectrum Disorder
INVESTIGATION A Discovery Resource of Rare Copy Number Variations in Individuals with Autism Spectrum Disorder Aparna Prasad,* Daniele Merico,* Bhooma Thiruvahindrapuram,* John Wei,* Anath C. Lionel,*,† Daisuke Sato,* Jessica Rickaby,* Chao Lu,* Peter Szatmari,‡ Wendy Roberts,§ Bridget A. Fernandez,** Christian R. Marshall,*,†† Eli Hatchwell,‡‡ Peggy S. Eis,‡‡ and Stephen W. Scherer*,†,††,1 *The Centre for Applied Genomics, Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto M5G 1L7, Canada, †Department of Molecular Genetics, University of Toronto, Toronto M5G 1L7, Canada, ‡Offord Centre for Child Studies, Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton L8P 3B6, § Canada, Autism Research Unit, The Hospital for Sick Children, Toronto M5G 1X8, Canada, **Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland A1B 3V6, Canada, ††McLaughlin Centre, University of Toronto, Toronto M5G 1L7, Canada, and ‡‡Population Diagnostics, Inc., Melville, New York 11747 ABSTRACT The identification of rare inherited and de novo copy number variations (CNVs) in human KEYWORDS subjects has proven a productive approach to highlight risk genes for autism spectrum disorder (ASD). A rare variants variety of microarrays are available to detect CNVs, including single-nucleotide polymorphism (SNP) arrays gene copy and comparative genomic hybridization (CGH) arrays. Here, we examine a cohort of 696 unrelated ASD number cases using a high-resolution one-million feature CGH microarray, the majority of which were previously chromosomal genotyped with SNP arrays. Our objective was to discover new CNVs in ASD cases that were not detected abnormalities by SNP microarray analysis and to delineate novel ASD risk loci via combined analysis of CGH and SNP array cytogenetics data sets on the ASD cohort and CGH data on an additional 1000 control samples. -
Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham a Thesis Submitted in Conformity
Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Molecular Genetics University of Toronto © Copyright by Edward James Higginbotham 2020 i Abstract Characterizing Genomic Duplication in Autism Spectrum Disorder Edward James Higginbotham Master of Science Graduate Department of Molecular Genetics University of Toronto 2020 Duplication, the gain of additional copies of genomic material relative to its ancestral diploid state is yet to achieve full appreciation for its role in human traits and disease. Challenges include accurately genotyping, annotating, and characterizing the properties of duplications, and resolving duplication mechanisms. Whole genome sequencing, in principle, should enable accurate detection of duplications in a single experiment. This thesis makes use of the technology to catalogue disease relevant duplications in the genomes of 2,739 individuals with Autism Spectrum Disorder (ASD) who enrolled in the Autism Speaks MSSNG Project. Fine-mapping the breakpoint junctions of 259 ASD-relevant duplications identified 34 (13.1%) variants with complex genomic structures as well as tandem (193/259, 74.5%) and NAHR- mediated (6/259, 2.3%) duplications. As whole genome sequencing-based studies expand in scale and reach, a continued focus on generating high-quality, standardized duplication data will be prerequisite to addressing their associated biological mechanisms. ii Acknowledgements I thank Dr. Stephen Scherer for his leadership par excellence, his generosity, and for giving me a chance. I am grateful for his investment and the opportunities afforded me, from which I have learned and benefited. I would next thank Drs. -
WO 2016/040794 Al 17 March 2016 (17.03.2016) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2016/040794 Al 17 March 2016 (17.03.2016) P O P C T (51) International Patent Classification: AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, C12N 1/19 (2006.01) C12Q 1/02 (2006.01) BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, C12N 15/81 (2006.01) C07K 14/47 (2006.01) DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IR, IS, JP, KE, KG, KN, KP, KR, (21) International Application Number: KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, MG, PCT/US20 15/049674 MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, (22) International Filing Date: PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, SC, 11 September 2015 ( 11.09.201 5) SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every (26) Publication Language: English kind of regional protection available): ARIPO (BW, GH, (30) Priority Data: GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, 62/050,045 12 September 2014 (12.09.2014) US TZ, UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, (71) Applicant: WHITEHEAD INSTITUTE FOR BIOMED¬ DK, EE, ES, FI, FR, GB, GR, HR, HU, IE, IS, IT, LT, LU, ICAL RESEARCH [US/US]; Nine Cambridge Center, LV, MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, Cambridge, Massachusetts 02142-1479 (US). -
MAGE-A Inhibit Apoptosis and Promote Proliferation in Multiple Myeloma Through Regulation of BIM and P21cip1
www.oncotarget.com Oncotarget, 2020, Vol. 11, (No. 7), pp: 727-739 Research Paper MAGE-A inhibit apoptosis and promote proliferation in multiple myeloma through regulation of BIM and p21Cip1 Anna Huo-Chang Mei1, Kaity Tung1, Jessie Han1, Deepak Perumal1, Alessandro Laganà2,3, Jonathan Keats4, Daniel Auclair5, Ajai Chari1, Sundar Jagannath1, Samir Parekh1 and Hearn Jay Cho1,5 1Tisch Cancer Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA 2Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mt. Sinai, New York, NY, USA 3Institute for Next Generation Healthcare, Icahn School of Medicine at Mt. Sinai, New York, NY, USA 4Translational Genomics Research Institute, Phoenix, AZ, USA 5The Multiple Myeloma Research Foundation, Norwalk, CT, USA Correspondence to: Hearn Jay Cho, email: [email protected] Keywords: MAGE-A3; multiple myeloma; apoptosis; cell cycle regulation; DNA repair Received: July 18, 2019 Accepted: January 29, 2020 Published: February 18, 2020 Copyright: Mei et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT The type I Melanoma Antigen Gene (MAGE) A3 is a functional target associated with survival and proliferation in multiple myeloma (MM). To investigate the mechanisms of these oncogenic functions, we performed gene expression profiling (GEP) of p53 wild- type human myeloma cell lines (HMCL) after MAGE-A knockdown, which identified a set of 201 differentially expressed genes (DEG) associated with apoptosis, DNA repair, and cell cycle regulation. -
Identification of a Novel Cancer-Germline Transcript Within the Mirna Harboring GABRA3 Gene
Identification of a novel cancer-germline transcript within the miRNA harboring GABRA3 gene. Epigenetic alterations of the locus in tumors. Aurélie VAN TONGELEN Mai 2017 Thèse présentée en vue de l’obtention du grade de docteur en sciences biomédicales et pharmaceutiques Secteur des sciences de la santé President of the jury Professor Frederic Lemaigre de Duve institute Université catholique de Louvain Jury members Doctor Paola Arimodo ETaC – Unité de pharmacochimie de la régulation épigénétique du cancer CNRS - Laboratoires Pierre Fabre Centre de recherche & développement Doctor Philippe Arnaud GReD – Génétique Reproduction et Développement CNRS - Clermont Université – INSERM Professor Anabelle Decottignies de Duve institute Université catholique de Louvain Professor Patrick Jacquemin de Duve institute Université catholique de Louvain Professor Guido Bommer de Duve institute Université catholique de Louvain Doctor Axelle Loriot de Duve institute Université catholique de Louvain Promoter Professor Charles De Smet de Duve institute Université catholique de Louvain This thesis was supported by PhD fellowship from F.R.S – FNRS Télévie and UCL – FSR Après avoir passé presque six années dans le laboratoire de Charles De Smet, j’en sors grandie d’expérience, d’ouverture d’esprit, de connaissance, d’organisation et d’indépendance. Mais ces six années n’ont pas seulement été faites de sciences, c’est aussi une grande expérience de vie. Je remercie toutes les personnes qui m’ont permis d’arriver où je suis aujourd’hui. Je tiens tout d’abord et tout particulièrement à remercier le professeur Charles De Smet, sans qui cette thèse n’aurait pu voir le jour. En tant que promoteur de thèse, il m’a constamment guidée dans mes recherches et m’a sans cesse aidée à trouver des solutions pour avancer. -
(12) United States Patent (10) Patent No.: US 8,841,436 B2 Gorodeski Et Al
USOO8841436B2 (12) United States Patent (10) Patent No.: US 8,841,436 B2 Gorodeski et al. (45) Date of Patent: Sep. 23, 2014 (54) SCREENING, DIAGNOSING, TREATING AND 5,139,941 A 8/1992 Muzyczka et al. ............ 435/456 PROGNOSIS OF PATHOPHYSIOLOGIC 5,252.479 A 10/1993 Srivastava .......... 435/235.1 5,427,916 A 6/1995 Gewirtz et al. ................... 435/5 STATUS BY RNA REGULATION 5,849,902 A 12/1998 Arrow et al. ... 536,245 2002fO086356 A1 7, 2002 TuSchlet al. ... ... 435/69.1 (75) Inventors: George Gorodeski, Beachwood, OH 2002/0173478 A1 11/2002 Gewirtz. ......... 514.f44 A (US); Judith Potashkin, Gurnee, IL 2004/0014113 A1 1/2004 Yang et al. ..... ... 435/6.11 (US); Bentley Cheatham, Durham, NC 2004/001817.6 A1 1/2004 Tolentino et al. .. 424.93.21 (US s s 2005/0022725 A1 2/2005 Jurgensen et al. ............ 117/104 2005. O153918 A1 7, 2005 Chabot et al. ...... 514.f44 A 2006/0105360 A1 5/2006 Croceet al. .... ... 435.6.18 (73) Assignees: University Hospitals Cleveland 2006/0292616 A1 12/2006 Neely et al. .................. 435/6.12 Medical Center, Cleveland, OH (US); 2007/00264.03 A1 2/2007 Hatzigeorgiou et al. ... 435/6.11 Rosalind Franklin University of 2008/0171715 A1 7/2008 Brown et al. ................... 514,44 Medicine and Science, an Illinois Corporation, North Chicago, IL (US) FOREIGN PATENT DOCUMENTS WO WO93/24641 12/1993 (*) Notice: Subject to any disclaimer, the term of this WO WO94f13788 6, 1994 patent is extended or adjusted under 35 WO WO 2005078139 A2 8, 2005 U.S.C. -
High Resolution X Chromosome-Specific Array-CGH Detects New Cnvs in Infertile Males
High Resolution X Chromosome-Specific Array-CGH Detects New CNVs in Infertile Males Csilla Krausz1,2*, Claudia Giachini1, Deborah Lo Giacco2,3, Fabrice Daguin1, Chiara Chianese1, Elisabet Ars3, Eduard Ruiz-Castane2, Gianni Forti4, Elena Rossi5 1 Unit of Sexual Medicine and Andrology, Molecular Genetic Laboratory, Department of Clinical Physiopathology, University of Florence, Florence, Italy, 2 Andrology Service, Fundacio´ Puigvert, Barcelona, Spain, 3 Molecular Biology Laboratory, Fundacio´ Puigvert, Universitat Auto`noma de Barcelona, Barcelona, Spain, 4 Endocrinology Unit, Department of Clinical Physiopathology, University of Florence, Florence, Italy, 5 Biology and Medical Genetics, University of Pavia, Pavia, Italy Abstract Context: The role of CNVs in male infertility is poorly defined, and only those linked to the Y chromosome have been the object of extensive research. Although it has been predicted that the X chromosome is also enriched in spermatogenesis genes, no clinically relevant gene mutations have been identified so far. Objectives: In order to advance our understanding of the role of X-linked genetic factors in male infertility, we applied high resolution X chromosome specific array-CGH in 199 men with different sperm count followed by the analysis of selected, patient-specific deletions in large groups of cases and normozoospermic controls. Results: We identified 73 CNVs, among which 55 are novel, providing the largest collection of X-linked CNVs in relation to spermatogenesis. We found 12 patient-specific deletions with potential clinical implication. Cancer Testis Antigen gene family members were the most frequently affected genes, and represent new genetic targets in relationship with altered spermatogenesis. One of the most relevant findings of our study is the significantly higher global burden of deletions in patients compared to controls due to an excessive rate of deletions/person (0.57 versus 0.21, respectively; p = 8.78561026) and to a higher mean sequence loss/person (11.79 Kb and 8.13 Kb, respectively; p = 3.43561024). -
RNA Binding Proteins As Drivers and Therapeutic Target Candidates in Pancreatic Ductal Adenocarcinoma
International Journal of Molecular Sciences Article RNA Binding Proteins as Drivers and Therapeutic Target Candidates in Pancreatic Ductal Adenocarcinoma Markus Glaß 1,* , Patrick Michl 2 and Stefan Hüttelmaier 1 1 Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120 Halle, Germany; [email protected] 2 Universitätsklinik und Poliklinik für Innere Medizin I, Universitätsklinikum Halle (Saale), Ernst-Grube-Str. 40, 06120 Halle (Saale), Germany; [email protected] * Correspondence: [email protected] Received: 8 May 2020; Accepted: 8 June 2020; Published: 11 June 2020 Abstract: Pancreatic ductal adenocarcinomas (PDAC) belong to the most frequent and most deadly malignancies in the western world. Mutations in KRAS and TP53 along with some other frequent polymorphisms occur almost universally and are likely to be responsible for tumor initiation. However, these mutations cannot explain the heterogeneity in therapeutic responses observed in PDAC patients, which limits efficiency of current therapeutic strategies. Instead, recent classifications of PDAC tumor samples are based on transcriptomics data and thus include information about epigenetic, transcriptomic, and post-transcriptomic deregulations. RNA binding proteins (RBPs) are important post-transcriptional regulators involved in every aspect of the RNA life cycle and thus considerably influence the transcriptome. In this study, we systematically investigated deregulated expression, prognostic value, and essentiality reported for RBPs in PDAC or PDAC cancer models using publicly available data. We identified 44 RBPs with suggested oncogenic potential. These include various proteins, e.g., IGF2 mRNA binding proteins (IGF2BPs), with reported tumor-promoting roles. We further characterized these RBPs and found common patterns regarding their expression, interaction, and regulation by microRNAs.