DOCSLIB.ORG

Mutational Analysis of ATP7B in North Chinese Patients with Wilson Disease

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mutational Analysis of ATP7B in North Chinese Patients with Wilson Disease Journal of Human Genetics (2013) 58, 67–72 & 2013 The Japan Society of Human Genetics All rights reserved 1434-5161/13 www.nature.com/jhg ORIGINAL ARTICLE Mutational analysis of ATP7B in north Chinese patients with Wilson disease Kui Li1, Wei-Min Zhang2, Sheng Lin1,6,LuWen1,7, Zi-Feng Wang1, Dan Xie3, Min Wei4, Zheng-Qing Qiu4, Yi Dai5, Marie C M Lin3, Hsiang-Fu Kung3 and Feng-Xia Yao2 Wilson disease (WD) is an autosomal recessive inherited disease caused by abnormalities of the copper-transporting protein encoding gene ATP7B. In this study, we examined ATP7B for mutations in 114 individuals of Chinese Han population living in north China who were diagnosed as WD. Totally, we identified 36 mutations and 11 single-nucleotide polymorphisms (SNPs), of which 14 mutations have never been reported previously and 5 were firstly described in Chinese. Among these, p.R778L (21.5%), p.A874V (7.5%) and p.P992L (6.1%) were the most frequent mutations. A genotype of p.L770L þ p.R778L þ p.P992L was the most frequent triple mutations and two pairs of mutations, p.L770L/p.R778L and p.A874V/ p.I929V, were closely related. In addition, a database was established to summarize all ATP7B mutations, including those reported previously and those identified in this study. Popular algorithms were used to predict the functional effects of these mutations, and finally, by comparative genomics approaches, we predicted a group of mutation hot spots for ATP7B. Our study will broaden our knowledge about ATP7B mutations in WD patients in north China, and be helpful for clinical genetic testing. Journal of Human Genetics (2013) 58, 67–72; doi:10.1038/jhg.2012.134; published online 13 December 2012 Keywords: ATP7B; Chinese; genotype; mutational analysis; susceptibility; Wilson disease INTRODUCTION ATP7B and its homolog ATP7A are the two main copper-transporting Wilson disease (WD/WND, NCBI MIM No. 277900) is an autosomal proteins.7 Defects of ATP7A impair the entry of copper from recessive inherited disease characterized by excess accumulation of enterocytes into circulation and thereby cause deficiency of copper, 8 intracellular hepatic copper with subsequent hepatic and neurologic known as the Menkes disease, an X-linked disorder. The role of abnormalities. It was first reported by Dr Samuel Alexander Kinnier ATP7B is quite different and it mainly functions as transforming Wilson in 1912 and since then a growing number of cases were apoceruloplasmin into ceruloplasmin and excreting copper into the identified worldwide.1 It is estimated that the disease frequency is biliary canaliculi. Defects of ATP7B reduce the blood ceruloplasmin about 1/5000 to 1/30 000 and the carrier frequency is even higher.2 and are harmful to hepatocytes. Many other organs, such as the brain WD patients have a very poor prognosis if not diagnosed at an early and kidney, can also be affected.9 stage and treated appropriately. A life-span treatment is required for Up to now, more than 500 forms of genetic mutations in ATP7B WD patients with severe symptom or early onset age, and an early have been reported and there are 1343 known single-nucleotide diagnosis and therapy will remarkably improve life quality with a polymorphisms (SNPs), suggesting that ATP7B is susceptible to hope of complete symptomatic recovery.3–5 Therefore, quick and mutation.10 In this study, we identified 36 mutations from 114 accurate genetic testing for WD patients and efficient screening for individuals in north China Han populations who were diagnosed as carriers in the population are urgently required. WD, of which 14 mutations have never been reported previously and WD is one of the most prevalent inherited diseases caused by 5 are firstly described in the Chinese. We also performed a abnormalities of a single gene, the ATP7B, which encodes a copper- bioinformatic analysis to predict the functional effects of these transporting ATPase 2 b protein.3,6 It is located at 13q14.3, spanning a mutations, and predicted a group of amino-acid residues of the genomic region of B78 kb and including 21 exons and 20 introns. ATP7B protein to be mutation hot spots. 1Laboratory of Integrated Biosciences, Life Science School, Sun Yat-sen University, Guangzhou, Guangdong, China; 2Clinical Research Lab, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 3State Key Laboratory of Oncology in South China, Cancer Center, Sun Yat-sen University, Guangzhou, China; 4Department of Pediatrics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China and 5Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China 6Current address: Laboratory of Medical Genetics, Research Institute of Population and Family Planning, ShenZhen, China. 7Current address: Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China. Correspondence: Dr F-X Yao, Clinical Research Lab, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical college, Beijing 100730, China. E-mail: [email protected] Received 7 April 2012; revised 19 September 2012; accepted 21 October 2012; published online 13 December 2012 ATP7B mutations in WD patients in north China KLiet al 68 MATERIALS AND METHODS Meanwhile, allele frequency and heterozygosity of SNPs identified in this study Subjects were also analyzed and subsequently compared with those obtained from the A total of 114 individuals, who belonged to the Han population from north dbSNP database. China and were diagnosed as WD, were recruited in this study, of which 76 A self-writing program was used for genotyping and paired relevance were males and 38 were females, with onset ages from 7 to 44 years and a analysis of the identified mutations. median age of 25. One hundred and eleven unrelated individuals and three siblings were set as the control, and all of them were fully informed and signed Computational prediction of deleterious variants of ATP7B for agreement. All the patients were diagnosed as WD at the Peking Union To predict the deleterious effects of a mutation to the structure and function Medical College Hospital generally based on the following criteria: (1) liver or of the protein, we applied three popular programs: PolyPhen-2 (http:// brain failure symptoms; (2) presence of K-F ring in the cornea by slit-lamp À1 genetics.bwh.harvard.edu/pph2/index.shtml), PMut (http://mmb2.pcb.ub.es: examination; (3) reduced serum ceruloplasmin (o0.20 g l )and/orelevated 8080/PMut/) and SNAP (http://rostlab.org/services/snap/).19–22 To predict 4 m 24-hour urinary copper excretion ( 1.0 mol per day) and/or hepatic copper deleterious SNPs located in the introns, upstream and downstream of the 4 m 11 content 250 g per g of dry weight. coding region, the FastSNP program was used (http://fastsnp.ibms.sinica. edu.tw/pages/input_CandidateGeneSearch.jsp).17 All the programs were run by Data source their default parameters with optimization. Reference ATP7B mRNA (NM_000053.3) and protein sequences (NP_000044.2) were retrieved from the NCBI Entrez database, and SNPs were retrieved from the NCBI database (db) SNP (http://www.ncbi.nlm.nih. Predication of mutation hot spots for ATP7B gov/snp/), including all SNPs in the ATP7B gene region except the clinical ATP7B protein sequences of 13 non-human organisms, including monkey submission items.12 (XP_001103242.2), rat (NP_036643.2), mouse (NP_031537.2), dog (NP_001020438.1), cattle (XP_002691840.1), sheep (NP_001009732.1), horse Multiple approaches were applied to obtain the known genetic mutations of ATP7B, including (1) the Wilson Disease Mutation Database in the University (XP_001488500.1), duck (XP_001378265.2), chicken (XP_417073.3), panda of Alberta, maintained by the Cox Lab (http://www.wilsondisease.med.ualberta (XP_002917723.1), platypus (XP_001513328.2), lizard (XP_003215344.1) .ca/database.asp);10 (2) the UniProt (Universal Protein Resource) accession and zebrafish (XP_684415.4), were retrieved from the NCBI database. Multiple sequences alignment of these sequences together with the human ATP7B of ATP7B protein P35670 (http://www.uniprot.org/uniprot/P35670); (3) the protein sequence was performed by the Clustal X software (http://www. Human Gene Mutation Database (HGMD) Professional at the Institute of 18 Medical Genetics in Cardiff, a product of BIOBASE (http://www.hgmd.org/).13 clustal.org/) with default parameters. Conservative scores of each residue HGMD is a commercial knowledge base service, being established and were calculated and outputted, ranging from 0 to 100. An amino-acid residue with the conservative score 480 was considered to be a high-conservative site maintained manually, and the last update was at 30 September 2011. This database is thought to be the most precise and complete collection of the and more than five consecutive such sites were defined as a conservative ATP7B gene variants. All the missense/nonsense mutations with an accession in segment. To identify mutation hot spots for ATP7B,allATP7B missense/nonsense the above databases were merged into a new set (Supplementary Table 1) and other forms of mutations, such as insert, deletion, indels, synonymous and mutations, including those identified in this study and those reported noncoding mutations, were mainly based on the HGMD database annotation. previously, were mapped into the conservative track. We defined a mutation hot spot when (1) there are more than one form of missense/nonsense mutations for a high-conservative site, or (2) there is only one form of DNA extraction, PCR and sequencing mutation, but it is within a conservative segment. Genomic DNAs were extracted from the peripheral blood leukocytes of the patients by QIAamp blood kits (Qiagen, Hilden, Germany) according to the manufacturer’s instruction. Eleven exons (2, 5, 8–12, 13, 16, 18 and 19) of the RESULTS ATP7B gene and their flanking intron sequences, which are a total of 5687 bp Identification of novel and/or prevalent ATP7B genetic variants of in length, were amplified by PCR.
Load more

Recommended publications
  • Molecular Mechanisms Regulating Copper Balance in Human Cells
    MOLECULAR MECHANISMS REGULATING COPPER BALANCE IN HUMAN CELLS by Nesrin M. Hasan A dissertation submitted to Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland August 2014 ©2014 Nesrin M. Hasan All Rights Reserved Intended to be blank ii ABSTRACT Precise copper balance is essential for normal growth, differentiation, and function of human cells. Loss of copper homeostasis is associated with heart hypertrophy, liver failure, neuronal de-myelination and other pathologies. The copper-transporting ATPases ATP7A and ATP7B maintain cellular copper homeostasis. In response to copper elevation, they traffic from the trans-Golgi network (TGN) to vesicles where they sequester excess copper for further export. The mechanisms regulating activity and trafficking of ATP7A/7B are not well understood. Our studies focused on determining the role of kinase-mediated phosphorylation in copper induced trafficking of ATP7B, and identifying and characterizing novel regulators of ATP7A. We have shown that Ser- 340/341 region of ATP7B plays an important role in interactions between the N-terminus and the nucleotide-binding domain and that mutations in these residues result in vesicular localization of the protein independent of the intracellular copper levels. We have determined that structural changes that alter the inter-domain interactions initiate exit of ATP7B from the TGN and that the role of copper-induced kinase-mediated hyperphosphorylation might be to maintain an open interface between the domains of ATP7B. In a separate study, seven proteins were identified, which upon knockdown result in increased intracellular copper levels. We performed an initial characterization of the knock-downs and obtained intriguing results indicating that these proteins regulate ATP7A protein levels, post-translational modifications, and copper-dependent trafficking.
    [Show full text]
  • ( 12 ) United States Patent
    US010428349B2 (12 ) United States Patent ( 10 ) Patent No. : US 10 , 428 ,349 B2 DeRosa et al . (45 ) Date of Patent: Oct . 1 , 2019 ( 54 ) MULTIMERIC CODING NUCLEIC ACID C12N 2830 / 50 ; C12N 9 / 1018 ; A61K AND USES THEREOF 38 / 1816 ; A61K 38 /45 ; A61K 38/ 44 ; ( 71 ) Applicant: Translate Bio , Inc ., Lexington , MA A61K 38 / 177 ; A61K 48 /005 (US ) See application file for complete search history . (72 ) Inventors : Frank DeRosa , Lexington , MA (US ) ; Michael Heartlein , Lexington , MA (56 ) References Cited (US ) ; Daniel Crawford , Lexington , U . S . PATENT DOCUMENTS MA (US ) ; Shrirang Karve , Lexington , 5 , 705 , 385 A 1 / 1998 Bally et al. MA (US ) 5 ,976 , 567 A 11/ 1999 Wheeler ( 73 ) Assignee : Translate Bio , Inc ., Lexington , MA 5 , 981, 501 A 11/ 1999 Wheeler et al. 6 ,489 ,464 B1 12 /2002 Agrawal et al. (US ) 6 ,534 ,484 B13 / 2003 Wheeler et al. ( * ) Notice : Subject to any disclaimer , the term of this 6 , 815 ,432 B2 11/ 2004 Wheeler et al. patent is extended or adjusted under 35 7 , 422 , 902 B1 9 /2008 Wheeler et al . 7 , 745 ,651 B2 6 / 2010 Heyes et al . U . S . C . 154 ( b ) by 0 days. 7 , 799 , 565 B2 9 / 2010 MacLachlan et al. (21 ) Appl. No. : 16 / 280, 772 7 , 803 , 397 B2 9 / 2010 Heyes et al . 7 , 901, 708 B2 3 / 2011 MacLachlan et al. ( 22 ) Filed : Feb . 20 , 2019 8 , 101 ,741 B2 1 / 2012 MacLachlan et al . 8 , 188 , 263 B2 5 /2012 MacLachlan et al . (65 ) Prior Publication Data 8 , 236 , 943 B2 8 /2012 Lee et al .
    [Show full text]
  • Cisplatin Inhibits MEK1/2
    www.impactjournals.com/oncotarget/ Oncotarget, Vol. 6, No. 27 Cisplatin inhibits MEK1/2 Tetsu Yamamoto1, Igor F. Tsigelny1,2,3, Andreas W. Götz3, Stephen B. Howell1 1 Moores Cancer Center and Department of Medicine, University of California, San Diego, La Jolla, CA 92093 2 Neuroscience Department, University of California, San Diego, La Jolla, CA 92093 3 San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093 Correspondence to: Stephen B. Howell, e-mail: [email protected] Keywords: MEK1, RAS, ERK, copper, cisplatin Received: March 11, 2015 Accepted: June 09, 2015 Published: June 20, 2015 ABSTRACT Cisplatin (cDDP) is known to bind to the CXXC motif of proteins containing a ferrodoxin-like fold but little is known about its ability to interact with other Cu-binding proteins. MEK1/2 has recently been identified as a Cu-dependent enzyme that does not contain a CXXC motif. We found that cDDP bound to and inhibited the activity of recombinant MEK1 with an IC50 of 0.28 μM and MEK1/2 in whole cells with +1 +2 an IC50 of 37.4 μM. The inhibition of MEK1/2 was relieved by both Cu and Cu in a concentration-dependent manner. cDDP did not inhibit the upstream pathways responsible for activating MEK1/2, and did not cause an acute depletion of cellular Cu that could account for the reduction in MEK1/2 activity. cDDP was found to bind MEK1/2 in whole cells and the extent of binding was augmented by supplementary Cu and reduced by Cu chelation. Molecular modeling predicts 3 Cu and cDDP binding sites and quantum chemistry calculations indicate that cDDP would be expected to displace Cu from each of these sites.
    [Show full text]
  • Biophysical Characterization of the First Four Metal-Binding Domains of Human Wilson Disease Protein
    Western Michigan University ScholarWorks at WMU Dissertations Graduate College 6-2014 Biophysical Characterization of the First Four Metal-Binding Domains of Human Wilson Disease Protein Alia V.H. Hinz Western Michigan University, [email protected] Follow this and additional works at: https://scholarworks.wmich.edu/dissertations Part of the Chemistry Commons, and the Medicinal and Pharmaceutical Chemistry Commons Recommended Citation Hinz, Alia V.H., "Biophysical Characterization of the First Four Metal-Binding Domains of Human Wilson Disease Protein" (2014). Dissertations. 280. https://scholarworks.wmich.edu/dissertations/280 This Dissertation-Open Access is brought to you for free and open access by the Graduate College at ScholarWorks at WMU. It has been accepted for inclusion in Dissertations by an authorized administrator of ScholarWorks at WMU. For more information, please contact [email protected]. BIOPHYSICAL CHARACTERIZATION OF THE FIRST FOUR METAL-BINDING DOMAINS OF HUMAN WILSON DISEASE PROTEIN by Alia V.H. Hinz A dissertation submitted to the Graduate College in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Chemistry Western Michigan University June 2014 Doctoral Committee: David Huffman, Ph.D., Chair Blair Szymczyna, Ph.D Gellert Mezei, Ph.D Douglas Coulter, Ph.D BIOPHYSICAL CHARACTERIZATION OF THE FIRST FOUR METAL-BINDING DOMAINS OF HUMAN WILSON DISEASE PROTEIN Alia V. H. Hinz, Ph.D. Western Michigan University, 2014 Wilson disease protein (WLNP) is a P1b-type ATPase crucial for maintaining copper homeostasis in humans. Mutations in this protein result in the autosomal recessive disorder Wilson disease, a condition characterized by copper accumulation in the liver and brain.
    [Show full text]
  • Benchmarking Computational Methods for Estimating the Pathogenicity of Wilson’S
    bioRxiv preprint doi: https://doi.org/10.1101/780924; this version posted September 25, 2019. 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-NC-ND 4.0 International license. Benchmarking Computational Methods for Estimating the Pathogenicity of Wilson’s Disease Mutations Ning Tang†, Thomas Sandahl§, Peter Ott§, and Kasper P. Kepp†* † Technical University of Denmark, DTU Chemistry, Kemitorvet 206, 2800 Kongens Lyngby, Denmark § The Danish Wilson Centre, Medical Department LMT, Hepatology, Aarhus University Hospital, Palle Juul Jensens Bouolevard 99, 8200 Aarhus, Denmark. *Corresponding author. E-mail: [email protected]. Phone: +045 45252409 Grants supporting this work: The Danish Council for Independent Research (DFF), grant case 7016-00079B, and The Memorial Foundation of Manufacturer Vilhelm Petersen & Wife. 1 bioRxiv preprint doi: https://doi.org/10.1101/780924; this version posted September 25, 2019. 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-NC-ND 4.0 International license. Abstract Genetic variations in the gene encoding the copper-transport protein ATP7B are the primary cause of Wilson’s disease. Controversially, clinical prevalence seems much smaller than prevalence estimated by genetic screening tools, causing fear that many people are undiagnosed although early diagnosis and treatment is essential. To address this issue, we benchmarked 16 state-of-the-art computational disease-prediction methods against established data of missense ATP7B mutations.
    [Show full text]
  • Hepatic Presentation of Wilson's Disease in Children
    Viral Hepatitis Foundation Bangladesh International Journal of Hepatology Review Article Hepatic presentation of Wilson’s Disease in children *Reema Afroza Alia1, A S M Bazlul Karim2, A K M Faizul Huq3, Nuzhat Choudhury4 Mamun-Al-Mahtab5 1Department of Pediatrics, Bangabandhu Sheikh Mujib University Dhaka, Bangladesh, 2Department of Pediatric Gastroenterology, Bangabandhu Sheikh Mujib University Dhaka, Bangladesh, 3Combined Military Hospital Dhaka, 4Department of Ophthalmology Bangabandhu Sheikh Mujib University Dhaka, Bangladesh,5Department of Hepatology, Bangabandhu Sheikh Mujib University, Dhaka, Bangladesh. *Correspondence to Department of Pediatrics. Bangabandhu Sheikh Mujib University, Shahbag, Dhaka, Bangladesh E-mail: [email protected], Mobile: +880-01190069729 Introduction Schematic representation of copper metabolism within a Wilson’s Disease is a rare autosomal recessive genetic liver cell. Abbreviation: ATP7B = Wilson’s disease gene. disorder of copper metabolism which is characterized by hepatic and neurological disease. The disease affects ATP7A and ATP7B are homologous copper-transporting between one in 30000 and one in 100000 individuals and proteins [6]. Mutation of the ATP7A gene results in the was first described as a syndrome by Kinnier Wilson in storage of copper in enterocytes, preventing entry of copper 1912. In affected individuals, there is accumulation of into the circulation and thereby causing a complete copper excess copper in the liver caused by reduced excretion of deficiency. This condition, known as Menkes disease, is copper in bile. The great danger is that Wilson’s disease is an X-linked disorder characterized by severe impairment progressive, can remain undiagnosed and is to be fatal if of neurological and connective tissue function. Discovery untreated [1]. Wilson’s disease presents mainly as hepatic of the mutated gene in Menkes disease helped to uncover disease in younger patients in their 1st and second decades the activity of the Wilson’s disease-associated gene within of life [2].
    [Show full text]
  • Structural Models of the Human Copper P-‐Type Atpases ATP7A
    Structural models of the human copper P-type ATPases ATP7A and ATP7B Pontus Gourdon1, Oleg Sitsel1, Jesper Lykkegaard Karlsen1, Lisbeth Birk Møller2 & Poul Nissen1 1 Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Aarhus University, Dept. of Molecular Biology and Genetics. Gustav Wieds Vej 10C, DK – 8000 Aarhus, Denmark 2 Center for Applied Human Molecular Genetics, Kennedy Center, Gl. Landevej 7, DK – 2600 Glostrup, Denmark * Correspondence e-mail: [email protected] Abstract The human copper exporters ATP7A and ATP7B contain domains common to all P-type ATPases, as well as class-specific features such as six sequential heavy metal binding domains (HMBD1-HMBD6) and a type-specific constellation of transmembrane helices. Despite the medical significance of ATP7A and ATP7B related to Menkes’ and Wilson’s diseases, respectively, structural information has only been available for isolated, soluble domains. Here we present homology models based on the existing structures of soluble domains and the recently determined structure of the homologous LpCopA, from the bacterium Legionella pneumophila. The models and sequence analyses show that the domains and residues involved in the catalytic phosphorylation events and copper transfer are highly conserved. In addition, there are only minor differences in the core structures of the two human proteins and the bacterial template, allowing protein-specific properties to be addressed. Furthermore, the mapping of known disease-causing missense mutations indicate that among the heavy-metal binding domains, HMBD5 and HMBD6 are the most crucial for function, thus mimicking the single or dual HMBD(s) found in most copper-specific P-type ATPases.
    [Show full text]
  • Copper Transporter 2 (CTR2) As a Regulator of Cisplatin Accumulation and Sensitivity
    UNIVERSITY OF CALIFORNIA SAN DIEGO Copper Transporter 2 (CTR2) as a Regulator of Cisplatin Accumulation and Sensitivity A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biomedical Sciences by Brian G. Blair Committee in charge: Professor Stephen B. Howell, Chair Professor Daniel J. Donoghue Professor Paul A. Insel Professor Stanley J. Opella Professor Nicholas J. Webster 2009 Copyright Brian G. Blair, 2009 All rights reserved. The dissertation of Brian G. Blair is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2009 iii DEDICATION To my parents and grandparents for their hard work and sacrifices that made my education possible, and for teaching me to follow my passions. To Erin, my loving and supportive wife, for encouraging me to be the best that I can be in everything that I do. iv TABLE OF CONTENTS Signature Page ……………………………………………………………… iii Dedication ……………………………..……………………………….…. iv Table of Contents …………………………………………………………. v List of Figures ……………………………………………………………... viii List of Tables ………………………………………………………………. xi Acknowledgements ………………………………………………………… xii Curriculum Vitae …………………………………………………………… xx Abstract of the Dissertation………………………………………………….. xxiii Chapter 1: Introduction ……………………………………………………… 1 Platinum Based Chemotherapy ……………………………………… 1 Resistance to Platinum-Drugs ……………………………………….. 4 Platinum-Drug Transport ...………………………………………….. 5 Copper Homeostasis ...……………………………………………….
    [Show full text]
  • Bhuiyan Et Al., 2018 Supplementary Data: Systematic Evaluation of Isoform Function
    Bhuiyan et al., 2018 Supplementary Data: Systematic evaluation of isoform function Systematic evaluation of isoform function in literature reports of alternative splicing: Supplemental Data Authors: Shamsuddin A. Bhuiyan1,2, Sophia Ly1, Minh Phan1, Brandon Huntington1, Ellie Hogan1, Chao Chun Liu1, James Liu1, Paul Pavlidis*1,2 1 Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada 2 Department of Psychiatry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada *To whom correspondence should be addressed. Tel: (604) 827-4157 Email: [email protected] 1 Bhuiyan et al., 2018 Supplementary Data: Systematic evaluation of isoform function Table of Contents SECTION 1: MASTER SPREADSHEET LEGEND ....................................................................................3 SECTION 2: CURATION STANDARDS (INSTRUCTIONS TO FILL OUT MASTER SPREADSHEET) ...............5 SECTION 3: PROBLEMATIC CASES OF LINKING FDSIs TO ENSEMBL ....................................................8 RNA binding protein, fox-1 homolog 1 (Rbfox1) ................................................................................................ 8 Ryanodine receptor 3 (Ryr3) .............................................................................................................................. 9 Sad1 and UNC84 domain containing 1 (SUN1) .................................................................................................. 9 SECTION 4: SUPPLEMENTAL TABLES AND FIGURES ........................................................................
    [Show full text]
  • Inhibition of Copper Transport Induces Apoptosis in Triple Negative Breast Cancer Cells and Suppresses Tumor Angiogenesis
    Author Manuscript Published OnlineFirst on March 1, 2019; DOI: 10.1158/1535-7163.MCT-18-0667 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Inhibition of Copper Transport Induces Apoptosis in Triple Negative Breast Cancer Cells and Suppresses Tumor Angiogenesis Olga Karginova*, 1, Claire M. Weekley*, 2, Akila Raoul1, Alhareth Alsayed1, Tong Wu2, Steve Seung-Young Lee 3, Chuan He2 and Olufunmilayo I. Olopade1, 4 *co-first authors 1Section of Hematology/Oncology, Department of Medicine, 2Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics and Howard Hughes Medical Institute, 3Department of Molecular Genetics and Cell Biology, 4Center for Clinical Cancer Genetics, The University of Chicago, Illinois, USA Current address for CM Weekley: Bio21 Institute and Department of Biochemistry and Molecular Biology, The University of Melbourne, VIC, Australia Current address for SS Lee: Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Illinois Running Title: Targeting copper transport in breast cancer Abbreviations: BSO, L-buthionine-sulfoximine; BSA, bovine serum albumin; CI, combination index; DRI, dose-reduction index; GSH, reduced glutathione; GSSG, oxidized glutathione; ICP- MS, inductively-coupled plasma mass spectrometry; LOX, lysyl oxidase; MAPK, mitogen- activated protein kinase; PI3K, phosphatidylinositol-3-kinase; ROS, reactive oxygen species; SOD, superoxide dismutase; TNBC, triple negative breast cancer; TM, tetrathiomolybdate; TGN, trans-Golgi network; XFM, X-ray fluorescence microscopy. Corresponding author: Olufunmilayo I. Olopade, MD, FACP, OON Knapp Center for Biomedical Discovery 900 E. 57th Street, 8th Floor Chicago, Illinois 60637 Phone: 773-702-4400 * Fax: 773-834-0778 Email: [email protected] Conflicts of Interest: C He is a scientific founder of Accent Therapeutics, Inc.
    [Show full text]
  • ATP7A-Regulated Enzyme Metalation and Trafficking in the Menkes
    biomedicines Review ATP7A-Regulated Enzyme Metalation and Trafficking in the Menkes Disease Puzzle Nina Horn 1,*,† and Pernilla Wittung-Stafshede 2 1 John F. Kennedy Institute, 2600 Glostrup, Denmark 2 Department of Biology and Biological Engineering, Chalmers University of Technology, 41296 Gothenburg, Sweden; [email protected] * Correspondence: [email protected] † Retired. Abstract: Copper is vital for numerous cellular functions affecting all tissues and organ systems in the body. The copper pump, ATP7A is critical for whole-body, cellular, and subcellular copper homeostasis, and dysfunction due to genetic defects results in Menkes disease. ATP7A dysfunction leads to copper deficiency in nervous tissue, liver, and blood but accumulation in other tissues. Site-specific cellular deficiencies of copper lead to loss of function of copper-dependent enzymes in all tissues, and the range of Menkes disease pathologies observed can now be explained in full by lack of specific copper enzymes. New pathways involving copper activated lysosomal and steroid sulfatases link patient symptoms usually related to other inborn errors of metabolism to Menkes disease. Additionally, new roles for lysyl oxidase in activation of molecules necessary for the innate immune system, and novel adapter molecules that play roles in ERGIC trafficking of brain receptors Citation: Horn, N.; and other proteins, are emerging. We here summarize the current knowledge of the roles of copper Wittung-Stafshede, P. ATP7A-Regulated Enzyme enzyme function in Menkes disease, with a focus on ATP7A-mediated enzyme metalation in the Metalation and Trafficking in the secretory pathway. By establishing mechanistic relationships between copper-dependent cellular Menkes Disease Puzzle. Biomedicines processes and Menkes disease symptoms in patients will not only increase understanding of copper 2021, 9, 391.
    [Show full text]
  • Cloning and Expression of the Two Isoforms of Copper Atpase in a Fish
    Multiple Cu-ATPase genes are differentially expressed and transcriptionally regulated by Cu exposure in sea bream, Sparus aurata Matteo Minghetti, Michael J. Leaver, Stephen G. George Institute of Aquaculture, University of Stirling, Stirling FK94LA, Scotland, UK 1. Introduction The variable valencies of copper (Cu) have been exploited during evolution as a cofactor for many vital enzymes (Kim et al., 2008). On the other hand, these same redox properties enable Cu to promote reactions which lead to the production of reactive oxygen species (ROS) that can have damaging oxidative effects on cellular macromolecules (Halliwell and Gutteridge 1984). In addition, Cu may also manifest toxicity by displacing Zn from functionally essential protein domains (Predki and Sarkar 1992). Thus, specific proteins have evolved for intracellular Cu transport and delivery to avoid damaging non-specific reactions and to enable targeting to cupro- proteins. These cuproproteins include Cu-ATPases which belong to the P1B-subfamily of P-type ATPases present in all eukaryotic phyla (Lutsenko et al., 2007b). Cu-ATPases transfer Cu from the cytosolic carrier, ATOX1 (Hamza et al., 2003), to secretory vesicles (Petris et al., 2000). The essentiality of Cu-ATPases in normal development and pigmentation was reported in Drosophila (Norgate et al., 2006), whilst in the zebrafish (Danio rerio) ATP7A was shown by mutagenetic analysis and genetic complementation to be essential for notochord formation and pigmentation (Mendelsohn et al., 2006). Two isoforms of Cu-ATPase (ATP7A and ATP7B) with differing functional roles have been identified in mammals, primarily by investigation of two human genetic disorders, Menkes syndrome and Wilson‟s disease. Menkes syndrome is caused by mutations of the gene encoding ATP7A (also known as Menkes protein) and is characterized by overall Cu deficiency and accumulation of Cu in intestinal enterocytes and the kidney.
    [Show full text]