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Screening of a Clinically and Biochemically Diagnosed SOD Patient Using Exome Sequencing: a Case Report with a Mutations/Variations Analysis Approach
The Egyptian Journal of Medical Human Genetics (2016) 17, 131–136 HOSTED BY Ain Shams University The Egyptian Journal of Medical Human Genetics www.ejmhg.eg.net www.sciencedirect.com CASE REPORT Screening of a clinically and biochemically diagnosed SOD patient using exome sequencing: A case report with a mutations/variations analysis approach Mohamad-Reza Aghanoori a,b,1, Ghazaleh Mohammadzadeh Shahriary c,2, Mahdi Safarpour d,3, Ahmad Ebrahimi d,* a Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran b Research and Development Division, RoyaBioGene Co., Tehran, Iran c Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz, Iran d Cellular and Molecular Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran Received 12 May 2015; accepted 15 June 2015 Available online 22 July 2015 KEYWORDS Abstract Background: Sulfite oxidase deficiency (SOD) is a rare neurometabolic inherited disor- Sulfite oxidase deficiency; der causing severe delay in developmental stages and premature death. The disease follows an auto- Case report; somal recessive pattern of inheritance and causes deficiency in the activity of sulfite oxidase, an Exome sequencing enzyme that normally catalyzes conversion of sulfite to sulfate. Aim of the study: SOD is an underdiagnosed disorder and its diagnosis can be difficult in young infants as early clinical features and neuroimaging changes may imitate some common diseases. Since the prognosis of the disease is poor, using exome sequencing as a powerful and efficient strat- egy for identifying the genes underlying rare mendelian disorders can provide important knowledge about early diagnosis, disease mechanisms, biological pathways, and potential therapeutic targets. -
Supplementary Table 1: Adhesion Genes Data Set
Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like, -
Human Robo3 Blocking Peptide (CDBP2568) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
Human Robo3 blocking peptide (CDBP2568) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Product Overview Blocking/Immunizing peptide for anti-ROBO3/RIG1 (internal) antibody Antigen Description This gene is a member of the Roundabout (ROBO) gene family that controls neurite outgrowth, growth cone guidance, and axon fasciculation. ROBO proteins are a subfamily of the immunoglobulin transmembrane receptor superfamily. SLIT proteins 1-3, a family of secreted chemorepellants, are ligands for ROBO proteins and SLIT/ROBO interactions regulate myogenesis, leukocyte migration, kidney morphogenesis, angiogenesis, and vasculogenesis in addition to neurogenesis. This gene, ROBO3, has a putative extracellular domain with five immunoglobulin (Ig)-like loops and three fibronectin (Fn) type III motifs, a transmembrane segment, and a cytoplasmic tail with three conserved signaling motifs: CC0, CC2, and CC3 (CC for conserved cytoplasmic). Unlike other ROBO family members, ROBO3 lacks motif CC1. The ROBO3 gene regulates axonal navigation at the ventral midline of the neural tube. In mouse, loss of Robo3 results in a complete failure of commissural axons to cross the midline throughout the spinal cord and the hindbrain. Mutations ROBO3 result in horizontal gaze palsy with progressive scoliosis (HGPPS); an autosomal recessive disorder characterized by congenital absence of horizontal gaze, progressive scoliosis, and failure of the corticospinal and somatosensory axon tracts to cross the midline in the medulla. -
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). -
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. -
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. -
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. -
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. -
Screening of a Clinically and Biochemically Diagnosed SOD Patient Using Exome Sequencing: a Case Report with a Mutations/Variations Analysis Approach
The Egyptian Journal of Medical Human Genetics (2016) 17, 131–136 HOSTED BY Ain Shams University The Egyptian Journal of Medical Human Genetics www.ejmhg.eg.net www.sciencedirect.com CASE REPORT Screening of a clinically and biochemically diagnosed SOD patient using exome sequencing: A case report with a mutations/variations analysis approach Mohamad-Reza Aghanoori a,b,1, Ghazaleh Mohammadzadeh Shahriary c,2, Mahdi Safarpour d,3, Ahmad Ebrahimi d,* a Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran b Research and Development Division, RoyaBioGene Co., Tehran, Iran c Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz, Iran d Cellular and Molecular Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran Received 12 May 2015; accepted 15 June 2015 Available online 22 July 2015 KEYWORDS Abstract Background: Sulfite oxidase deficiency (SOD) is a rare neurometabolic inherited disor- Sulfite oxidase deficiency; der causing severe delay in developmental stages and premature death. The disease follows an auto- Case report; somal recessive pattern of inheritance and causes deficiency in the activity of sulfite oxidase, an Exome sequencing enzyme that normally catalyzes conversion of sulfite to sulfate. Aim of the study: SOD is an underdiagnosed disorder and its diagnosis can be difficult in young infants as early clinical features and neuroimaging changes may imitate some common diseases. Since the prognosis of the disease is poor, using exome sequencing as a powerful and efficient strat- egy for identifying the genes underlying rare mendelian disorders can provide important knowledge about early diagnosis, disease mechanisms, biological pathways, and potential therapeutic targets. -
Mouse Robo3 Conditional Knockout Project (CRISPR/Cas9)
https://www.alphaknockout.com Mouse Robo3 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Robo3 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Robo3 gene (NCBI Reference Sequence: NM_001164767 ; Ensembl: ENSMUSG00000032128 ) is located on Mouse chromosome 9. 28 exons are identified, with the ATG start codon in exon 1 and the TGA stop codon in exon 28 (Transcript: ENSMUST00000115038). Exon 8~11 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Robo3 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-439O11 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: Homozygous mutants display perinatal lethality, abnormal commissural axon growth, and fragile floor plates. Exon 8 starts from about 27.56% of the coding region. The knockout of Exon 8~11 will result in frameshift of the gene. The size of intron 7 for 5'-loxP site insertion: 1647 bp, and the size of intron 11 for 3'-loxP site insertion: 541 bp. The size of effective cKO region: ~1989 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 6 7 8 9 10 11 12 13 14 15 28 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Robo3 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. -
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. -
Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands That Promote Axonal Growth
Research Article: New Research Development Peripheral Nerve Single-Cell Analysis Identifies Mesenchymal Ligands that Promote Axonal Growth Jeremy S. Toma,1 Konstantina Karamboulas,1,ª Matthew J. Carr,1,2,ª Adelaida Kolaj,1,3 Scott A. Yuzwa,1 Neemat Mahmud,1,3 Mekayla A. Storer,1 David R. Kaplan,1,2,4 and Freda D. Miller1,2,3,4 https://doi.org/10.1523/ENEURO.0066-20.2020 1Program in Neurosciences and Mental Health, Hospital for Sick Children, 555 University Avenue, Toronto, Ontario M5G 1X8, Canada, 2Institute of Medical Sciences University of Toronto, Toronto, Ontario M5G 1A8, Canada, 3Department of Physiology, University of Toronto, Toronto, Ontario M5G 1A8, Canada, and 4Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1A8, Canada Abstract Peripheral nerves provide a supportive growth environment for developing and regenerating axons and are es- sential for maintenance and repair of many non-neural tissues. This capacity has largely been ascribed to paracrine factors secreted by nerve-resident Schwann cells. Here, we used single-cell transcriptional profiling to identify ligands made by different injured rodent nerve cell types and have combined this with cell-surface mass spectrometry to computationally model potential paracrine interactions with peripheral neurons. These analyses show that peripheral nerves make many ligands predicted to act on peripheral and CNS neurons, in- cluding known and previously uncharacterized ligands. While Schwann cells are an important ligand source within injured nerves, more than half of the predicted ligands are made by nerve-resident mesenchymal cells, including the endoneurial cells most closely associated with peripheral axons. At least three of these mesen- chymal ligands, ANGPT1, CCL11, and VEGFC, promote growth when locally applied on sympathetic axons.