Cilia—Where Two Wnts Collide
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Hydroxylation of the Eukaryotic Ribosomal Decoding Center Affects Translational Accuracy
Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy Christoph Loenarza,1, Rok Sekirnika,2, Armin Thalhammera,2, Wei Gea, Ekaterina Spivakovskya, Mukram M. Mackeena,b,3, Michael A. McDonougha, Matthew E. Cockmanc, Benedikt M. Kesslerb, Peter J. Ratcliffec, Alexander Wolfa,4, and Christopher J. Schofielda,1 aChemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3TA, United Kingdom; bTarget Discovery Institute, University of Oxford, Oxford OX3 7FZ, United Kingdom; and cCentre for Cellular and Molecular Physiology, University of Oxford, Oxford OX3 7BN, United Kingdom Edited by William G. Kaelin, Jr., Harvard Medical School, Boston, MA, and approved January 24, 2014 (received for review July 31, 2013) The mechanisms by which gene expression is regulated by oxygen Enzyme-catalyzed hydroxylation of intracellularly localized are of considerable interest from basic science and therapeutic proteins was once thought to be rare, but accumulating recent perspectives. Using mass spectrometric analyses of Saccharomyces evidence suggests it is widespread (11). Motivated by these cerevisiae ribosomes, we found that the amino acid residue in findings, we investigated whether the translation of mRNA to closest proximity to the decoding center, Pro-64 of the 40S subunit protein is affected by oxygen-dependent modifications. A rapidly ribosomal protein Rps23p (RPS23 Pro-62 in humans) undergoes growing eukaryotic cell devotes most of its resources to the tran- posttranslational hydroxylation. We identify RPS23 hydroxylases scription, splicing, and transport of ribosomal proteins and rRNA as a highly conserved eukaryotic subfamily of Fe(II) and 2-oxoglu- (12). We therefore reasoned that ribosomal modification is a tarate dependent oxygenases; their catalytic domain is closely re- candidate mechanism for the regulation of protein expression. -
The Emerging Landscape of Dynamic DNA Methylation in Early Childhood
The emerging landscape of dynamic DNA methylation in early childhood Cheng-Jian Xu, Marc Jan Bonder, Cilla Söderhäll, Mariona Bustamante, Nour Baïz, Ulrike Gehring, Soesma Jankipersadsing, Pieter van der Vlies, Cleo van Diemen, Bianca van Rijkom, et al. To cite this version: Cheng-Jian Xu, Marc Jan Bonder, Cilla Söderhäll, Mariona Bustamante, Nour Baïz, et al.. The emerg- ing landscape of dynamic DNA methylation in early childhood. BMC Genomics, BioMed Central, 2017, 18, pp.25. 10.1186/s12864-016-3452-1. hal-01792686 HAL Id: hal-01792686 https://hal.archives-ouvertes.fr/hal-01792686 Submitted on 26 May 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Xu et al. BMC Genomics (2017) 18:25 DOI 10.1186/s12864-016-3452-1 RESEARCHARTICLE Open Access The emerging landscape of dynamic DNA methylation in early childhood Cheng-Jian Xu1,2*, Marc Jan Bonder2, Cilla Söderhäll3,4, Mariona Bustamante5,6,7,8, Nour Baïz9, Ulrike Gehring10, Soesma A. Jankipersadsing1,2, Pieter van der Vlies2, Cleo C. van Diemen2, Bianca van Rijkom2, Jocelyne Just9,11, Inger Kull12, Juha Kere3,13, Josep Maria Antó5,7,8,14, Jean Bousquet15,16,17,18, Alexandra Zhernakova2, Cisca Wijmenga2, Isabella Annesi-Maesano9, Jordi Sunyer5,7,8,14, Erik Melén19, Yang Li2*, Dirkje S. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Splicing-Correcting Therapeutic Approaches for Retinal Dystrophies: Where Endogenous Gene Regulation and Specificity Matter
New Developments Splicing-Correcting Therapeutic Approaches for Retinal Dystrophies: Where Endogenous Gene Regulation and Specificity Matter Niccolo` Bacchi,1 Simona Casarosa,1,2 and Michela A. Denti1,3 1Centre for Integrative Biology (CIBIO) - University of Trento, Trento, Italy 2Neuroscience Institute - National Research Council (CNR), Pisa, Italy 3Neuroscience Institute - National Research Council (CNR), Padova, Italy Correspondence: Simona Casarosa, Splicing is an important and highly regulated step in gene expression. The ability to modulate Centre for Integrative Biology it can offer a therapeutic option for many genetic disorders. Antisense-mediated splicing- (CIBIO) - University of Trento, Via correction approaches have recently been successfully exploited for some genetic diseases, Sommarive 9, 38123 Trento, Italy; and are currently demonstrating safety and efficacy in different clinical trials. Their [email protected]. application for the treatment of retinal dystrophies could potentially solve a vast panel of Michela A. Denti, Centre for Inte- grative Biology (CIBIO) - University cases, as illustrated by the abundance of mutations that could be targeted and the versatility of ofTrento,ViaSommarive9,38123 the technique. In this review, we will give an insight of the different therapeutic strategies, Trento, Italy; focusing on the current status of their application for retinal dystrophies. [email protected]. Keywords: splicing correction, antisense oligonucleotides, retinal dystrophy, gene therapy SC and MAD contributed equally to the work presented here and should therefore be regarded as equivalent authors. Submitted: April 8, 2014 Accepted: April 11, 2014 Citation: Bacchi N, Casarosa S, Denti MA. Splicing-correcting therapeutic approaches for retinal dystrophies: where endogenous gene regulation and specificity matter. Invest Oph- thalmol Vis Sci. -
Ciliopathies Gene Panel
Ciliopathies Gene Panel Contact details Introduction Regional Genetics Service The ciliopathies are a heterogeneous group of conditions with considerable phenotypic overlap. Levels 4-6, Barclay House These inherited diseases are caused by defects in cilia; hair-like projections present on most 37 Queen Square cells, with roles in key human developmental processes via their motility and signalling functions. Ciliopathies are often lethal and multiple organ systems are affected. Ciliopathies are London, WC1N 3BH united in being genetically heterogeneous conditions and the different subtypes can share T +44 (0) 20 7762 6888 many clinical features, predominantly cystic kidney disease, but also retinal, respiratory, F +44 (0) 20 7813 8578 skeletal, hepatic and neurological defects in addition to metabolic defects, laterality defects and polydactyly. Their clinical variability can make ciliopathies hard to recognise, reflecting the ubiquity of cilia. Gene panels currently offer the best solution to tackling analysis of genetically Samples required heterogeneous conditions such as the ciliopathies. Ciliopathies affect approximately 1:2,000 5ml venous blood in plastic EDTA births. bottles (>1ml from neonates) Ciliopathies are generally inherited in an autosomal recessive manner, with some autosomal Prenatal testing must be arranged dominant and X-linked exceptions. in advance, through a Clinical Genetics department if possible. Referrals Amniotic fluid or CV samples Patients presenting with a ciliopathy; due to the phenotypic variability this could be a diverse set should be sent to Cytogenetics for of features. For guidance contact the laboratory or Dr Hannah Mitchison dissecting and culturing, with ([email protected]) / Prof Phil Beales ([email protected]) instructions to forward the sample to the Regional Molecular Genetics Referrals will be accepted from clinical geneticists and consultants in nephrology, metabolic, laboratory for analysis respiratory and retinal diseases. -
OFD1 and Flotillins Are Integral Components of a Ciliary Signaling Protein Complex Organized by Polycystins in Renal Epithelia and Odontoblasts
OFD1 and Flotillins Are Integral Components of a Ciliary Signaling Protein Complex Organized by Polycystins in Renal Epithelia and Odontoblasts Stephanie Jerman1, Heather H. Ward2, Rebecca Lee1, Carla A. M. Lopes3, Andrew M. Fry3, Mary MacDougall4, Angela Wandinger-Ness1* 1 Department of Pathology MSC08-4640 and Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America, 2 Department of Internal Medicine, Division of Nephrology MSC10-5550, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, United States of America, 3 Department of Biochemistry, University of Leicester, Leicester, United Kingdom, 4 Institute of Oral Health Research & Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama, Birmingham, Alabama, United States of America Abstract Mutation of the X-linked oral-facial-digital syndrome type 1 (OFD1) gene is embryonic lethal in males and results in craniofacial malformations and adult onset polycystic kidney disease in females. While the OFD1 protein localizes to centriolar satellites, centrosomes and basal bodies, its cellular function and how it relates to cystic kidney disease is largely unknown. Here, we demonstrate that OFD1 is assembled into a protein complex that is localized to the primary cilium and contains the epidermal growth factor receptor (EGFR) and domain organizing flotillin proteins. This protein complex, which has similarity to a basolateral adhesion domain formed during cell polarization, also contains the polycystin proteins that when mutant cause autosomal dominant polycystic kidney disease (ADPKD). Importantly, in human ADPKD cells where mutant polycystin-1 fails to localize to cilia, there is a concomitant loss of localization of polycystin-2, OFD1, EGFR and flotillin-1 to cilia. -
X-Linked Diseases: Susceptible Females
REVIEW ARTICLE X-linked diseases: susceptible females Barbara R. Migeon, MD 1 The role of X-inactivation is often ignored as a prime cause of sex data include reasons why women are often protected from the differences in disease. Yet, the way males and females express their deleterious variants carried on their X chromosome, and the factors X-linked genes has a major role in the dissimilar phenotypes that that render women susceptible in some instances. underlie many rare and common disorders, such as intellectual deficiency, epilepsy, congenital abnormalities, and diseases of the Genetics in Medicine (2020) 22:1156–1174; https://doi.org/10.1038/s41436- heart, blood, skin, muscle, and bones. Summarized here are many 020-0779-4 examples of the different presentations in males and females. Other INTRODUCTION SEX DIFFERENCES ARE DUE TO X-INACTIVATION Sex differences in human disease are usually attributed to The sex differences in the effect of X-linked pathologic variants sex specific life experiences, and sex hormones that is due to our method of X chromosome dosage compensation, influence the function of susceptible genes throughout the called X-inactivation;9 humans and most placental mammals – genome.1 5 Such factors do account for some dissimilarities. compensate for the sex difference in number of X chromosomes However, a major cause of sex-determined expression of (that is, XX females versus XY males) by transcribing only one disease has to do with differences in how males and females of the two female X chromosomes. X-inactivation silences all X transcribe their gene-rich human X chromosomes, which is chromosomes but one; therefore, both males and females have a often underappreciated as a cause of sex differences in single active X.10,11 disease.6 Males are the usual ones affected by X-linked For 46 XY males, that X is the only one they have; it always pathogenic variants.6 Females are biologically superior; a comes from their mother, as fathers contribute their Y female usually has no disease, or much less severe disease chromosome. -
Ciliary Exclusion of Polycystin-2 Promotes Kidney Cystogenesis in an Autosomal Dominant Polycystic Kidney Disease Model
ARTICLE https://doi.org/10.1038/s41467-019-12067-y OPEN Ciliary exclusion of Polycystin-2 promotes kidney cystogenesis in an autosomal dominant polycystic kidney disease model Rebecca V. Walker 1,3, Jennifer L. Keynton1, Daniel T. Grimes 1,4, Vrinda Sreekumar1, Debbie J. Williams1, Chris Esapa1, Dongsheng Wu 2, Martin M. Knight 2 & Dominic P. Norris 1 PKD2 1234567890():,; The human locus encodes Polycystin-2 (PC2), a TRPP channel that localises to several distinct cellular compartments, including the cilium. PKD2 mutations cause Autosomal Dominant Polycystic Kidney Disease (ADPKD) and affect many cellular pathways. Data underlining the importance of ciliary PC2 localisation in preventing PKD are limited because PC2 function is ablated throughout the cell in existing model systems. Here, we dissect the ciliary role of PC2 by analysing mice carrying a non-ciliary localising, yet channel-functional, PC2 mutation. Mutants develop embryonic renal cysts that appear indistinguishable from mice completely lacking PC2. Despite not entering the cilium in mutant cells, mutant PC2 accumulates at the ciliary base, forming a ring pattern consistent with distal appendage localisation. This suggests a two-step model of ciliary entry; PC2 first traffics to the cilium base before TOP domain dependent entry. Our results suggest that PC2 localisation to the cilium is necessary to prevent PKD. 1 MRC Harwell Institute, Harwell Science Campus, Oxfordshire OX11 0RD, UK. 2 Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK. 3Present address: School of Medicine, University of Maryland, Baltimore, MD 21201, USA. 4Present address: Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR, USA. -
Ciliary Dyneins and Dynein Related Ciliopathies
cells Review Ciliary Dyneins and Dynein Related Ciliopathies Dinu Antony 1,2,3, Han G. Brunner 2,3 and Miriam Schmidts 1,2,3,* 1 Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Mathildenstrasse 1, 79106 Freiburg, Germany; [email protected] 2 Genome Research Division, Human Genetics Department, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands; [email protected] 3 Radboud Institute for Molecular Life Sciences (RIMLS), Geert Grooteplein Zuid 10, 6525 KL Nijmegen, The Netherlands * Correspondence: [email protected]; Tel.: +49-761-44391; Fax: +49-761-44710 Abstract: Although ubiquitously present, the relevance of cilia for vertebrate development and health has long been underrated. However, the aberration or dysfunction of ciliary structures or components results in a large heterogeneous group of disorders in mammals, termed ciliopathies. The majority of human ciliopathy cases are caused by malfunction of the ciliary dynein motor activity, powering retrograde intraflagellar transport (enabled by the cytoplasmic dynein-2 complex) or axonemal movement (axonemal dynein complexes). Despite a partially shared evolutionary developmental path and shared ciliary localization, the cytoplasmic dynein-2 and axonemal dynein functions are markedly different: while cytoplasmic dynein-2 complex dysfunction results in an ultra-rare syndromal skeleto-renal phenotype with a high lethality, axonemal dynein dysfunction is associated with a motile cilia dysfunction disorder, primary ciliary dyskinesia (PCD) or Kartagener syndrome, causing recurrent airway infection, degenerative lung disease, laterality defects, and infertility. In this review, we provide an overview of ciliary dynein complex compositions, their functions, clinical disease hallmarks of ciliary dynein disorders, presumed underlying pathomechanisms, and novel Citation: Antony, D.; Brunner, H.G.; developments in the field. -
Characterization of Primary Cilia and Intraflagellar Transport 20 in the Epidermis
Characterization of Primary Cilia and Intraflagellar Transport 20 in the Epidermis Steven H. Su 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 2020 © 2020 Steven H. Su All Rights Reserved Abstract Characterization of Primary Cilia and Intraflagellar Transport 20 in the Epidermis Steven H. Su Mammalian skin is a dynamic organ that constantly undergoes self-renewal during homeostasis and regenerates in response to injury. Crucial for the skin’s self-renewal and regenerative capabilities is the epidermis and its stem cell populations. Here we have interrogated the role of primary cilia and Intraflagellar Transport 20 (Ift20) in epidermal development as well as during homeostasis and wound healing in postnatal, adult skin. Using a transgenic mouse model with fluorescent markers for primary cilia and basal bodies, we characterized epidermal primary cilia during embryonic development as well as in postnatal and adult skin and find that both the Interfollicular Epidermis (IFE) and hair follicles (HFs) are highly ciliated throughout development as well as in postnatal and adult skin. Leveraging this transgenic mouse, we also developed a technique for live imaging of epidermal primary cilia in ex vivo mouse embryos and discovered that epidermal primary cilia undergo ectocytosis, a ciliary mechanism previously only observed in vitro. We also generated a mouse model for targeted ablation of Ift20 in the hair follicle stem cells (HF-SCs) of adult mice. We find that loss of Ift20 in HF-SCs inhibits ciliogenesis, as expected, but strikingly it also inhibits hair regrowth. -
Perkinelmer Genomics to Request the Saliva Swab Collection Kit for Patients That Cannot Provide a Blood Sample As Whole Blood Is the Preferred Sample
Eye Disorders Comprehensive Panel Test Code D4306 Test Summary This test analyzes 211 genes that have been associated with ocular disorders. Turn-Around-Time (TAT)* 3 - 5 weeks Acceptable Sample Types Whole Blood (EDTA) (Preferred sample type) DNA, Isolated Dried Blood Spots Saliva Acceptable Billing Types Self (patient) Payment Institutional Billing Commercial Insurance Indications for Testing Individuals with an eye disease suspected to be genetic in origin Individuals with a family history of eye disease Individuals suspected to have a syndrome associated with an eye disease Test Description This panel analyzes 211 genes that have been associated with ocular disorders. Both sequencing and deletion/duplication (CNV) analysis will be performed on the coding regions of all genes included (unless otherwise marked). All analysis is performed utilizing Next Generation Sequencing (NGS) technology. CNV analysis is designed to detect the majority of deletions and duplications of three exons or greater in size. Smaller CNV events may also be detected and reported, but additional follow-up testing is recommended if a smaller CNV is suspected. All variants are classified according to ACMG guidelines. Condition Description Diseases associated with this panel include microphtalmia, anophthalmia, coloboma, progressive external ophthalmoplegia, optic nerve atrophy, retinal dystrophies, retinitis pigementosa, macular degeneration, flecked-retinal disorders, Usher syndrome, albinsm, Aloprt syndrome, Bardet Biedl syndrome, pulmonary fibrosis, and Hermansky-Pudlak -
An EMT-Primary Cilium-GLIS2 Signaling Axis Regulates Mammogenesis and Claudin-Low Breast Tumorigenesis
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.29.424695; this version posted December 29, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 An EMT-primary cilium-GLIS2 signaling axis regulates mammogenesis 2 and claudin-low breast tumorigenesis 3 4 5 6 7 Molly M. Wilson1, Céline Callens2, Matthieu Le Gallo3,4, Svetlana Mironov2, Qiong Ding5, 8 Amandine Salamagnon2, Tony E. Chavarria1, Abena D. Peasah6, Arjun Bhutkar1, Sophie 9 Martin3,4, Florence Godey3,4, Patrick Tas3,4, Anton M. Jetten8, Jane E. Visvader7, Robert A. 10 Weinberg9, Massimo Attanasio5, Claude Prigent2, Jacqueline A. Lees1, Vincent J Guen2* 11 12 13 14 1Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts 15 Institute of Technology, Cambridge, MA, USA. 16 2Institut de Génétique et Développement de Rennes - Centre National de la Recherche 17 Scientifique, Rennes, France. 18 3INSERM U1242, Rennes 1 University, Rennes, France. 19 4Centre de Lutte Contre le Cancer Eugène Marquis, Rennes, France. 20 5Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, 21 USA. 22 6Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 23 USA. 24 7Stem Cells and Cancer Division, The Walter and Eliza Hall Institute of Medical Research and 25 Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia. 26 8Cell Biology Section, Division of Intramural Research, National Institute of Environmental Health 27 Sciences, National Institutes of Health, Research Triangle Park, NC, USA. 28 9MIT Department of Biology and the Whitehead Institute, Cambridge, MA, USA.