DOCSLIB.ORG

Membrane Proteins Take Different Trafficking Pathways to the Primary Cilium

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Membrane Proteins Take Different Trafficking Pathways to the Primary Cilium University of Massachusetts Medical School eScholarship@UMMS GSBS Dissertations and Theses Graduate School of Biomedical Sciences 2017-12-14 Membrane Proteins Take Different Trafficking Pathways to the Primary Cilium William Joseph Monis University of Massachusetts Medical School Let us know how access to this document benefits ou.y Follow this and additional works at: https://escholarship.umassmed.edu/gsbs_diss Part of the Cell Biology Commons, and the Developmental Biology Commons Repository Citation Monis WJ. (2017). Membrane Proteins Take Different Trafficking Pathways to the Primary Cilium. GSBS Dissertations and Theses. https://doi.org/10.13028/M2GX0S. Retrieved from https://escholarship.umassmed.edu/gsbs_diss/946 This material is brought to you by eScholarship@UMMS. It has been accepted for inclusion in GSBS Dissertations and Theses by an authorized administrator of eScholarship@UMMS. For more information, please contact [email protected]. MEMBRANE PROTEINS TAKE DIFFERENT TRAFFICKING PATHWAYS TO THE PRIMARY CILIUM A Dissertation Presented By William Joseph Monis Submitted to the Faculty of the University of Massachusetts Graduate School of Biomedical Sciences, Worcester in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY (DECEMBER, 14, 2017) INTERDISCIPLINARY GRADUATE PROGRAM MEMBRANE PROTEINS TAKE DIFFERENT TRAFFICKING PATHWAYS TO THE PRIMARY CILIUM A Dissertation Presented By William Joseph Monis This work was undertaken in the Graduate School of Biomedical Sciences Interdisciplinary Graduate Program The signature of the Thesis Advisor signifies validation of Dissertation content ⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯ Gregory J. Pazour, Ph.D., Thesis Advisor The signatures of the Dissertation Defense Committee signify completion and approval as to style and content of the Dissertation ⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯ Julie A. Jonassen, Ph.D., Member of Committee ⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯ Mary Munson, Ph.D., Member of Committee ⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯ Silvia Corvera, M.D., Member of Committee ⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯ Jagesh V. Shah, Ph.D., External Member of Committee The signature of the Chair of the Committee signifies that the written dissertation meets the requirements of the Dissertation Committee ⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯ George B. Witman, Ph.D., Chair of Committee The signature of the Dean of the Graduate School of Biomedical Sciences signifies that the student has met all graduation requirements of the School ⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯ Anthony Carruthers, Ph.D., Dean of the Graduate School of Biomedical Sciences December 14, 2017 iii Dedication For My Mother “The untold want by life and land ne’er granted, Now voyager sail thou forth to seek and find.” - Walt Whitman, Leaves of Grass, 1855 iv Acknowledgments I thank my thesis advisor Gregory Pazour for his mentorship and for the opportunity to conduct research in his lab. I express my gratitude to all the members of my thesis/dissertation committee for their interest, enthusiasm, and valuable advice that helped me move my thesis project forward. Additionally, I thank all the past and present members of the Pazour Lab along with all my friends at UMass Medical School for their support. v Abstract Cilia are conserved organelles that extend from the surface of most eukaryotic cells. During development cilia play key roles in force generation and perception of the extracellular environment. Ciliary defects cause a broad class of human diseases called ciliopathies characterized by pleiotropic symptoms including cystic kidneys, retinal degeneration, cardiac malformations and skeletal deformations. Perception of the environment relies on specific proteins being localized to the ciliary membrane compartment. The mechanism for sorting and trafficking membrane proteins to the cilium is poorly understood. To address this question, I developed a fluorescence-based pulse-chase assay to measure the transport kinetics of ciliary membrane proteins. This assay was used to determine the importance of candidate proteins to the delivery of fibrocystin, polycystin-2, and smoothened to cilia. Using this assay, I found that ciliary delivery of fibrocystin and polycystin-2 requires IFT20, GMAP210, and the exocyst while smoothened delivery is largely independent of these proteins. In addition, I determined that polycystin-2, but not smoothened or fibrocystin require the biogenesis of lysosome related organelles complex-1 (BLOC-1) for ciliary delivery. Consistent with a requirement for BLOC-1 in ciliary transport of polycystin-2, BLOC-1 mutant mice have cystic kidney disease. BLOC-1 functions in endosomal sorting and I find that disrupting the recycling endosome also reduced ciliary polycystin-2 and causes its accumulation in the recycling vi endosome. This is the first demonstration of a role for BLOC-1 in ciliary biogenesis and highlights the complexity of trafficking pathways to the cilium. vii Table of Contents Signature Page.....................................................................................................ii Dedication ...........................................................................................................iii Acknowledgments ..............................................................................................iv Abstract ................................................................................................................v Table of Contents ..............................................................................................vii List of Tables.......................................................................................................ix List of Figures ......................................................................................................x List of Copyrighted Material .............................................................................xii Preface...............................................................................................................xiv Chapter I : Introduction .......................................................................................1 Primary Cilia Structure and Trafficking Barriers...................................................... 1 The Primary Cilium.................................................................................................... 2 Photoreceptors Have A Modified Primary Cilium ...................................................... 2 The Ciliary Gate ........................................................................................................ 5 Vesicle Docking and Fusion Sites ..................................................................................... 5 Transition Fibers ................................................................................................................ 6 Transition Zone.................................................................................................................. 7 Ciliary Targeting Sequences...................................................................................... 8 Apical and Basolateral Membrane Protein Sorting ................................................... 8 Cystoproteins ............................................................................................................ 9 G Protein Coupled Receptors ................................................................................. 15 Trafficking Pathways to the Cilium ......................................................................... 20 Lateral Trafficking Pathway..................................................................................... 21 Direct Trafficking Pathway ...................................................................................... 26 Recycling Trafficking Pathway ................................................................................ 28 Proteins Implicated in Ciliary Trafficking ............................................................... 30 IFT Complex A and B.............................................................................................. 31 Golgi-IFT Complex .................................................................................................. 34 BBSome .................................................................................................................. 37 Molecular Motors..................................................................................................... 39 Small GTPases ....................................................................................................... 40 Arf Small GTPases .......................................................................................................... 41 Arl Small GTPases .......................................................................................................... 43 Rab Small GTPases ........................................................................................................ 46 Exocyst.................................................................................................................... 49 SNAREs .................................................................................................................. 51 BLOC-1 ................................................................................................................... 52 Conclusion................................................................................................................. 53 Chapter II : BLOC-1 is required for selective membrane protein trafficking from endosomes
Load more

Recommended publications
  • Educational Paper Ciliopathies
    Eur J Pediatr (2012) 171:1285–1300 DOI 10.1007/s00431-011-1553-z REVIEW Educational paper Ciliopathies Carsten Bergmann Received: 11 June 2011 /Accepted: 3 August 2011 /Published online: 7 September 2011 # The Author(s) 2011. This article is published with open access at Springerlink.com Abstract Cilia are antenna-like organelles found on the (NPHP) . Ivemark syndrome . Meckel syndrome (MKS) . surface of most cells. They transduce molecular signals Joubert syndrome (JBTS) . Bardet–Biedl syndrome (BBS) . and facilitate interactions between cells and their Alstrom syndrome . Short-rib polydactyly syndromes . environment. Ciliary dysfunction has been shown to Jeune syndrome (ATD) . Ellis-van Crefeld syndrome (EVC) . underlie a broad range of overlapping, clinically and Sensenbrenner syndrome . Primary ciliary dyskinesia genetically heterogeneous phenotypes, collectively (Kartagener syndrome) . von Hippel-Lindau (VHL) . termed ciliopathies. Literally, all organs can be affected. Tuberous sclerosis (TSC) . Oligogenic inheritance . Modifier. Frequent cilia-related manifestations are (poly)cystic Mutational load kidney disease, retinal degeneration, situs inversus, cardiac defects, polydactyly, other skeletal abnormalities, and defects of the central and peripheral nervous Introduction system, occurring either isolated or as part of syn- dromes. Characterization of ciliopathies and the decisive Defective cellular organelles such as mitochondria, perox- role of primary cilia in signal transduction and cell isomes, and lysosomes are well-known
    [Show full text]
  • Synergistic Genetic Interactions Between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models
    BASIC RESEARCH www.jasn.org Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models Rory J. Olson,1 Katharina Hopp ,2 Harrison Wells,3 Jessica M. Smith,3 Jessica Furtado,1,4 Megan M. Constans,3 Diana L. Escobar,3 Aron M. Geurts,5 Vicente E. Torres,3 and Peter C. Harris 1,3 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background Autosomal recessive polycystic kidney disease (ARPKD) and autosomal dominant polycystic kidney disease (ADPKD) are genetically distinct, with ADPKD usually caused by the genes PKD1 or PKD2 (encoding polycystin-1 and polycystin-2, respectively) and ARPKD caused by PKHD1 (encoding fibrocys- tin/polyductin [FPC]). Primary cilia have been considered central to PKD pathogenesis due to protein localization and common cystic phenotypes in syndromic ciliopathies, but their relevance is questioned in the simple PKDs. ARPKD’s mild phenotype in murine models versus in humans has hampered investi- gating its pathogenesis. Methods To study the interaction between Pkhd1 and Pkd1, including dosage effects on the phenotype, we generated digenic mouse and rat models and characterized and compared digenic, monogenic, and wild-type phenotypes. Results The genetic interaction was synergistic in both species, with digenic animals exhibiting pheno- types of rapidly progressive PKD and early lethality resembling classic ARPKD. Genetic interaction be- tween Pkhd1 and Pkd1 depended on dosage in the digenic murine models, with no significant enhancement of the monogenic phenotype until a threshold of reduced expression at the second locus was breached.
    [Show full text]
  • Table 2. Significant
    Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S.
    [Show full text]
  • University of Oklahoma
    UNIVERSITY OF OKLAHOMA GRADUATE COLLEGE MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION SUBMITTED TO THE GRADUATE FACULTY in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY By JOSHUA THOMAS COOPER Norman, Oklahoma 2017 MACRONUTRIENTS SHAPE MICROBIAL COMMUNITIES, GENE EXPRESSION AND PROTEIN EVOLUTION A DISSERTATION APPROVED FOR THE DEPARTMENT OF MICROBIOLOGY AND PLANT BIOLOGY BY ______________________________ Dr. Boris Wawrik, Chair ______________________________ Dr. J. Phil Gibson ______________________________ Dr. Anne K. Dunn ______________________________ Dr. John Paul Masly ______________________________ Dr. K. David Hambright ii © Copyright by JOSHUA THOMAS COOPER 2017 All Rights Reserved. iii Acknowledgments I would like to thank my two advisors Dr. Boris Wawrik and Dr. J. Phil Gibson for helping me become a better scientist and better educator. I would also like to thank my committee members Dr. Anne K. Dunn, Dr. K. David Hambright, and Dr. J.P. Masly for providing valuable inputs that lead me to carefully consider my research questions. I would also like to thank Dr. J.P. Masly for the opportunity to coauthor a book chapter on the speciation of diatoms. It is still such a privilege that you believed in me and my crazy diatom ideas to form a concise chapter in addition to learn your style of writing has been a benefit to my professional development. I’m also thankful for my first undergraduate research mentor, Dr. Miriam Steinitz-Kannan, now retired from Northern Kentucky University, who was the first to show the amazing wonders of pond scum. Who knew that studying diatoms and algae as an undergraduate would lead me all the way to a Ph.D.
    [Show full text]
  • XP725 Antibody List Lot 129K4830
    Panorama® Antibody Microarray-XPRESS Profiler725, XP725 List of Antibodies Lot: 129K4830 Reactivity Number Antibody Sigma No. Gene Ids Gene Symbols P/M Accessions Human Mouse Rat 3 Actin A5060 58 ACTA1 P NP_001091.1 n/d n/d n/d 5 Actin, αβ-Smooth Muscle A5228 59 ACTA2 M NP_001135417.1, NP_001604.1, yyy 6 β-Actin A1978 60 ACTB M NP_001092.1 yyy 7 β-Actin A2228 60 ACTB M NP_001092.1 yyy 8 a-Actinin A5044 87 ACTN1 M NP_001093.1 y y n/d 555 PARP P7605 142 PARP1 P NP_001609.2 y n/d n/d 11 β1 and β2-Adaptins A4450 162 AP1B1 M NP_001118.3 y n/d y 167 Chondroitin Sulfate C8035 176 ACAN M NP_001126.3, NP_037359.3 yyy 574 Protein Kinase Ba /Akt1 P2482 207 AKT1 M NP_001014431.1,NP_001014432.1 , NP_005154.2, yyy 575 Protein Kinase Ba /Akt1 P1601 207 AKT1 P NP_001014431.1,NP_001014432.1 , NP_005154.2, yyy 577 phospho-PKB (pSer473) P4112 207 AKT1 P NP_001014431.1,NP_001014432.1 , NP_005154.2, n/d y y 578 phospho-PKB (pThr308) P3862 207 AKT1 P NP_001014431.1,NP_001014432.1 , NP_005154.2, n/d y y 22 Annexin V A8604 308 ANXA5 M NP_001145.1 y n/d n/d 23 Annexin VII A4475 310 ANXA7 M NP_001147.1 yyy 29 Apaf1, N-Terminal A8469 317 APAF1 P NP_001151.1 y y n/d 457 Mint2 M3319 321 APBA2 P NP_001123886.1 n/d n/d y 28 AP Endonuclease A2105 328 APEX1 M NP_001632.2,NP_542379.1,NP_542380.1 yyy 692 Survivin S8191 332 BIRC5 P NP_001012270.1 yyy 17 β-Amyloid A8354 351 APP M NP_000475.1,NP_001129488.1 ,NP_001129601.1 ,NP_001129602.1 ,NP_001129603.1 ,NP_001191230.1 ,NP_001191231.1 ,NP_001191232.1,NP_958816.1,NP_9 y n/d n/d 18 Amyloid Precursor Protein, C-Terminal A8717
    [Show full text]
  • Jimmunol.1701087.Full.Pdf
    A Novel Pkhd1 Mutation Interacts with the Nonobese Diabetic Genetic Background To Cause Autoimmune Cholangitis This information is current as Wenting Huang, Daniel B. Rainbow, Yuehong Wu, David of September 28, 2021. Adams, Pranavkumar Shivakumar, Leah Kottyan, Rebekah Karns, Bruce Aronow, Jorge Bezerra, M. Eric Gershwin, Laurence B. Peterson, Linda S. Wicker and William M. Ridgway J Immunol published online 20 November 2017 Downloaded from http://www.jimmunol.org/content/early/2017/11/23/jimmun ol.1701087 Supplementary http://www.jimmunol.org/content/suppl/2017/11/20/jimmunol.170108 http://www.jimmunol.org/ Material 7.DCSupplemental Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on September 28, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2017 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published November 27, 2017, doi:10.4049/jimmunol.1701087 The Journal of Immunology ANovelPkhd1 Mutation Interacts with the Nonobese Diabetic Genetic Background To Cause Autoimmune Cholangitis Wenting Huang,*,1 Daniel B. Rainbow,†,1 Yuehong Wu,* David Adams,* Pranavkumar Shivakumar,‡ Leah Kottyan,x Rebekah Karns,{ Bruce Aronow,{ Jorge Bezerra,‡ M.
    [Show full text]
  • Missense Mutation in Sterile Motif of Novel Protein Samcystin Is
    Missense Mutation in Sterile ␣ Motif of Novel Protein SamCystin is Associated with Polycystic Kidney Disease in (cy/؉) Rat Joanna H. Brown,* Marie-The´re`se Bihoreau,* Sigrid Hoffmann,† Bettina Kra¨nzlin,† Iulia Tychinskaya,† Nicholas Obermu¨ ller,‡ Dirk Podlich,† Suzanne N. Boehn,† Pamela J. Kaisaki,* Natalia Megel,† Patrick Danoy,§ Richard R. Copley,* John Broxholme,* ʈ Ralph Witzgall, Mark Lathrop,§ Norbert Gretz,† and Dominique Gauguier* *The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom; †Medical Research Centre, Klinikum Mannheim, University of Heidelberg, Mannheim, Germany; ‡Division of Nephrology, Medical Clinic ʈ III, University of Frankfurt, Frankfurt, Germany; §Centre National de Ge´notypage, Evry, France; and Institute for Molecular and Cellular Anatomy, University of Regensburg, Regensburg, Germany Autosomal dominant polycystic kidney disease (PKD) is the most common genetic disease that leads to kidney failure in humans. In addition to the known causative genes PKD1 and PKD2, there are mutations that result in cystic changes in the kidney, such as nephronophthisis, autosomal recessive polycystic kidney disease, or medullary cystic kidney disease. Recent efforts to improve the understanding of renal cystogenesis have been greatly enhanced by studies in rodent models of PKD. Genetic studies in the (cy/؉) rat showed that PKD spontaneously develops as a consequence of a mutation in a gene different from the rat orthologs of PKD1 and PKD2 or other genes that are known to be involved in human cystic kidney diseases. This article reports the positional cloning and mutation analysis of the rat PKD gene, which revealedaCtoTtransition that replaces an arginine by a tryptophan at amino acid 823 in the protein sequence.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Investigations Into Neuronal Cilia Utilizing Mouse Models
    INVESTIGATIONS INTO NEURONAL CILIA UTILIZING MOUSE MODELS OF BARDET-BIEDL SYNDROME Dissertation Presented In Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of the Ohio State University By Nicolas F. Berbari, BS ***** The Ohio State University 2008 Dissertation Committee: Approved by: Kirk Mykytyn, PhD, Adviser Virginia Sanders, PhD __________________________________________ Georgia Bishop, PhD Adviser Michael Robinson, PhD Integrated Biomedical Sciences Graduate Program ABSTRACT Cilia are hair-like microtubule based cellular appendages that extend 5-30 microns from the surface of most vertebrate cells. Since their initial discovery over a hundred years ago, cilia have been of interest to microbiologists and others studying the dynamics and physiological relevance of their motility. The more recent realization that immotile or primary cilia dysfunction is the basis of several human genetic disorders and diseases has brought the efforts of the biomedical research establishment to bear on this long overlooked and underappreciated organelle. Several human genetic disorders caused by cilia defects have been identified, and include Bardet-Biedl syndrome, Joubert syndrome, Meckel-Gruber syndrome, Alstrom syndrome and orofaciodigital syndrome. One theme of these disorders is their multitude of clinical features such as blindness, cystic kidneys, cognitive deficits and obesity. The fact that many of these cilia disorders present with several features may be due to the ubiquitous nature of the primary cilium and their unrecognized roles in most tissues and cell types. The lack of known function for most primary cilia is no more apparent than in the central nervous system. While it has been known for some time that neurons throughout the brain have primary cilia, their functions remain unknown.
    [Show full text]
  • Supplemental Information For
    Supplemental Information for: Gene Expression Profiling of Pediatric Acute Myelogenous Leukemia Mary E. Ross, Rami Mahfouz, Mihaela Onciu, Hsi-Che Liu, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Stanley Pounds, Cheng Cheng, Jing Ma, Raul C. Ribeiro, Jeffrey E. Rubnitz, Kevin Girtman, W. Kent Williams, Susana C. Raimondi, Der-Cherng Liang, Lee-Yung Shih, Ching-Hon Pui & James R. Downing Table of Contents Section I. Patient Datasets Table S1. Diagnostic AML characteristics Table S2. Cytogenetics Summary Table S3. Adult diagnostic AML characteristics Table S4. Additional T-ALL characteristics Section II. Methods Table S5. Summary of filtered probe sets Table S6. MLL-PTD primers Additional Statistical Methods Section III. Genetic Subtype Discriminating Genes Figure S1. Unsupervised Heirarchical clustering Figure S2. Heirarchical clustering with class discriminating genes Table S7. Top 100 probe sets selected by SAM for t(8;21)[AML1-ETO] Table S8. Top 100 probe sets selected by SAM for t(15;17) [PML-RARα] Table S9. Top 63 probe sets selected by SAM for inv(16) [CBFβ-MYH11] Table S10. Top 100 probe sets selected by SAM for MLL chimeric fusion genes Table S11. Top 100 probe sets selected by SAM for FAB-M7 Table S12. Top 100 probe sets selected by SAM for CBF leukemias (whole dataset) Section IV. MLL in combined ALL and AML dataset Table S13. Top 100 probe sets selected by SAM for MLL chimeric fusions irrespective of blast lineage (whole dataset) Table S14. Class discriminating genes for cases with an MLL chimeric fusion gene that show uniform high expression, irrespective of blast lineage Section V.
    [Show full text]
  • Cilium Structure, Assembly, and Disassembly Regulated by the Cytoskeleton
    Biochemical Journal (2018) 475 2329–2353 https://doi.org/10.1042/BCJ20170453 Review Article Cilium structure, assembly, and disassembly regulated by the cytoskeleton Mary Mirvis1,*, Tim Stearns2,3 and W. James Nelson1,2 1Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, U.S.A.; 2Department of Biology, Stanford University, Stanford, CA 94305, U.S.A.; 3Department of Genetics, Stanford University, Stanford, CA 94305, U.S.A. Correspondence: W. James Nelson ([email protected]) The cilium, once considered a vestigial structure, is a conserved, microtubule-based organelle critical for transducing extracellular chemical and mechanical signals that control cell polarity, differentiation, and proliferation. The cilium undergoes cycles of assembly and disassembly that are controlled by complex inter-relationships with the cytoskeleton. Microtubules form the core of the cilium, the axoneme, and are regulated by post-translational modifications, associated proteins, and microtubule dynamics. Although actin and septin cytoskeletons are not major components of the axoneme, they also regulate cilium organization and assembly state. Here, we discuss recent advances on how these different cytoskeletal systems affect cilium function, structure, and organization. Introduction Cilia are specialized, conserved organelles that are evolutionarily optimized for interaction with the world outside of the cell. They protrude into the extracellular space, are structurally resilient but also flexible and dynamic, and have unique mechanisms to tightly control their internal and membrane composition. These features ensure that the cilium is primed to perform highly regulated signaling, mechanosensory, and motile functions. In this review, we consider cilia mostly from the perspective of vertebrate animal cells, with additional information from the wide range of ciliated eukaryotes where appropriate.
    [Show full text]
  • PKHD1 Gene PKHD1, Fibrocystin/Polyductin
    PKHD1 gene PKHD1, fibrocystin/polyductin Normal Function The PKHD1 gene provides instructions for making a protein called fibrocystin ( sometimes known as polyductin). This protein is present in fetal and adult kidney cells, and is also present at low levels in the liver and pancreas. Fibrocystin spans the cell membrane of kidney cells, so that one end of the protein remains inside the cell and the other end projects from the outer surface of the cell. Based on its structure, fibrocystin may act as a receptor, interacting with molecules outside the cell and receiving signals that help the cell respond to its environment. This protein also may be involved in connecting cells together (adhesion), keeping cells apart (repulsion), and promoting the growth and division of cells (proliferation). Fibrocystin is also found in cell structures called primary cilia. Primary cilia are tiny, fingerlike projections that line the small tubes where urine is formed (renal tubules). Researchers believe that primary cilia play an important role in maintaining the size and structure of these tubules; however, the function of fibrocystin in primary cilia remains unclear. Health Conditions Related to Genetic Changes Polycystic kidney disease More than 270 mutations in the PKHD1 gene have been identified in people with polycystic kidney disease. These mutations cause autosomal recessive polycystic kidney disease (ARPKD), which is a severe type of the disorder that is usually evident at birth or in early infancy. PKHD1 mutations include changes in single DNA building blocks (base pairs) and insertions or deletions of a small number of base pairs in the gene. These mutations disrupt the normal structure and function of the fibrocystin protein, or lead to the production of an abnormally small, nonfunctional version of the protein.
    [Show full text]