DOCSLIB.ORG

Characterising the Role of Amigo3 in Oligodendrocytes and Demyelinating Diseases

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Characterising the Role of Amigo3 in Oligodendrocytes and Demyelinating Diseases CHARACTERISING THE ROLE OF AMIGO3 IN OLIGODENDROCYTES AND DEMYELINATING DISEASES By Simon Foale A thesis submitted to the University of Birmingham for the degree of DOCTOR OF PHILOSOPHY Neuroscience and Ophthalmology Institute of Inflammation and Ageing (IIA) College of Medical and Dental Sciences University of Birmingham August 2018 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. Abstract Demyelination disrupts neuronal signalling and can have profound effects on neurological control. No therapies currently exist to encourage remyelination and treatment options are based on preventing further demyelination highlighting the need to develop effective therapies for demyelinating diseases. Recent trials aimed at the leucine rich repeat (LRR) protein, LINGO1 to encourage remyelination have shown promising preclinical data however phase II clinical trials have been unsuccessful. The analogous LRR protein, AMIGO3 is predicted to overcome LINGO1 inhibition and therefore needs to be investigated for its role in oligodendroglia. We have investigated the expression profile of AMIGO3 in myelination and demyelinating disease. AMIGO3 is upregulated rapidly in oligodendrocyte precursor cells (OPCs) following trauma and in experimental autoimmune encephalomyelitis (EAE). Downregulation of AMIGO3 also corresponds with development myelination however AMIGO3 mRNA levels do not change following induction of OPC maturation in vitro. As AMIGO3 is raised following trauma, AMIGO3 could provide a pathological inhibition of OPC maturation in demyelinating diseases. We have also identified the NgR1 receptor complex on OPCs highlighting a potential biding partner that AMIGO3 could function through in disease. These data suggest that therapies aimed at inhibiting AMIGO3 will be promising in encouraging remyelination and treating demyelinating diseases. Acknowledgements I would like to thank everyone in the Neuroscience and Ophthalmology group for all the time and patience they have set aside to support and guide my work. Thanks to Zubair Ahmed, and especially to Daniel Fulton, Ghazala Begum and Masahiro Otsu who committed extensive time to help me develop the skills required for this research. Special mention has to be made to Adam Thompson and Chloe Thomas for their help and day-to-day support which has made this possible. Along with the guidance I have received, my friends both within and outside of Birmingham cannot be overlooked. Without the support of many of them I would have struggled to keep myself going. I have to mention; Patrick Sherlock for having to deal with my constant complaints, Ben Gannon for keeping me uplifted by comparing how much we were both getting overwhelmed, as well as Tom Salmon, Greg Carty, Louise Rayfield, Pippi Hornsby, Matt Knights, Thomas Helfer, Leigh O’Connor, Ben Wiggins, Hannah Eadies and Muhammed Rassul, all of whom have been invaluable to me during this process. Notably, I also have to thank Jenny Kirby for listening to me, guiding me and just generally for helping me through the toughest period. She has had an influential role in ensuring that this work was completed. Sincere thanks as well has to go to my wonderful partner, Maya Bhalla, who was invaluable, providing me with the motivation I needed during the write up period. I do not know if I could have finished putting the final components together without her backing, for which I will always be grateful. Finally I would like to thank my family, Janine Foale, Mike Foale and Richard Foale, for always being behind me and helping me throughout this long a trying period. I am extremely grateful for everything that they have provided, I am forever in their debt and cannot thank them enough for everything that they have done. Contents Chapter 1 Introduction………………………………………………………….1 1.1 Myelin and the mammalian nervous system .................................................. 2 1.1.1 The role of myelin in saltatory conduction and the metabolic and trophic support of axons ...................................................................................................... 2 1.1.2 Structure of myelin ................................................................................... 5 1.1.3 Myelin production in mammals ................................................................ 7 1.1.3.1 Myelin in the central nervous system ................................................ 7 1.1.3.2 Peripheral nervous system .............................................................. 12 1.2 Demyelination and demyelinating diseases ................................................. 13 1.2.1 Remyelination ........................................................................................ 14 1.2.2 Multiple sclerosis ................................................................................... 15 1.2.2.1 Aetiology of MS ............................................................................... 19 1.2.2.2 Current treatments .......................................................................... 23 1.3 Leucine rich repeat molecules in the mammalian CNS ................................ 27 1.3.1 LRR Molecules in Central Nervous System Disorders ........................... 27 1.4 LINGO1 and AMIGO3 .................................................................................. 28 1.4.1 Endogenous expression ........................................................................ 29 1.4.2 LINGO1: CNS disease ........................................................................... 31 1.4.2.1 CNS Trauma ................................................................................... 31 1.4.2.2 Demyelinating diseases .................................................................. 32 1.5 AMIGO3 ....................................................................................................... 39 1.5.1 Endogenous expression ........................................................................ 40 1.5.2 Expression profile in disease ................................................................. 41 1.6 Study rationale ............................................................................................. 45 1.7 Hypothesis and aims .................................................................................... 47 2.1 In vivo procedures ........................................................................................ 49 2.1.1 Animals .................................................................................................. 49 2.1.2 Experimental autoimmune encephalomyelitis ........................................ 49 2.1.2.1 Principles of EAE ............................................................................ 49 2.1.2.2 Advantages of EAE over other models of demyelination ................ 52 2.1.2.3 EAE protocol ................................................................................... 54 2.2 Ex vivo procedures ....................................................................................... 57 2.2.1 Cell culture ............................................................................................. 57 2.2.1.1 Primary OLG ................................................................................... 57 2.3 In vitro procedures........................................................................................ 61 2.3.1 Cell culturing .......................................................................................... 61 2.3.1.1 Oli-neu............................................................................................. 61 2.3.2 Histology ................................................................................................ 62 2.3.2.1 Principles of Histology ..................................................................... 62 2.3.2.2 Processing of tissue for histology .................................................... 65 2.3.2.3 Processing of cell cultures for histology .......................................... 66 2.3.2.4 Immunohistology Protocol ............................................................... 66 2.3.2.5 Antibodies ....................................................................................... 67 2.3.2.6 Imaging and analysis ...................................................................... 68 2.3.2.7 Semi-quantification of images ......................................................... 68 2.3.3 Total pixel counts ................................................................................... 70 2.3.3.1 Pixel intensity .................................................................................. 70 2.3.3.2 Cell counts ...................................................................................... 70 2.3.3.3 Cell co-expression ........................................................................... 70 2.3.4 Western Blot .......................................................................................... 71 2.3.4.1 Principles of Western Blot ..............................................................
Load more

Recommended publications
  • Novel Therapeutic Targets for Axonal Degeneration in Multiple Sclerosis
    J Neuropathol Exp Neurol Vol. 69, No. 4 Copyright Ó 2010 by the American Association of Neuropathologists, Inc. April 2010 pp. 323Y334 REVIEW ARTICLE Novel Therapeutic Targets for Axonal Degeneration in Multiple Sclerosis Steven Petratos, PhD, Michael F. Azari, PhD, Ezgi Ozturk, BSc(Hons), Roula Papadopoulos, PhD, and Claude C.A. Bernard, DSc Downloaded from https://academic.oup.com/jnen/article/69/4/323/2917137 by guest on 30 September 2021 INTRODUCTION Abstract Multiple sclerosis (MS) is a major neurological disorder Multiple sclerosis (MS) is a devastating neurological condition in which there is inflammation, demyelination, and axonal that mainly affects young adults and is associated with long-standing damage in the brain and spinal cord. Approximately 2.5 million morbidity. The pathophysiology of MS is believed to involve people currently live with MS globally, and this causes a immune-mediated multifocal lesions in the CNS that are charac- significant health burden; more than 400,000 people in the terized by inflammation, demyelination, and axonal injury. Most United States alone are diagnosed with the disease. Women are research efforts to date have concentrated on the mechanisms of at least 2 to 3 times more likely to develop the disease than immune-mediated demyelination, whereas mechanisms of axonal men, and the disease onset is most often between the ages injury, the major determinant of neurological deficits in MS patients, of 20 and 50 years (1). Although MS occurs in most ethnic have been elusive beyond observational analyses. This review dis- groups (some more than others, particularly individuals from cusses current understanding of the pathology and novel clinical northern Europe or their direct descendants), strong genetic investigations of axonal injury in MS and the commonly used MS or environmental risk factors are still to be elucidated (2).
    [Show full text]
  • LINGO-1 Antagonist Promotes Spinal Cord Remyelination and Axonal Integrity in MOG-Induced Experimental Autoimmune Encephalomyelitis
    ARTICLES LINGO-1 antagonist promotes spinal cord remyelination and axonal integrity in MOG-induced experimental autoimmune encephalomyelitis Sha Mi1,7, Bing Hu2,7,8, Kyungmin Hahm1,YiLuo1, Edward Sai Kam Hui6, Qiuju Yuan2, Wai Man Wong2, Li Wang2, Huanxing Su2, Tak-Ho Chu2, Jiasong Guo2, Wenming Zhang2, Kwok-Fai So2–4, Blake Pepinsky1, Zhaohui Shao1, Christilyn Graff1, Ellen Garber1, Vincent Jung1, Ed Xuekui Wu6 & Wutian Wu2,3,5,7 Demyelinating diseases, such as multiple sclerosis, are characterized by the loss of the myelin sheath around neurons, owing to inflammation and gliosis in the central nervous system (CNS). Current treatments therefore target anti-inflammatory mechanisms http://www.nature.com/naturemedicine to impede or slow disease progression. The identification of a means to enhance axon myelination would present new therapeutic approaches to inhibit and possibly reverse disease progression. Previously, LRR and Ig domain–containing, Nogo receptor– interacting protein (LINGO-1) has been identified as an in vitro and in vivo negative regulator of oligodendrocyte differentiation and myelination. Here we show that loss of LINGO-1 function by Lingo1 gene knockout or by treatment with an antibody antagonist of LINGO-1 function leads to functional recovery from experimental autoimmune encephalomyelitis. This is reflected biologically by improved axonal integrity, as confirmed by magnetic resonance diffusion tensor imaging, and by newly formed myelin sheaths, as determined by electron microscopy. Antagonism of LINGO-1 or its pathway is therefore a promising approach for the treatment of demyelinating diseases of the CNS. In multiple sclerosis, the myelin and oligodendrocytes of brain and multiple sclerosis. The model has previously been used to demon- Nature Publishing Group Group Nature Publishing 7 spinal cord white matter are the targets of T cell–mediated immune strate that fostering remyelination can be effective in moderating 1 4 200 attacks , resulting in demyelination and the consequent progressive disease progression .
    [Show full text]
  • Supplemental Information
    Supplemental information Dissection of the genomic structure of the miR-183/96/182 gene. Previously, we showed that the miR-183/96/182 cluster is an intergenic miRNA cluster, located in a ~60-kb interval between the genes encoding nuclear respiratory factor-1 (Nrf1) and ubiquitin-conjugating enzyme E2H (Ube2h) on mouse chr6qA3.3 (1). To start to uncover the genomic structure of the miR- 183/96/182 gene, we first studied genomic features around miR-183/96/182 in the UCSC genome browser (http://genome.UCSC.edu/), and identified two CpG islands 3.4-6.5 kb 5’ of pre-miR-183, the most 5’ miRNA of the cluster (Fig. 1A; Fig. S1 and Seq. S1). A cDNA clone, AK044220, located at 3.2-4.6 kb 5’ to pre-miR-183, encompasses the second CpG island (Fig. 1A; Fig. S1). We hypothesized that this cDNA clone was derived from 5’ exon(s) of the primary transcript of the miR-183/96/182 gene, as CpG islands are often associated with promoters (2). Supporting this hypothesis, multiple expressed sequences detected by gene-trap clones, including clone D016D06 (3, 4), were co-localized with the cDNA clone AK044220 (Fig. 1A; Fig. S1). Clone D016D06, deposited by the German GeneTrap Consortium (GGTC) (http://tikus.gsf.de) (3, 4), was derived from insertion of a retroviral construct, rFlpROSAβgeo in 129S2 ES cells (Fig. 1A and C). The rFlpROSAβgeo construct carries a promoterless reporter gene, the β−geo cassette - an in-frame fusion of the β-galactosidase and neomycin resistance (Neor) gene (5), with a splicing acceptor (SA) immediately upstream, and a polyA signal downstream of the β−geo cassette (Fig.
    [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]
  • Functions of Nogo Proteins and Their Receptors in the Nervous System
    REVIEWS Functions of Nogo proteins and their receptors in the nervous system Martin E. Schwab Abstract | The membrane protein Nogo-A was initially characterized as a CNS-specific inhibitor of axonal regeneration. Recent studies have uncovered regulatory roles of Nogo proteins and their receptors — in precursor migration, neurite growth and branching in the developing nervous system — as well as a growth-restricting function during CNS maturation. The function of Nogo in the adult CNS is now understood to be that of a negative regulator of neuronal growth, leading to stabilization of the CNS wiring at the expense of extensive plastic rearrangements and regeneration after injury. In addition, Nogo proteins interact with various intracellular components and may have roles in the regulation of endoplasmic reticulum (ER) structure, processing of amyloid precursor protein and cell survival. Nogo proteins were discovered, and have been exten- The amino-terminal segments of the proteins sively studied, in the context of injury and repair of fibre encoded by the different RTN genes have differing tracts in the CNS1 — a topic of great research interest lengths and there is no homology between them3,5. The and clinical relevance. However, much less in known N termini of the RTN4 products Nogo-A and Nogo-B are about the physiological functions of Nogo proteins in identical, consisting of a 172-amino acid sequence that development and in the intact adult organism, including is encoded by a single exon (exon 1) that is followed by in the brain. Through a number of recent publications, a short exon 2 and, in Nogo-A, by the very long exon Nogo proteins have emerged as important regulators of 3 encoding 800 amino acids2,6 (FIG.
    [Show full text]
  • Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
    medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened.
    [Show full text]
  • Behavioral Abnormalities with Disruption of Brain Structure in Mice Overexpressing
    www.nature.com/scientificreports Correction: Author Correction OPEN Behavioral abnormalities with disruption of brain structure in mice overexpressing VGF Received: 12 October 2016 Takahiro Mizoguchi, Hiroko Minakuchi, Mitsue Ishisaka, Kazuhiro Tsuruma, Masamitsu Accepted: 10 May 2017 Shimazawa & Hideaki Hara Published online: 05 July 2017 VGF nerve growth factor inducible (VGF) is a neuropeptide induced by nerve growth factor and brain- derived neurotrophic factor. This peptide is involved in synaptic plasticity, neurogenesis, and neurite growth in the brain. Patients with depression and bipolar disorder have lower-than-normal levels of VGF, whereas patients with schizophrenia and other cohorts of patients with depression have higher- than-normal levels. VGF knockout mice display behavioral abnormalities such as higher depressive behavior and memory dysfunction. However, it is unclear whether upregulation of VGF afects brain function. In the present study, we generated mice that overexpress VGF and investigated several behavioral phenotypes and the brain structure. These adult VGF-overexpressing mice showed (a) hyperactivity, working memory impairment, a higher depressive state, and lower sociality compared with wild-type mice; (b) lower brain weight without a change in body weight; (c) increased lateral ventricle volume compared with wild-type mice; and (d) striatal morphological defects. These results suggest that VGF may modulate a variety of behaviors and brain development. This transgenic mouse line may provide a useful model for research on mental illnesses. Mental illnesses are high prevalence1. Suicide is a common cause of death worldwide and a leading cause of death in young people2. Suicide rates are much higher in people with mental health problems3. Although many studies have investigated candidate genes for mental illnesses, these disorders still have no cure4–8.
    [Show full text]
  • Single Cell Derived Clonal Analysis of Human Glioblastoma Links
    SUPPLEMENTARY INFORMATION: Single cell derived clonal analysis of human glioblastoma links functional and genomic heterogeneity ! Mona Meyer*, Jüri Reimand*, Xiaoyang Lan, Renee Head, Xueming Zhu, Michelle Kushida, Jane Bayani, Jessica C. Pressey, Anath Lionel, Ian D. Clarke, Michael Cusimano, Jeremy Squire, Stephen Scherer, Mark Bernstein, Melanie A. Woodin, Gary D. Bader**, and Peter B. Dirks**! ! * These authors contributed equally to this work.! ** Correspondence: [email protected] or [email protected]! ! Supplementary information - Meyer, Reimand et al. Supplementary methods" 4" Patient samples and fluorescence activated cell sorting (FACS)! 4! Differentiation! 4! Immunocytochemistry and EdU Imaging! 4! Proliferation! 5! Western blotting ! 5! Temozolomide treatment! 5! NCI drug library screen! 6! Orthotopic injections! 6! Immunohistochemistry on tumor sections! 6! Promoter methylation of MGMT! 6! Fluorescence in situ Hybridization (FISH)! 7! SNP6 microarray analysis and genome segmentation! 7! Calling copy number alterations! 8! Mapping altered genome segments to genes! 8! Recurrently altered genes with clonal variability! 9! Global analyses of copy number alterations! 9! Phylogenetic analysis of copy number alterations! 10! Microarray analysis! 10! Gene expression differences of TMZ resistant and sensitive clones of GBM-482! 10! Reverse transcription-PCR analyses! 11! Tumor subtype analysis of TMZ-sensitive and resistant clones! 11! Pathway analysis of gene expression in the TMZ-sensitive clone of GBM-482! 11! Supplementary figures and tables" 13" "2 Supplementary information - Meyer, Reimand et al. Table S1: Individual clones from all patient tumors are tumorigenic. ! 14! Fig. S1: clonal tumorigenicity.! 15! Fig. S2: clonal heterogeneity of EGFR and PTEN expression.! 20! Fig. S3: clonal heterogeneity of proliferation.! 21! Fig.
    [Show full text]
  • LINGO-1 and AMIGO3, Potential Therapeutic Targets for Neurological and Dysmyelinating Disorders?
    [Downloaded free from http://www.nrronline.org on Wednesday, February 28, 2018, IP: 147.188.108.81] NEURAL REGENERATION RESEARCH August 2017, Volume 12, Issue 8 www.nrronline.org INVITED REVIEW LINGO-1 and AMIGO3, potential therapeutic targets for neurological and dysmyelinating disorders? Simon Foale, Martin Berry, Ann Logan, Daniel Fulton, Zubair Ahmed* Neuroscience and Ophthalmology, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK How to cite this article: Foale S, Berry M, Logan A, Fulton D, Ahmed Z (2017) LINGO-1 and AMIGO3, potential therapeutic targets for neu- rological and dysmyelinating disorders?. Neural Regen Res 12(8):1247-1251. Funding: This work was supported by a grant from The University of Birmingham. Abstract *Correspondence to: Zubair Ahmed, Ph.D., Leucine rich repeat proteins have gained considerable interest as therapeutic targets due to their expres- [email protected]. sion and biological activity within the central nervous system. LINGO-1 has received particular attention since it inhibits axonal regeneration after spinal cord injury in a RhoA dependent manner while inhibiting orcid: leucine rich repeat and immunoglobulin-like domain-containing protein 1 (LINGO-1) disinhibits neuron 0000-0001-6267-6492 outgrowth. Furthermore, LINGO-1 suppresses oligodendrocyte precursor cell maturation and myelin (Zubair Ahmed) production. Inhibiting the action of LINGO-1 encourages remyelination both in vitro and in vivo. Accord- ingly, LINGO-1 antagonists show promise as therapies for demyelinating diseases. An analogous protein doi: 10.4103/1673-5374.213538 to LINGO-1, amphoterin-induced gene and open reading frame-3 (AMIGO3), exerts the same inhibitory effect on the axonal outgrowth of central nervous system neurons, as well as interacting with the same re- Accepted: 2017-07-17 ceptors as LINGO-1.
    [Show full text]
  • Linking LINGO1 to Essential Tremor
    European Journal of Human Genetics (2010) 18, 739–740 & 2010 Macmillan Publishers Limited All rights reserved 1018-4813/10 www.nature.com/ejhg of ET is problematic without a biological or NEWS AND COMMENTARY objective diagnostic marker. ET is essentially a clinical diagnosis and despite proposed diag- nostic criteria by experts in the field, we do LINGO1 and Essential Tremor: linking the shakes not know for certain whether ET is a single ............................................. disorder or a disease syndrome with varied etiologies.1 Some people with ET also have Linking LINGO1 to essential tremor other associated movement disorders, while others progress to develop Parkinson’s disease Eng-King Tan years after the initial ET diagnosis. Even ........................................................................... limited post-mortem studies seem to suggest that the condition is likely to be hetero- European Journal of Human Genetics (2010) 18, 739–740; doi:10.1038/ejhg.2010.25; geneous. Most cases have cerebellar changes published online 7 April 2010 without Lewy bodies, whereas intriguingly some cases have brainstem Lewy bodies.7 It is arguable whether the inclusion of the latter ssential tremor (ET), one of the most of ‘definite’, ‘probable’ or ‘possible’ cases and group would compound genetic association E common neurological conditions, is showed that the strength of association with studies. One study showed that one in three characterized by postural and action tremor.1 rs9652490 was stronger in those with a more patients with tremor have been wrongly diag- The prevalence has been reported to be as definitive diagnosis. They also alluded to the nosed as having ET.8 These problems are high as 39 cases per 1000.
    [Show full text]
  • Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer
    Epigenetic mechanisms are involved in the oncogenic properties of ZNF518B in colorectal cancer Francisco Gimeno-Valiente, Ángela L. Riffo-Campos, Luis Torres, Noelia Tarazona, Valentina Gambardella, Andrés Cervantes, Gerardo López-Rodas, Luis Franco and Josefa Castillo SUPPLEMENTARY METHODS 1. Selection of genomic sequences for ChIP analysis To select the sequences for ChIP analysis in the five putative target genes, namely, PADI3, ZDHHC2, RGS4, EFNA5 and KAT2B, the genomic region corresponding to the gene was downloaded from Ensembl. Then, zoom was applied to see in detail the promoter, enhancers and regulatory sequences. The details for HCT116 cells were then recovered and the target sequences for factor binding examined. Obviously, there are not data for ZNF518B, but special attention was paid to the target sequences of other zinc-finger containing factors. Finally, the regions that may putatively bind ZNF518B were selected and primers defining amplicons spanning such sequences were searched out. Supplementary Figure S3 gives the location of the amplicons used in each gene. 2. Obtaining the raw data and generating the BAM files for in silico analysis of the effects of EHMT2 and EZH2 silencing The data of siEZH2 (SRR6384524), siG9a (SRR6384526) and siNon-target (SRR6384521) in HCT116 cell line, were downloaded from SRA (Bioproject PRJNA422822, https://www.ncbi. nlm.nih.gov/bioproject/), using SRA-tolkit (https://ncbi.github.io/sra-tools/). All data correspond to RNAseq single end. doBasics = TRUE doAll = FALSE $ fastq-dump -I --split-files SRR6384524 Data quality was checked using the software fastqc (https://www.bioinformatics.babraham. ac.uk /projects/fastqc/). The first low quality removing nucleotides were removed using FASTX- Toolkit (http://hannonlab.cshl.edu/fastxtoolkit/).
    [Show full text]
  • Systematic Elucidation of Neuron-Astrocyte Interaction in Models of Amyotrophic Lateral Sclerosis Using Multi-Modal Integrated Bioinformatics Workflow
    ARTICLE https://doi.org/10.1038/s41467-020-19177-y OPEN Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow Vartika Mishra et al.# 1234567890():,; Cell-to-cell communications are critical determinants of pathophysiological phenotypes, but methodologies for their systematic elucidation are lacking. Herein, we propose an approach for the Systematic Elucidation and Assessment of Regulatory Cell-to-cell Interaction Net- works (SEARCHIN) to identify ligand-mediated interactions between distinct cellular com- partments. To test this approach, we selected a model of amyotrophic lateral sclerosis (ALS), in which astrocytes expressing mutant superoxide dismutase-1 (mutSOD1) kill wild-type motor neurons (MNs) by an unknown mechanism. Our integrative analysis that combines proteomics and regulatory network analysis infers the interaction between astrocyte-released amyloid precursor protein (APP) and death receptor-6 (DR6) on MNs as the top predicted ligand-receptor pair. The inferred deleterious role of APP and DR6 is confirmed in vitro in models of ALS. Moreover, the DR6 knockdown in MNs of transgenic mutSOD1 mice attenuates the ALS-like phenotype. Our results support the usefulness of integrative, systems biology approach to gain insights into complex neurobiological disease processes as in ALS and posit that the proposed methodology is not restricted to this biological context and could be used in a variety of other non-cell-autonomous communication
    [Show full text]