Pyramidal Cells: Role in Primate Prefrontal Cortex Circuitry During Postnatal Development and Schizophrenia

Total Page:16

File Type:pdf, Size:1020Kb

Pyramidal Cells: Role in Primate Prefrontal Cortex Circuitry During Postnatal Development and Schizophrenia PYRAMIDAL CELLS: ROLE IN PRIMATE PREFRONTAL CORTEX CIRCUITRY DURING POSTNATAL DEVELOPMENT AND SCHIZOPHRENIA by Dibyadeep Datta Bachelor of Arts, Neuroscience, Colgate University, 2010 Submitted to the Graduate Faculty of the Kenneth P. Dietrich School of Arts and Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Pittsburgh 2015 UNIVERSITY OF PITTSBURGH DIETRICH SCHOOL OF ARTS AND SCIENCES This dissertation was presented by Dibyadeep Datta It was defended on September 24, 2015 and approved by Vikaas Sohal, MD/PhD, Department of Neuroscience, University of California, San Francisco J. Patrick Card, PhD, Department of Neuroscience Kenneth N. Fish, PhD, Department of Psychiatry Stephen D. Meriney, PhD, Department of Neuroscience Etienne L. Sibille, PhD, Centre for Addiction and Mental Health Dissertation Advisor: David A. Lewis, MD, Department of Psychiatry ii Copyright © by Dibyadeep Datta 2015 iii PYRAMIDAL CELLS: ROLE IN PRIMATE PREFRONTAL CORTEX CIRCUITRY DURING POSTNATAL DEVELOPMENT AND SCHIZOPHRENIA Dibyadeep Datta, PhD University of Pittsburgh, 2015 Cognitive deficits constitute a core feature of schizophrenia, are persistent across the course of the illness and are the best predictor of long-term functional outcome. Dysfunction in certain cognitive processes, such as working memory, are common in subjects with schizophrenia and have been attributed to aberrant function of the dorsolateral prefrontal cortex (DLPFC). This dysfunction appears to reflect, at least in part, alterations in excitatory neurotransmission. Cortical pyramidal neurons, the principal source of cortical glutamate neurotransmission, exhibit highly robust molecular and morphological alterations in schizophrenia. These alterations appear to be most pronounced in DLPFC deep layer 3, the same microcircuit necessary for the generation of neural oscillations in the γ-frequency range that sustain working memory function. Understanding how dysfunction in DLPFC cortical circuits in deep layer 3 might give rise to the pathophysiology of altered γ-frequency oscillations and working memory deficits in schizophrenia require an interrogation of the mechanisms by which these neuropathological alterations may arise, but also the normal developmental trajectories of these vulnerable microcircuits. In this dissertation, we provide evidence for pyramidal cell type- specific molecular disturbances and synapse-specific structural impairments in DLPFC deep layer 3, and cell type-specific and layer-specific nature of postnatal developmental refinements in pyramidal cells in the DLPFC, within the circuitry that subserves γ-frequency oscillations and working memory. Accordingly, we have identified alterations in the expression of numerous molecular regulators of the actin cytoskeleton in a layer-specific and cell type-specific manner in DLPFC deep layer 3 in individuals with schizophrenia that might be a critical “upstream” cause iv in the pathogenesis of the illness. Additionally, using novel triple-label fluorescence immunohistochemistry and spinning-disk confocal microscopy, we characterize specific synaptic connections onto DLPFC deep layer 3 pyramidal cells in schizophrenia. Finally, we demonstrate that the developmental trajectories of primate DLPFC deep layer 3 pyramidal neurons are protracted, and layer-specific and posit that the molecular maturation of GABA synapses on pyramidal cells may account, at least in part, for the maturation of synchronized pyramidal cell firing which is crucial for γ-frequency oscillations. v TABLE OF CONTENTS PREFACE ................................................................................................................... XXI 1.0 GENERAL INTRODUCTION ........................................................................... 1 1.1 OVERVIEW OF SCHIZOPHRENIA .......................................................... 1 1.1.1 Burden of schizophrenia .................................................................... 1 1.1.2 Etiology of Schizophrenia .................................................................. 2 1.1.3 Epidemiology and clinical features of schizophrenia ...................... 4 1.1.4 Cognitive impairments as a critical component of schizophrenia . 6 1.1.5 Treatment and outcome ..................................................................... 7 1.2 DORSOLATERAL PREFRONTAL CORTEX AND PYRAMIDAL CELLS: CRITICAL MEDIATORS OF WORKING MEMORY AND COGNITIVE FUNCTION ................................................................................................................................. 8 1.2.1 Cognitive dysfunction and the dorsolateral prefrontal cortex in schizophrenia ................................................................................................. 8 1.2.2 Deep layer 3 pyramidal cells: “cellular” basis of working memory ..............................................................................................................10 1.2.3 Cortical pyramidal neurons in different laminar locations subserve unique functions .......................................................................................... 11 1.2.4 Spatial tuning of deep layer 3 pyramidal cells is determined by GABA interneurons ...................................................................................... 15 vi 1.2.5 Role of DLPFC GABA interneurons in sculpting pyramidal cell activity for cognitive control ....................................................................... 16 1.2.6 Molecular heterogeneity in GABA receptors .................................. 18 1.3 EVIDENCE FOR ALTERED EXCITATION AND INHIBITION IN SCHIZOPHRENIA ................................................................................................. 21 1.3.1 Aberration in excitatory neurotransmission in schizophrenia ..... 21 1.3.2 Dendritic spines: structure and function ........................................ 23 1.3.3 Actin cytoskeleton: Crucial regulators of Dendritic Spines .......... 25 1.3.4 Impairments in actin cytoskeleton in schizophrenia ..................... 29 1.3.5 Alterations in presynaptic afferents in the DLPFC: Potential source of dendritic spine alterations .......................................................... 31 1.3.6 Alterations in GABA interneurons are most pronounced in DLPFC deep layer 3 in schizophrenia ..................................................................... 33 1.4 DEVELOPMENTAL REFINEMENTS IN DLPFC DEEP LAYER 3 MICROCIRCUITS DURING POSTNATAL MATURATION ................................... 37 1.4.1 Protracted developmental maturation of pyramidal and GABA cells.................................................................................................................37 1.4.2 Pyramidal cell and GABA interneuron circuitry in layer 3 is crucial for generating γ oscillations ....................................................................... 41 1.5 GOALS AND RELEVANCE OF THIS DISSERTATION ........................ 43 2.0 ALTERED EXPRESSION OF CDC42 SIGNALING PATHWAY COMPONENTS IN CORTICAL LAYER 3 PYRAMIDAL CELLS IN SCHIZOPHRENIA .......................................................................................................................................45 vii 2.1 INTRODUCTION .................................................................................... 45 2.2 MATERIALS AND METHODS ............................................................... 50 2.2.1 Human subjects ................................................................................ 50 2.2.2 Laser microdissection procedure.................................................... 52 2.2.3 qPCR analyses .................................................................................. 54 2.2.4 Microarray analyses .......................................................................... 54 2.2.5 Antipsychotic-exposed monkeys .................................................... 55 2.2.6 Data analysis and statistics ............................................................. 55 2.3 RESULTS ............................................................................................... 57 2.3.1 Expression of CDC42-related mRNAs in DLPFC deep layer 3 ...... 57 2.3.2 Effects of psychotropic medications and other confounding variables ........................................................................................................ 61 2.4 DISCUSSION ......................................................................................... 64 2.4.1 Differences in layer-specific vs. cell type-specific pathology in schizophrenia ............................................................................................... 65 2.4.2 Contribution of CDC42-related signaling to dendritic spine abnormalities in DLPFC layer 3 pyramidal cells ........................................ 66 2.4.3 Conclusion ........................................................................................ 68 3.0 IDENTITY OF INPUTS TO DENDRITIC SPINES ON DEEP LAYER 3 PYRAMIDAL CELLS IN THE DORSOLATERAL PREFRONTAL CORTEX IN SCHIZOPHRENIA......................................................................................................... 70 3.1 INTRODUCTION .................................................................................... 70 3.2 MATERIALS AND METHODS ............................................................... 73 viii 3.2.1 Human Subjects ................................................................................ 73 3.2.2 Immunohistochemistry ....................................................................
Recommended publications
  • Regulation of Cdc42 and Its Effectors in Epithelial Morphogenesis Franck Pichaud1,2,*, Rhian F
    © 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs217869. doi:10.1242/jcs.217869 REVIEW SUBJECT COLLECTION: ADHESION Regulation of Cdc42 and its effectors in epithelial morphogenesis Franck Pichaud1,2,*, Rhian F. Walther1 and Francisca Nunes de Almeida1 ABSTRACT An overview of Cdc42 Cdc42 – a member of the small Rho GTPase family – regulates cell Cdc42 was discovered in yeast and belongs to a large family of small – polarity across organisms from yeast to humans. It is an essential (20 30 kDa) GTP-binding proteins (Adams et al., 1990; Johnson regulator of polarized morphogenesis in epithelial cells, through and Pringle, 1990). It is part of the Ras-homologous Rho subfamily coordination of apical membrane morphogenesis, lumen formation and of GTPases, of which there are 20 members in humans, including junction maturation. In parallel, work in yeast and Caenorhabditis elegans the RhoA and Rac GTPases, (Hall, 2012). Rho, Rac and Cdc42 has provided important clues as to how this molecular switch can homologues are found in all eukaryotes, except for plants, which do generate and regulate polarity through localized activation or inhibition, not have a clear homologue for Cdc42. Together, the function of and cytoskeleton regulation. Recent studies have revealed how Rho GTPases influences most, if not all, cellular processes. important and complex these regulations can be during epithelial In the early 1990s, seminal work from Alan Hall and his morphogenesis. This complexity is mirrored by the fact that Cdc42 can collaborators identified Rho, Rac and Cdc42 as main regulators of exert its function through many effector proteins.
    [Show full text]
  • Differentially Expressed on Collagen Networks 1, 2, 10 © 2000-2009 Ingenuity Systems, Inc. All Rights Reserved. Symbol Entrez
    Differentially expressed on collagen Networks 1, 2, 10 © 2000-2009 Ingenuity Systems, Inc. All rights reserved. Symbol Entrez Gene Name Affymetrix Fold Change Location Family ALDH1A3 aldehyde dehydrogenase 1 family, member A3 203180_at -5.43125168 Cytoplasm enzyme 209772_s_ Plasma CD24 CD24 molecule at -4.32890229 Membrane other HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 204130_at -4.1099197 Cytoplasm enzyme Plasma AMOTL2 angiomotin like 2 203002_at -2.82872773 Membrane other transcription DLX2 distal-less homeobox 2 207147_at -2.74996362 Nucleus regulator 221215_s_ RIPK4 receptor-interacting serine-threonine kinase 4 at -2.56556472 Nucleus kinase PLK2 polo-like kinase 2 (Drosophila) 201939_at -2.47054478 Nucleus kinase ALDH3A1 aldehyde dehydrogenase 3 family, memberA1 205623_at -2.30532989 Cytoplasm enzyme TXNRD1 thioredoxin reductase 1 201266_at -2.27936909 Cytoplasm enzyme Extracellular CYR61 cysteine-rich, angiogenic inducer, 61 201289_at -2.09052668 Space other 214212_x_ FERMT2 fermitin family homolog 2 (Drosophila) at -1.87478183 Cytoplasm other Plasma RIT1 Ras-like without CAAX 1 209882_at -1.77586775 Membrane enzyme 210297_s_ Extracellular MSMB microseminoprotein, beta- at -1.72177723 Space other Extracellular PI3 peptidase inhibitor 3, skin-derived 203691_at -1.68135697 Space other ALDH3B1 aldehyde dehydrogenase 3 family, member B1 205640_at -1.67376791 Cytoplasm enzyme 202124_s_ Plasma TRAK2 trafficking protein, kinesin binding 2 at -1.6367793 Membrane transporter BMP and activin membrane-bound inhibitor Plasma BAMBI
    [Show full text]
  • The Borg Family of Cdc42 Effector Proteins Cdc42ep1–5
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Institute of Cancer Research Repository Biochemical Society Transactions (2016) 0 1–8 DOI: 10.1042/BST20160219 1 2 The Borg family of Cdc42 effector proteins 3 4 Cdc42EP1–5 5 6 Aaron J. Farrugia and Fernando Calvo 7 8 Tumour Microenvironment Team, Division of Cancer Biology, Institute of Cancer Research, 237 Fulham Road, London SW2 6JB, U.K. 9 Correspondence: Fernando Calvo ([email protected]) 10 11 12 13 Despite being discovered more than 15 years ago, the Borg (binder of Rho GTPases) 14 – family of Cdc42 effector proteins (Cdc42EP1 5) remains largely uncharacterised and rela- 15 tively little is known about their structure, regulation and role in development and disease. 16 Recent studies are starting to unravel some of the key functional and mechanistic 17 aspects of the Borg proteins, including their role in cytoskeletal remodelling and signal- 18 ling. In addition, the participation of Borg proteins in important cellular processes such as 19 cell shape, directed migration and differentiation is slowly emerging, directly linking Borgs 20 with important physiological and pathological processes such as angiogenesis, neuro- 21 fi transmission and cancer-associated desmoplasia. Here, we review some of these nd- 22 ings and discuss future prospects. 23 24 25 26 27 28 29 Introduction 30 The Rho GTPase family member Cdc42 regulates a diverse range of cellular functions including cyto- 31 kinesis, cytoskeletal remodelling and cell polarity [1,2]. Like other Rho family members, Cdc42 cycles 32 between two tightly regulated conformational states, a GTP-bound active state and a GDP-bound 33 inactive state [3].
    [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]
  • Characterizing Humidity, Sex, and B-Cell Gene Regulation in Fungal Allergic
    CHARACTERIZING HUMIDITY, SEX, AND B-CELL GENE REGULATION IN FUNGAL ALLERGIC ASTHMA A Thesis Submitted to the Graduate Faculty of the North Dakota State University of Agriculture and Applied Science By Emma Claire Kusick In Partial Fulfillment of the Requirements for the Degree of MASTER OF SCIENCE Major Department: Microbiological Sciences April 2020 Fargo, North Dakota North Dakota State University Graduate School Title CHARACTERIZING HUMIDITY, SEX, AND B-CELL GENE REGULATION IN FUNGAL ALLERGIC ASTHMA By EMMA KUSICK The Supervisory Committee certifies that this disquisition complies with North Dakota State University’s regulations and meets the accepted standards for the degree of MASTER OF SCIENCE SUPERVISORY COMMITTEE: Dr. Jane Schuh Chair Dr. Teresa Bergholz Dr. Penelope Gibbs Dr. Sumit Ghosh Approved: 5/4/2020 Dr. John McEvoy Date Department Chair ABSTRACT Asthma is a debilitating lung disease that affects nearly 300 million people worldwide. Environments with high humidity and subsequent mold exposure often trigger allergic asthma. Sex differences have been reported in the incidence, prevalence, and severity of asthma. B-lymphocytes are recruited in high numbers to the allergic lung in response to the inhalation of Aspergillus fumigatus mold spores (conidia). In this work, we used a mouse model of allergic fungal asthma to assess environmental humidity, sex, and B-lymphocytes in an inhalational model of allergic fungal asthma. Our results showed that animals sensitized in low humidity conditions had no airway hyperresponsiveness (AHR), inflammation, but an increase in IgG3 antibody production. Males weighed more than females, female mice had more fibrosis and produced more IgG3 Ab, but sex showed no impact on low humidity.
    [Show full text]
  • CDC42EP4 (NM 012121) Human Tagged ORF Clone Product Data
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC201162L3 CDC42EP4 (NM_012121) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: CDC42EP4 (NM_012121) Human Tagged ORF Clone Tag: Myc-DDK Symbol: CDC42EP4 Synonyms: BORG4; CEP4; KAIA1777 Vector: pLenti-C-Myc-DDK-P2A-Puro (PS100092) E. coli Selection: Chloramphenicol (34 ug/mL) Cell Selection: Puromycin ORF Nucleotide The ORF insert of this clone is exactly the same as(RC201162). Sequence: Restriction Sites: SgfI-MluI Cloning Scheme: ACCN: NM_012121 ORF Size: 1068 bp This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 CDC42EP4 (NM_012121) Human Tagged ORF Clone – RC201162L3 OTI Disclaimer: The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. polymorphisms), each with its own valid existence. This clone is substantially in agreement with the reference, but a complete review of all prevailing variants is recommended prior to use. More info OTI Annotation: This clone was engineered to express the complete ORF with an expression tag. Expression varies depending on the nature of the gene. RefSeq: NM_012121.4 RefSeq Size: 3121 bp RefSeq ORF: 1071 bp Locus ID: 23580 UniProt ID: Q9H3Q1, B2R6D8 Domains: PBD MW: 38 kDa Gene Summary: The product of this gene is a member of the CDC42-binding protein family.
    [Show full text]
  • Molecular Analyses of Malignant Pleural Mesothelioma
    Molecular Analyses of Malignant Pleural Mesothelioma Shir Kiong Lo National Heart and Lung Institute Imperial College Dovehouse Street London SW3 6LY A thesis submitted for MD (Res) Faculty of Medicine, Imperial College London 2016 1 Abstract Malignant pleural mesothelioma (MPM) is an aggressive cancer that is strongly associated with asbestos exposure. Majority of patients with MPM present with advanced disease and the treatment paradigm mainly involves palliative chemotherapy and best supportive care. The current chemotherapy options are limited and ineffective hence there is an urgent need to improve patient outcomes. This requires better understanding of the genetic alterations driving MPM to improve diagnostic, prognostic and therapeutic strategies. This research aims to gain further insights in the pathogenesis of MPM by exploring the tumour transcriptional and mutational profiles. We compared gene expression profiles of 25 MPM tumours and 5 non-malignant pleura. This revealed differentially expressed genes involved in cell migration, invasion, cell cycle and the immune system that contribute to the malignant phenotype of MPM. We then constructed MPM-associated co-expression networks using weighted gene correlation network analysis to identify clusters of highly correlated genes. These identified three distinct molecular subtypes of MPM associated with genes involved in WNT and TGF-ß signalling pathways. Our results also revealed genes involved in cell cycle control especially the mitotic phase correlated significantly with poor prognosis. Through exome analysis of seven paired tumour/blood and 29 tumour samples, we identified frequent mutations in BAP1 and NF2. Additionally, the mutational profile of MPM is enriched with genes encoding FAK, MAPK and WNT signalling pathways.
    [Show full text]
  • Shear Stress Modulates Gene Expression in Normal Human Dermal Fibroblasts
    University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2017 Shear Stress Modulates Gene Expression in Normal Human Dermal Fibroblasts Zabinyakov, Nikita Zabinyakov, N. (2017). Shear Stress Modulates Gene Expression in Normal Human Dermal Fibroblasts (Unpublished master's thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/27775 http://hdl.handle.net/11023/3639 master thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Shear Stress Modulates Gene Expression in Normal Human Dermal Fibroblasts by Nikita Zabinyakov A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE GRADUATE PROGRAM IN BIOMEDICAL ENGINEERING CALGARY, ALBERTA JANUARY 2017 © Nikita Zabinyakov 2017 Abstract Applied mechanical forces, such as those resulting from fluid flow, trigger cells to change their functional behavior or phenotype. However, there is little known about how fluid flow affects fibroblasts. The hypothesis of this thesis is that dermal fibroblasts undergo significant changes of expression of differentiation genes after exposure to fluid flow (or shear stress). To test the hypothesis, human dermal fibroblasts were exposed to laminar steady fluid flow for 20 and 40 hours and RNA was collected for microarray analysis.
    [Show full text]
  • Identification of Key Genes and Pathways for Alzheimer's Disease
    Biophys Rep 2019, 5(2):98–109 https://doi.org/10.1007/s41048-019-0086-2 Biophysics Reports RESEARCH ARTICLE Identification of key genes and pathways for Alzheimer’s disease via combined analysis of genome-wide expression profiling in the hippocampus Mengsi Wu1,2, Kechi Fang1, Weixiao Wang1,2, Wei Lin1,2, Liyuan Guo1,2&, Jing Wang1,2& 1 CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, Beijing 100101, China 2 Department of Psychology, University of Chinese Academy of Sciences, Beijing 10049, China Received: 8 August 2018 / Accepted: 17 January 2019 / Published online: 20 April 2019 Abstract In this study, combined analysis of expression profiling in the hippocampus of 76 patients with Alz- heimer’s disease (AD) and 40 healthy controls was performed. The effects of covariates (including age, gender, postmortem interval, and batch effect) were controlled, and differentially expressed genes (DEGs) were identified using a linear mixed-effects model. To explore the biological processes, func- tional pathway enrichment and protein–protein interaction (PPI) network analyses were performed on the DEGs. The extended genes with PPI to the DEGs were obtained. Finally, the DEGs and the extended genes were ranked using the convergent functional genomics method. Eighty DEGs with q \ 0.1, including 67 downregulated and 13 upregulated genes, were identified. In the pathway enrichment analysis, the 80 DEGs were significantly enriched in one Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, GABAergic synapses, and 22 Gene Ontology terms. These genes were mainly involved in neuron, synaptic signaling and transmission, and vesicle metabolism. These processes are all linked to the pathological features of AD, demonstrating that the GABAergic system, neurons, and synaptic function might be affected in AD.
    [Show full text]
  • Genome-Wide Gene Expression Profiling of the Angelman Syndrome
    European Journal of Human Genetics (2010) 18, 1228–1235 & 2010 Macmillan Publishers Limited All rights reserved 1018-4813/10 www.nature.com/ejhg ARTICLE Genome-wide gene expression profiling of the Angelman syndrome mice with Ube3a mutation Daren Low1 and Ken-Shiung Chen*,1 Angelman syndrome (AS) is a human neurological disorder caused by lack of maternal UBE3A expression in the brain. UBE3A is known to function as both an ubiquitin-protein ligase (E3) and a coactivator for steroid receptors. Many ubiquitin targets, as well as interacting partners, of UBE3A have been identified. However, the pathogenesis of AS, and how deficiency of maternal UBE3A can upset cellular homeostasis, remains vague. In this study, we performed a genome-wide microarray analysis on the maternal Ube3a-deficient (Ube3amÀ/p+) AS mouse to search for genes affected in the absence of Ube3a. We observed 64 differentially expressed transcripts (7 upregulated and 57 downregulated) showing more than 1.5-fold differences in expression (Po0.05). Pathway analysis shows that these genes are implicated in three major networks associated with cell signaling, nervous system development and cell death. Using quantitative reverse-transcription PCR, we validated the differential expression of genes (Fgf7, Glra1, Mc1r, Nr4a2, Slc5a7 and Epha6) that show functional relevance to AS phenotype. We also show that the protein level of melanocortin 1 receptor (Mc1r) and nuclear receptor subfamily 4, group A, member 2 (Nr4a2) in the AS mice cerebellum is decreased relative to that of the wild-type mice. Consistent with this finding, expression of small-interfering RNA that targets Ube3a in P19 cells caused downregulation of Mc1r and Nr4a2, whereas overexpression of Ube3a results in the upregulation of Mc1r and Nr4a2.
    [Show full text]
  • (Siberian Roe Deer and Grey Brocket Deer) Unravelled by Chromosome-Specific DNA Sequencing Alexey I
    Nova Southeastern University NSUWorks Biology Faculty Articles Department of Biological Sciences 8-11-2016 Contrasting Origin of B Chromosomes in Two Cervids (Siberian Roe Deer and Grey Brocket Deer) Unravelled by Chromosome-Specific DNA Sequencing Alexey I. Makunin Institute of Molecular and Cell Biology - Novosibirsk, Russia; St. Petersburg State University - Russia Ilya G. Kichigin Institute of Molecular and Cell Biology - Novosibirsk, Russia Denis M. Larkin University of London - United Kingdom Patricia C. M. O'Brien Cambridge University - United Kingdom Malcolm A. Ferguson-Smith University of Cambridge - United Kingdom See next page for additional authors Follow this and additional works at: https://nsuworks.nova.edu/cnso_bio_facarticles Part of the Animal Sciences Commons, and the Genetics and Genomics Commons NSUWorks Citation Makunin, Alexey I.; Ilya G. Kichigin; Denis M. Larkin; Patricia C. M. O'Brien; Malcolm A. Ferguson-Smith; Fengtang Yang; Anastasiya A. Proskuryakova; Nadezhda V. Vorobieva; Ekaterina N. Chernyaeva; Stephen J. O'Brien; Alexander S. Graphodatsky; and Vladimir Trifonov. 2016. "Contrasting Origin of B Chromosomes in Two Cervids (Siberian Roe Deer and Grey Brocket Deer) Unravelled by Chromosome-Specific DNA eS quencing." BMC Genomics 17, (618): 1-14. doi:10.1186/s12864-016-2933-6. This Article is brought to you for free and open access by the Department of Biological Sciences at NSUWorks. It has been accepted for inclusion in Biology Faculty Articles by an authorized administrator of NSUWorks. For more information, please contact [email protected]. Authors Alexey I. Makunin, Ilya G. Kichigin, Denis M. Larkin, Patricia C. M. O'Brien, Malcolm A. Ferguson-Smith, Fengtang Yang, Anastasiya A.
    [Show full text]
  • Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants Associated with Diabetic Nephropathy
    BASIC RESEARCH www.jasn.org Whole-Genome Sequencing of Finnish Type 1 Diabetic Siblings Discordant for Kidney Disease Reveals DNA Variants associated with Diabetic Nephropathy Jing Guo ,1,2 Owen J. L. Rackham ,2 Niina Sandholm ,3,4,5 Bing He ,1 Anne-May Österholm,1,2 Erkka Valo ,3,4,5 Valma Harjutsalo ,3,4,5,6 Carol Forsblom,3,4,5 Iiro Toppila,3,4,5 Maija Parkkonen,3,4,5 Qibin Li,7 Wenjuan Zhu,7 Nathan Harmston ,2,8 Sonia Chothani,2 Miina K. Öhman ,2 Eudora Eng,2 Yang Sun,2 Enrico Petretto ,2,9 Per-Henrik Groop,3,4,5,10 and Karl Tryggvason1,2,11 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background Several genetic susceptibility loci associated with diabetic nephropathy have been documen- ted, but no causative variants implying novel pathogenetic mechanisms have been elucidated. Methods We carried out whole-genome sequencing of a discovery cohort of Finnish siblings with type 1 diabetes who were discordant for the presence (case) or absence (control) of diabetic nephropathy. Con- trols had diabetes without complications for 15–37 years. We analyzed and annotated variants at genome, gene, and single-nucleotide variant levels. We then replicated the associated variants, genes, and regions in a replication cohort from the Finnish Diabetic Nephropathy study that included 3531 unrelated Finns with type 1 diabetes. Results We observed protein-altering variants and an enrichment of variants in regions associated with the presence or absence of diabetic nephropathy. The replication cohort confirmed variants in both regulatory and protein-coding regions.
    [Show full text]