DOCSLIB.ORG

In Vivo Transcriptional Profile Analysis Reveals RNA Splicing and Chromatin Remodeling As Prominent Processes for Adult Neurogenesis

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
In Vivo Transcriptional Profile Analysis Reveals RNA Splicing and Chromatin Remodeling As Prominent Processes for Adult Neurogenesis www.elsevier.com/locate/ymcne Mol. Cell. Neurosci. 31 (2006) 131 – 148 In vivo transcriptional profile analysis reveals RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis Daniel A. Lim,a,* Mayte Sua´rez-Farin˜as,b Felix Naef,b Coleen R. Hacker,c Benedicte Menn,a Hirohide Takebayashi,a Marcelo Magnasco,b Nila Patil,c and Arturo Alvarez-Buyllaa,* aDepartment of Neurological Surgery and Developmental and Stem Cell Biology Program, University of California, San Francisco, CA 94143, USA bThe Rockefeller University, 1230 York Ave., New York, NY 10021, USA cPerlegen Sciences Inc., 3380 Central Expressway, Santa Clara, CA 95051, USA Received 10 May 2005; revised 21 August 2005; accepted 4 October 2005 Available online 5 December 2005 Neural stem cells and neurogenesis persist in the adult mammalian SVZ neurogenesis and reveal RNA splicing and chromatin remodel- brain subventricular zone (SVZ). Cells born in the rodent SVZ ing as prominent biological processes for these germinal cells. migrate to the olfactory bulb (Ob) where they differentiate into D 2005 Elsevier Inc. All rights reserved. interneurons. To determine the gene expression and functional profile of SVZ neurogenesis, we performed three complementary Keywords: Subventricular zone (SVZ); Neurogenesis; Stem cell; Adult sets of transcriptional analysis experiments using Affymetrix brain; Microarray; Transcription; Transcriptional profile; Chromatin GeneChips: (1) comparison of adult mouse SVZ and Ob gene remodeling; RNA splicing expression profiles with those of the striatum, cerebral cortex, and hippocampus; (2) profiling of SVZ stem cells and ependyma isolated by fluorescent-activated cell sorting (FACS); and (3) analysis of gene expression changes during in vivo SVZ regeneration after anti- Introduction mitotic treatment. Gene Ontology (GO) analysis of data from these three separate approaches showed that in adult SVZ neurogenesis, The adult brain harbors neurogenic stem cells within the RNA splicing and chromatin remodeling are biological processes as statistically significant as cell proliferation, transcription, and subventricular zone (SVZ) of the lateral ventricle wall (Garcia- neurogenesis. In non-neurogenic brain regions, RNA splicing and Verdugo et al., 1998; Gage, 2000). In neonatal (Luskin, 1993) and chromatin remodeling were not prominent processes. Fourteen adult mice (Lois and Alvarez-Buylla, 1994; Doetsch and Alvarez- mRNA splicing factors including Sf3b1, Sfrs2, Lsm4, and Khdrbs1/ Buylla, 1996; Jankovski and Sotelo, 1996; Thomas et al., 1996), Sam68 were detected along with 9 chromatin remodeling genes cells born in the SVZ migrate a long distance to the olfactory bulb including Mll, Bmi1, Smarcad1, Baf53a, and Hat1. We validated the (Ob) where they differentiate into interneurons. SVZ astrocytes transcriptional profile data with Northern blot analysis and in situ (type B cells) are neural stem cells (Doetsch et al., 1999a,b; Laywell hybridization. The data greatly expand the catalogue of cell cycle et al., 2000) and give rise to rapidly dividing, immature-appearing components, transcription factors, and migration genes for adult cells (type C cells) that generate migratory neuroblasts (type A cells) (Lois and Alvarez-Buylla, 1994; Peretto et al., 1997; Luskin, 1998; Doetsch et al., 1999a,b). See Figs. 1B, C. SVZ ependymal cells are themselves not neurogenic (Chiasson et al., 1999; Laywell et al., 2000; Capela and Temple, 2002) but may be important for generating the SVZ neurogenic niche (Lim et al., 2000; Goldman, Abbreviations: SVZ, subventricular zone; Ob, olfactory bulb; ObC, 2003; Peretto et al., 2004). Although the SVZ cellular architecture olfactory bulb core; Ctx, cortex; St, striatum; Hp, hippocampus; ds cDNA, (Gates et al., 1995; Jankovski and Sotelo, 1996; Doetsch et al., double-stranded complementary DNA; cRNA, complementary (antisense) 1997; Peretto et al., 1997), stem cell identity (Chiasson et al., 1999; RNA; FACS, fluorescent-activated cell sorting; ECM, extracellular matrix; Doetsch et al., 1999a,b; Laywell et al., 2000; Rietze et al., 2001; RMS, rostral migratory stream; EGF, epidermal growth factor; FGF, fibroblast growth factor. Capela and Temple, 2002; Imura et al., 2003), and neurogenic * Corresponding authors. lineage (Doetsch et al., 1999a,b) have been defined, the genetic E-mail addresses: [email protected] (D.A. Lim), program for adult SVZ neurogenesis is poorly understood. [email protected] (A. Alvarez-Buylla). The transcriptional changes of differentiating neocortical (East- Available online on ScienceDirect (www.sciencedirect.com). erday et al., 2003; Karsten et al., 2003) and postnatal SVZ-derived 1044-7431/$ - see front matter D 2005 Elsevier Inc. All rights reserved. doi:10.1016/j.mcn.2005.10.005 132 D.A. Lim et al. / Mol. Cell. Neurosci. 31 (2006) 131–148 to have a similar migration capacity. Therefore, transcriptional analysis of in vivo SVZ neurogenesis is required to identify genes and biological processes involved in this continual generation of neurons for the Ob. Using high-density oligonucleotide (GeneChip) arrays, we undertook three complementary approaches to determine the transcriptional profile of in vivo SVZ neurogenesis. We first compared gene expression differences of the SVZ-Ob system with that of three other brain regions. We then utilized FACS methods to compare the transcriptional profiles of type B cells – the neurogenic stem cell – and the non-neurogenic ependyma. Finally, we analyzed the transcriptional changes of the SVZ as it regenerated type C and A cells from a population of type B cells. Data integrated from these three approaches identified genes, signaling pathways, and biological processes related to SVZ neurogenesis. In addition to expanding the catalogue of cell cycle components, transcription factors, and genes for migration, we identified RNA splicing and chromatin remodeling as prominent processes for adult neurogenesis. The importance of RNA splicing and chromatin remodeling has not been described for SVZ neuro- genesis, and we here provide evidence that these processes are as upregulated as the expected processes of cell cycle, transcription, and neurogenesis. We focused our Results and Discussion below only on a subset of genes with special attention to RNA splicing and chromatin remodeling, however, both the raw chip image data and other data analyses are available (Supplementary data and at http:// asterion.rockefeller.edu/mayte/Neurogenesis) for future compara- tive expression profile analyses with other developmental, adult, or tumor cell populations. Results Fig. 1. (A) Brain regions dissected for the brain region transcriptional analysis. Dissected areas are shown in yellow. The SVZ contains three Brain region transcriptional profile analysis identified genes with populations of neurogenic precursors—type B, C, and A cells. (B) The increased expression in the SVZ-ObC neurogenic system lineage of SVZ neurogenesis. Type B cells (blue) are SVZ astrocytes that self- renew and give rise to a rapidly dividing population of immature-appearing We analyzed the transcriptional profiles of the SVZ, Ob core cells—type C cells (green). The transit-amplifying type C cells then become (ObC), and three other brain regions indicated in Fig. 1A. The ObC type A cells (red), the neuroblasts that migrate into the ObC. (C) Architecture dissection excluded the mitral and periglomerular layers, providing a of the SVZ. The ventricle is to the left. Ciliated ependymal cells (gray) line RNA sample primarily representing migratory type A cells, the ventricle wall. Some type B cells (blue) make contact with the ventricle maturing neuroblasts, and mature granule cells. The hippocampus lumen (arrow). Both type C (green) and A cells (red) are in direct contact with (Hp) dissection included the non-neurogenic CA1–CA3 regions as the type B cells. In this panel, type A cells are migrating toward the ObC in a well the dentate gyrus. The striatum (St) was the region directly direction perpendicular to the page. (D) Sagittal view of the mouse brain. Within the SVZ, there is an extensive network of type A cells migrating underlying the SVZ dissection. The cortex (Ctx) did not include the tangentially toward the ObC. This network of pathways coalesces at the corpus callosum. Biotin-labeled complementary RNAs (cRNAs) anterior of the SVZ to form the rostral migratory stream (curved arrow). The derived from each brain region were analyzed on GeneChip Mu11k rostral migratory stream enters the ObC where type A cells then migrate expression arrays, which contain more than 13,000 probe sets radially and disperse (red dots) throughout the Ob. The major biological analyzing the expression of over 11,000 unique genes. Each brain processes that occur in the SVZ alone (SVZ profile), SVZ and ObC (SO region was analyzed independently twice; the data among the profile), and ObC alone (ObC profile) are listed to the left, middle, and right, duplicates were consistent (Supplementary data S1). respectively; the cell types of the SVZ and ObC profiles are in bold. To focus our analysis on those genes more likely to be involved in SVZ neurogenesis, we filtered the data (see Experimental (Gurok et al., 2004) neurospheres have also been studied in vitro. methods) for those genes that are (1) increased in the SVZ—the Many neurospheres are derived from transit-amplifying cells (type SVZ profile, (2) increased in the ObC—the ObC profile, and (3) C cells) (Doetsch et al., 2002), and their exposure
Load more

Recommended publications
  • Molecular Basis for the Distinct Cellular Functions of the Lsm1-7 and Lsm2-8 Complexes
    bioRxiv preprint doi: https://doi.org/10.1101/2020.04.22.055376; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes Eric J. Montemayor1,2, Johanna M. Virta1, Samuel M. Hayes1, Yuichiro Nomura1, David A. Brow2, Samuel E. Butcher1 1Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA. 2Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA. Correspondence should be addressed to E.J.M. ([email protected]) and S.E.B. ([email protected]). Abstract Eukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1-7 complex initiates mRNA decay, while the nuclear Lsm2-8 complex acts as a chaperone for U6 spliceosomal RNA. It has been unclear how these complexes perform their distinct functions while differing by only one out of seven subunits. Here, we elucidate the molecular basis for Lsm-RNA recognition and present four high-resolution structures of Lsm complexes bound to RNAs. The structures of Lsm2-8 bound to RNA identify the unique 2′,3′ cyclic phosphate end of U6 as a prime determinant of specificity. In contrast, the Lsm1-7 complex strongly discriminates against cyclic phosphates and tightly binds to oligouridylate tracts with terminal purines.
    [Show full text]
  • Bppart and Bpmax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model
    BPPart and BPMax: RNA-RNA Interaction Partition Function and Structure Prediction for the Base Pair Counting Model Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, and Hamidreza Chitsaz ∗ Department of Computer Science, Colorado State University Abstract A few elite classes of RNA-RNA interaction (RRI), with complex roles in cellular functions such as miRNA-target and lncRNAs in human health, have already been studied. Accordingly, RRI bioinfor- matics tools tailored for those elite classes have been proposed in the last decade. Interestingly, there are somewhat unnoticed mRNA-mRNA interactions in the literature with potentially drastic biological roles. Hence, there is a need for high-throughput generic RRI bioinformatics tools. We revisit our RRI partition function algorithm, piRNA, which happens to be the most comprehensive and computationally-intensive thermodynamic model for RRI. We propose simpler models that are shown to retain the vast majority of the thermodynamic information that piRNA captures. We simplify the energy model and instead consider only weighted base pair counting to obtain BPPart for Base-pair Partition function and BPMax for Base-pair Maximization which are 225 and 1350 faster ◦ × × than piRNA, with a correlation of 0.855 and 0.836 with piRNA at 37 C on 50,500 experimentally charac- terized RRIs. This correlation increases to 0.920 and 0.904, respectively, at 180◦C. − Finally, we apply our algorithm BPPart to discover two disease-related RNAs, SNORD3D and TRAF3, and hypothesize their potential roles in Parkinson's disease and Cerebral Autosomal Dominant Arteri- opathy with Subcortical Infarcts and Leukoencephalopathy (CADASIL). 1 Introduction Since mid 1990s with the advent of RNA interference discovery, RNA-RNA interaction (RRI) has moved to the spotlight in modern, post-genome biology.
    [Show full text]
  • Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
    Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement.
    [Show full text]
  • Dissertation
    Regulation of gene silencing: From microRNA biogenesis to post-translational modifications of TNRC6 complexes DISSERTATION zur Erlangung des DOKTORGRADES DER NATURWISSENSCHAFTEN (Dr. rer. nat.) der Fakultät Biologie und Vorklinische Medizin der Universität Regensburg vorgelegt von Johannes Danner aus Eggenfelden im Jahr 2017 Das Promotionsgesuch wurde eingereicht am: 12.09.2017 Die Arbeit wurde angeleitet von: Prof. Dr. Gunter Meister Johannes Danner Summary ‘From microRNA biogenesis to post-translational modifications of TNRC6 complexes’ summarizes the two main projects, beginning with the influence of specific RNA binding proteins on miRNA biogenesis processes. The fate of the mature miRNA is determined by the incorporation into Argonaute proteins followed by a complex formation with TNRC6 proteins as core molecules of gene silencing complexes. miRNAs are transcribed as stem-loop structured primary transcripts (pri-miRNA) by Pol II. The further nuclear processing is carried out by the microprocessor complex containing the RNase III enzyme Drosha, which cleaves the pri-miRNA to precursor-miRNA (pre-miRNA). After Exportin-5 mediated transport of the pre-miRNA to the cytoplasm, the RNase III enzyme Dicer cleaves off the terminal loop resulting in a 21-24 nt long double-stranded RNA. One of the strands is incorporated in the RNA-induced silencing complex (RISC), where it directly interacts with a member of the Argonaute protein family. The miRNA guides the mature RISC complex to partially complementary target sites on mRNAs leading to gene silencing. During this process TNRC6 proteins interact with Argonaute and recruit additional factors to mediate translational repression and target mRNA destabilization through deadenylation and decapping leading to mRNA decay.
    [Show full text]
  • Analysis of Alternative Splicing Associated with Aging and Neurodegeneration in the Human Brain
    Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Research Analysis of alternative splicing associated with aging and neurodegeneration in the human brain James R. Tollervey,1 Zhen Wang,1 Tibor Hortoba´gyi,2 Joshua T. Witten,1 Kathi Zarnack,3 Melis Kayikci,1 Tyson A. Clark,4 Anthony C. Schweitzer,4 Gregor Rot,5 Tomazˇ Curk,5 Blazˇ Zupan,5 Boris Rogelj,2 Christopher E. Shaw,2 and Jernej Ule1,6 1MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, United Kingdom; 2MRC Centre for Neurodegeneration Research, King’s College London, Institute of Psychiatry, De Crespigny Park, London SE5 8AF, United Kingdom; 3EMBL–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom; 4Expression Research, Affymetrix, Inc., Santa Clara, California 95051, USA; 5Faculty of Computer and Information Science, University of Ljubljana, Trzˇasˇka 25, SI-1000 Ljubljana, Slovenia Age is the most important risk factor for neurodegeneration; however, the effects of aging and neurodegeneration on gene expression in the human brain have most often been studied separately. Here, we analyzed changes in transcript levels and alternative splicing in the temporal cortex of individuals of different ages who were cognitively normal, affected by frontotemporal lobar degeneration (FTLD), or affected by Alzheimer’s disease (AD). We identified age-related splicing changes in cognitively normal individuals and found that these were present also in 95% of individuals with FTLD or AD, independent of their age. These changes were consistent with increased polypyrimidine tract binding protein (PTB)– dependent splicing activity. We also identified disease-specific splicing changes that were present in individuals with FTLD or AD, but not in cognitively normal individuals.
    [Show full text]
  • Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation Chip-Sequencing Data Processing Pipeline
    Bioinformatics Tools for the Analysis of Gene-Phenotype Relationships Coupled with a Next Generation ChIP-Sequencing Data Processing Pipeline Erinija Pranckeviciene Thesis submitted to the Faculty of Graduate and Postdoctoral Studies in partial fulfillment of the requirements for the Doctorate in Philosophy degree in Cellular and Molecular Medicine Department of Cellular and Molecular Medicine Faculty of Medicine University of Ottawa c Erinija Pranckeviciene, Ottawa, Canada, 2015 Abstract The rapidly advancing high-throughput and next generation sequencing technologies facilitate deeper insights into the molecular mechanisms underlying the expression of phenotypes in living organisms. Experimental data and scientific publications following this technological advance- ment have rapidly accumulated in public databases. Meaningful analysis of currently avail- able data in genomic databases requires sophisticated computational tools and algorithms, and presents considerable challenges to molecular biologists without specialized training in bioinfor- matics. To study their phenotype of interest molecular biologists must prioritize large lists of poorly characterized genes generated in high-throughput experiments. To date, prioritization tools have primarily been designed to work with phenotypes of human diseases as defined by the genes known to be associated with those diseases. There is therefore a need for more prioritiza- tion tools for phenotypes which are not related with diseases generally or diseases with which no genes have yet been associated in particular. Chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) is a method of choice to study the gene regulation processes responsible for the expression of cellular phenotypes. Among publicly available computational pipelines for the processing of ChIP-Seq data, there is a lack of tools for the downstream analysis of composite motifs and preferred binding distances of the DNA binding proteins.
    [Show full text]
  • Supplementary Table 3 Gene Microarray Analysis: PRL+E2 Vs
    Supplementary Table 3 Gene microarray analysis: PRL+E2 vs. control ID1 Field1 ID Symbol Name M Fold P Value 69 15562 206115_at EGR3 early growth response 3 2,36 5,13 4,51E-06 56 41486 232231_at RUNX2 runt-related transcription factor 2 2,01 4,02 6,78E-07 41 36660 227404_s_at EGR1 early growth response 1 1,99 3,97 2,20E-04 396 54249 36711_at MAFF v-maf musculoaponeurotic fibrosarcoma oncogene homolog F 1,92 3,79 7,54E-04 (avian) 42 13670 204222_s_at GLIPR1 GLI pathogenesis-related 1 (glioma) 1,91 3,76 2,20E-04 65 11080 201631_s_at IER3 immediate early response 3 1,81 3,50 3,50E-06 101 36952 227697_at SOCS3 suppressor of cytokine signaling 3 1,76 3,38 4,71E-05 16 15514 206067_s_at WT1 Wilms tumor 1 1,74 3,34 1,87E-04 171 47873 238623_at NA NA 1,72 3,30 1,10E-04 600 14687 205239_at AREG amphiregulin (schwannoma-derived growth factor) 1,71 3,26 1,51E-03 256 36997 227742_at CLIC6 chloride intracellular channel 6 1,69 3,23 3,52E-04 14 15038 205590_at RASGRP1 RAS guanyl releasing protein 1 (calcium and DAG-regulated) 1,68 3,20 1,87E-04 55 33237 223961_s_at CISH cytokine inducible SH2-containing protein 1,67 3,19 6,49E-07 78 32152 222872_x_at OBFC2A oligonucleotide/oligosaccharide-binding fold containing 2A 1,66 3,15 1,23E-05 1969 32201 222921_s_at HEY2 hairy/enhancer-of-split related with YRPW motif 2 1,64 3,12 1,78E-02 122 13463 204015_s_at DUSP4 dual specificity phosphatase 4 1,61 3,06 5,97E-05 173 36466 227210_at NA NA 1,60 3,04 1,10E-04 117 40525 231270_at CA13 carbonic anhydrase XIII 1,59 3,02 5,62E-05 81 42339 233085_s_at OBFC2A oligonucleotide/oligosaccharide-binding
    [Show full text]
  • Mrna Editing, Processing and Quality Control in Caenorhabditis Elegans
    | WORMBOOK mRNA Editing, Processing and Quality Control in Caenorhabditis elegans Joshua A. Arribere,*,1 Hidehito Kuroyanagi,†,1 and Heather A. Hundley‡,1 *Department of MCD Biology, UC Santa Cruz, California 95064, †Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and ‡Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405 ABSTRACT While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes. KEYWORDS Caenorhabditis elegans; splicing; RNA editing; RNA modification; polyadenylation; quality control; WormBook TABLE OF CONTENTS Abstract 531 RNA Editing and Modification 533 Adenosine-to-inosine RNA editing 533 The C. elegans A-to-I editing machinery 534 RNA editing in space and time 535 ADARs regulate the levels and fates of endogenous dsRNA 537 Are other modifications present in C.
    [Show full text]
  • Chromosome 17Q25 Genes, RHBDF2 and CYGB, in Ovarian Cancer
    INTERNATIONAL JOURNAL OF ONCOLOGY 40: 1865-1880, 2012 Chromosome 17q25 genes, RHBDF2 and CYGB, in ovarian cancer PAULINA M. WOJNAROWICZ1, DIANE M. PROVENCHER2-4, ANNE-MARIE MES-MASSON2,5 and PATRICIA N. TONIN1,6,7 1Department of Human Genetics, McGill University; 2Research Centre of the University of Montreal Hospital Centre (CRCHUM)/Montreal Cancer Institute; 3Division of Gynecologic Oncology, University of Montreal; 4Department of Obstetrics and Gynecology, University of Montreal; 5Department of Medicine, University of Montreal; 6The Research Institute of the McGill University Health Centre; 7Department of Medicine, McGill University, Montreal, Quebec, Canada Received November 15, 2011; Accepted December 29, 2011 DOI: 10.3892/ijo.2012.1371 Abstract. It has been proposed that the frequent loss of Introduction heterozygosity (LOH) of an entire chromosome 17 contig in epithelial ovarian cancers (EOC) is the consequence of It is well established that loss of chromosome 17 is a common the inactivation of multiple tumour suppressor genes on this occurrence in epithelial ovarian cancers (EOCs), as suggested chromosome. We report the characterization of a 453 Kb 17q25 by karyotype and loss of heterozygosity (LOH) studies (1,2). locus shown previously to exhibit a high frequency of LOH This observation, together with complementation studies in EOC samples. LOH analysis further defined the minimal involving the transfer of chromosome 17 which resulted in region of deletion to a 65 Kb interval flanked by D17S2239 reduced tumourigenicity of an EOC cell line (3), suggest that and D17S2244, which contains RHBDF2, CYGB and PRCD as this chromosome harbours tumour suppressor genes (TSGs). tumour suppressor gene candidates. Tissue specific expression Chromosome 17 contains a number of very well characterized excluded PRCD as a candidate.
    [Show full text]
  • Global Profiles of Gene Expression Induced by Adrenocorticotropin in Y1 Mouse Adrenal Cells
    0013-7227/06/$15.00/0 Endocrinology 147(5):2357–2367 Printed in U.S.A. Copyright © 2006 by The Endocrine Society doi: 10.1210/en.2005-1526 Global Profiles of Gene Expression Induced by Adrenocorticotropin in Y1 Mouse Adrenal Cells Bernard P. Schimmer, Martha Cordova, Henry Cheng, Andrew Tsao, Andrew B. Goryachev, Aaron D. Schimmer, and Quaid Morris Banting and Best Department of Medical Research (B.P.S., M.C., H.C., A.T., A.B.G., Q.M.), Department of Pharmacology (B.P.S.) and Department of Computer Science (Q.M.), University of Toronto, Princess Margaret Hospital and Ontario Cancer Institute (A.D.S.), Toronto, Ontario, Canada M5G 1L6 ACTH regulates the steroidogenic capacity, size, and struc- transcripts, i.e. only 10% of the ACTH-affected transcripts, tural integrity of the adrenal cortex through a series of actions were represented in the categories above; most of these had involving changes in gene expression; however, only a limited not been described as ACTH-regulated previously. The con- number of ACTH-regulated genes have been identified, and tributions of protein kinase A and protein kinase C to these these only partly account for the global effects of ACTH on the genome-wide effects of ACTH were evaluated in microarray adrenal cortex. In this study, a National Institute on Aging 15K experiments after treatment of Y1 cells and derivative protein mouse cDNA microarray was used to identify genome-wide kinase A-defective mutants with pharmacological probes of changes in gene expression after treatment of Y1 mouse ad- each pathway. Protein kinase A-dependent signaling ac- renocortical cells with ACTH.
    [Show full text]
  • Renoprotective Effect of Combined Inhibition of Angiotensin-Converting Enzyme and Histone Deacetylase
    BASIC RESEARCH www.jasn.org Renoprotective Effect of Combined Inhibition of Angiotensin-Converting Enzyme and Histone Deacetylase † ‡ Yifei Zhong,* Edward Y. Chen, § Ruijie Liu,*¶ Peter Y. Chuang,* Sandeep K. Mallipattu,* ‡ ‡ † | ‡ Christopher M. Tan, § Neil R. Clark, § Yueyi Deng, Paul E. Klotman, Avi Ma’ayan, § and ‡ John Cijiang He* ¶ *Department of Medicine, Mount Sinai School of Medicine, New York, New York; †Department of Nephrology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China; ‡Department of Pharmacology and Systems Therapeutics and §Systems Biology Center New York, Mount Sinai School of Medicine, New York, New York; |Baylor College of Medicine, Houston, Texas; and ¶Renal Section, James J. Peters Veterans Affairs Medical Center, New York, New York ABSTRACT The Connectivity Map database contains microarray signatures of gene expression derived from approximately 6000 experiments that examined the effects of approximately 1300 single drugs on several human cancer cell lines. We used these data to prioritize pairs of drugs expected to reverse the changes in gene expression observed in the kidneys of a mouse model of HIV-associated nephropathy (Tg26 mice). We predicted that the combination of an angiotensin-converting enzyme (ACE) inhibitor and a histone deacetylase inhibitor would maximally reverse the disease-associated expression of genes in the kidneys of these mice. Testing the combination of these inhibitors in Tg26 mice revealed an additive renoprotective effect, as suggested by reduction of proteinuria, improvement of renal function, and attenuation of kidney injury. Furthermore, we observed the predicted treatment-associated changes in the expression of selected genes and pathway components. In summary, these data suggest that the combination of an ACE inhibitor and a histone deacetylase inhibitor could have therapeutic potential for various kidney diseases.
    [Show full text]
  • (Mir-539-5P) Interaction and Its Potential Impact on the NSCLC Risk
    Feng et al. Journal of Experimental & Clinical Cancer Research (2020) 39:157 https://doi.org/10.1186/s13046-020-01652-5 RESEARCH Open Access A SNP-mediated lncRNA (LOC146880) and microRNA (miR-539-5p) interaction and its potential impact on the NSCLC risk Tienan Feng1,2†, Nannan Feng1†, Tengteng Zhu1, Qiang Li1, Qi Zhang1, Yu Wang1, Ming Gao3, Baosen Zhou4, Herbert Yu5, Min Zheng6 and Biyun Qian1,7* Abstract Background: Many cancer-associated single nucleotide polymorphisms (SNPs) are located in the genomic regions of long non-coding RNAs (lncRNAs). Mechanisms of these SNPs in connection to cancer risk are not fully understood. Methods: Association of SNP (rs140618127) in lncRNA LOC146880 with non-small cell lung cancer (NSCLC) was evaluated in a case-control study of 2707 individuals. The mechanism of the SNP’s biologic influence was explored with in vitro and in vivo experiments, including plasmid transfection, siRNA knockdown, flow cytometry assessment, and assays of cell proliferation, migration, invasion, and colony formation. Results: Association analysis showed that A allele of SNP rs140618127 was associated with low risk of NSCLC in the Chinese population. Lab experiments indicated that SNP rs140618127 contained a binding site for miR-539-5p and the binding between miR-539-5p and LOC146880 resulted in declined phosphorylation of an oncogene, ENO1. The reduced phosphorylation of ENO1 led to decreased phosphorylation of PI3K and Akt, which is further linked to the decline in cell proliferation and tumor progression. Conclusion: The study demonstrates that SNP rs140618127 in lncRNA loc146880 provides an alternate binding site for microRNA miR-539-5p which affects the phosphorylation of ENO1 and activation of the PI3K and Akt pathway.
    [Show full text]