DOCSLIB.ORG

Derived Neurons of Children with Neurodevelopmental Disorders

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Derived Neurons of Children with Neurodevelopmental Disorders Alterations in Transcription and Connectivity in Stem Cell- Derived Neurons of Children with Neurodevelopmental Disorders by Kirill Zaslavsky A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Molecular Genetics University of Toronto © Copyright by Kirill Zaslavsky 2017 Alterations in Transcription and Connectivity in Stem Cell-Derived Neurons of Children with Neurodevelopmental Disorders Kirill Zaslavsky Doctor of Philosophy Department of Molecular Genetics University of Toronto 2017 Abstract Many neurodevelopmental disorders (NDD) have a genetic etiology. Some arise from mutations at a specific locus whereas others are polygenic. For example, Williams-Beuren Syndrome (WBS) is caused by hemizygous deletions at 7q11.23 that result in intellectual disability and increased socialization. In contrast, autism spectrum disorder (ASD) is common, results in impaired socialization, and has a polygenic, sex-dependent pattern of inheritance. While these NDDs involve genes in transcription and synapse function, it has been challenging to discover associated neuronal phenotypes owing to a lack of suitable human tissue. The recent development of human induced pluripotent stem cells (IPSC) allows to bridge this gap by providing a renewable source of neurons specific to individuals with NDDs. To examine transcription, I used IPSCs from a child with WBS and two children with ASD with mutations at the PTCHD1/PTCHD1AS locus, which encodes a protein and long non-coding RNA (lncRNA) of unknown function. In WBS neurons, I found an overall reduction in expression of synapse, voltage-gated potassium channel and extracellular matrix genes. In ASD neurons, I found a reduction in genes involved in RNA splicing, export, cellular respiration, and an increase in ii extracellular matrix genes. The large range of transcriptional alterations suggests that mechanisms of disease in these NDDs are complex and varied. To assess synaptic connectivity in ASD, I compared IPSC-derived neurons from two cases with mutations in SHANK2, a synaptic scaffolding gene, and engineered SHANK2 knockouts to parental and isogenic controls. Because heterogeneity among IPSC-derived neurons can compromise connectivity comparisons, I developed a Sparse coculture for Connectivity (SparCon) assay that increases statistical power by sparsely plating differentially labeled control and mutant neurons onto a lawn of unlabeled control neurons. Using SparCon, I found that dendrite complexity and total synapse number are increased in SHANK2 mutant cells, which was paralleled by increased excitatory synaptic activity. These findings are the first example of excitatory hyperconnectivity in IPSC-derived neurons from subjects with ASD and provide evidence that SHANK2 functions in early neuronal development as a suppressor of dendrite branching. In summary, IPSC-derived neurons are beginning to reveal transcriptional and synaptic neuronal phenotypes in vitro that are associated with NDDs. As the model system matures, methodological refinements like SparCon will further increase the ability of this system to discover disease phenotypes. Investigating alterations in transcription of synaptic genes in WBS, RNA splicing in PTCHD1/PTCHD1AS ASD, and hyperconnectivity in SHANK2 ASD will yield further insight into the pathophysiology of these NDDs. iii Acknowledgments The PhD is a physically and mentally draining process. I would not have been able to complete it without the support of my laboratory, my supervisor, my dear friends, and relatives. In particular, I want to thank my supervisor James Ellis for giving me the opportunity to work in his lab and for allowing me to pursue my ideas. I am indebted to Joel Ross for inspiring me to work in this field. I am lucky I have found a great friend in labmate Deivid Rodrigues, who helped me keep Fresh Start in business by dutifully buying coffee every day and lending a patient ear. He has helped me shape my ideas and has been crucial source of support. I would also like to thank Eric Deneault, for I have not seen anybody that works harder. My work would also not have been possible without the great support of the lab technicians who help us feed and differentiate our cells – namely Alina Piekna, Wei Wei, and Asli Romm. Peter Pasceri, our lab manager, made the lab a welcoming and warm place to work. I also thank Rebecca Mok for helpful discussions on the project. My friends have been an unwavering source of support. I’d like to thank Ilya Mukovozov, who has been by my side for the past 7 years going through MD and PhD together. Richard Wu has been the most amazing workout buddy and has kept me focused. I would be remiss if I did not acknowledge others that have helped me through it all: Rob Vanner for being a great mentor, Brian Ballios for always being an inspiration, Amanda Khan for her unwavering positivity and support, Priya Dhir for listening to me rant about things that almost always turned out better than I expected, and Richard Gao for being my one of my best friends since grade 8. Lastly, this would not have been possible without the support of my parents. I thank my mother, Elena, who is the living embodiment of the American Dream, an immigrant who arrived with nothing and achieved so much. I am also thankful to my father, Ilya, for helpful discussion iv and support. I am constantly inspired by my little brother, Maxim, who is the smartest person I know and at the age of 20 is set to begin grad school. I cannot wait to see what you will accomplish. v Table of Contents Acknowledgments ........................................................................................................................ iv Table of Contents ......................................................................................................................... vi List of Tables ................................................................................................................................. x List of Figures ............................................................................................................................... xi Chapter 1 Introduction ................................................................................................................ 1 1.1 Overview of NDDs ......................................................................................................................1 1.2 Overview of WBS .......................................................................................................................3 1.2.1 Brief History of WBS ..............................................................................................................3 1.2.2 Neurodevelopmental Alterations in WBS ................................................................................4 1.2.3 Genetic Architecture of WBS ..................................................................................................5 1.2.4 Structural brain changes in WBS .............................................................................................7 1.2.5 Transcriptional and connectivity alterations in WBS ..............................................................8 1.3 1.3 Overview of ASD ................................................................................................................10 1.3.1 Brief history of ASD ..............................................................................................................10 1.3.2 Diagnosis and Clinical Presentation ......................................................................................12 1.3.3 Genetic Architecture of ASD .................................................................................................14 1.3.4 Transcriptional and morphological alterations in post-mortem ASD brains .........................20 1.3.5 Genetic evidence for PTCHD1/PTCHD1AS ..........................................................................22 1.3.6 Genetic evidence for SHANK2 ...............................................................................................23 1.4 SHANK proteins are critical for development of synaptic connectivity. ............................24 1.4.1 SHANKs coordinate synapse development and function ......................................................25 1.4.2 SHANK1, SHANK2, and SHANK3 have overlapping and distinct functions. ....................27 1.4.3 Non-synaptic roles of SHANK ..............................................................................................29 1.4.4 Mouse models of SHANK2-associated ASD exhibit inconsistent phenotypes ......................30 1.5 IPSC in NDD modeling & Drug Discovery ............................................................................32 1.5.1 Gene editing in human iPSC ..................................................................................................33 1.5.2 Three Broad Types of Neuronal Differentiation Protocols ....................................................36 1.5.3 Recent Progress in IPSC models of NDDs ............................................................................41 1.5.4 Challenges in IPSC models of NDDs. ...................................................................................43 1.6 1.6 Rationale ..............................................................................................................................46 vi Chapter 2 Transcriptional Alterations in WBS and ASD ....................................................... 49 ....................................................................................................................................................
Load more

Recommended publications
  • Exploring the Mechanisms Underlying Excitation/Inhibition Imbalance in Human Ipsc-Derived Models of ASD Lorenza Culotta1,3 and Peter Penzes1,2,3*
    Culotta and Penzes Molecular Autism (2020) 11:32 https://doi.org/10.1186/s13229-020-00339-0 REVIEW Open Access Exploring the mechanisms underlying excitation/inhibition imbalance in human iPSC-derived models of ASD Lorenza Culotta1,3 and Peter Penzes1,2,3* Abstract Autism spectrum disorder (ASD) is a range of neurodevelopmental disorders characterized by impaired social interaction and communication, and repetitive or restricted behaviors. ASD subjects exhibit complex genetic and clinical heterogeneity, thus hindering the discovery of pathophysiological mechanisms. Considering that several ASD-risk genes encode proteins involved in the regulation of synaptic plasticity, neuronal excitability, and neuronal connectivity, one hypothesis that has emerged is that ASD arises from a disruption of the neuronal network activity due to perturbation of the synaptic excitation and inhibition (E/I) balance. The development of induced pluripotent stem cell (iPSC) technology and recent advances in neuronal differentiation techniques provide a unique opportunity to model complex neuronal connectivity and to test the E/I hypothesis of ASD in human-based models. Here, we aim to review the latest advances in studying the different cellular and molecular mechanisms contributing to E/I balance using iPSC-based in vitro models of ASD. Keywords: Autism spectrum disorder, Induced pluripotent stem cell, Excitation/inhibition balance Background ASD can be classified into syndromic and non- Autism spectrum disorder (ASD) represents a spectrum of syndromic forms [4–7]. Syndromic ASD accounts for a early-onset neurodevelopmental disorders characterized by small percentage of total ASD cases; it typically occurs persistent deficits in social interaction and communication, with a clinical presentation in association with secondary as well as repetitive patterns of behavior and restricted inter- phenotypes and/or dysmorphic features [6].
    [Show full text]
  • Identification and Functional Characterization of Rare SHANK2
    OPEN Molecular Psychiatry (2015) 20, 1489–1498 © 2015 Macmillan Publishers Limited All rights reserved 1359-4184/15 www.nature.com/mp ORIGINAL ARTICLE Identification and functional characterization of rare SHANK2 variants in schizophrenia S Peykov1, S Berkel1, M Schoen2, K Weiss3, F Degenhardt4, J Strohmaier5, B Weiss1, C Proepper2, G Schratt3, MM Nöthen4,5, TM Boeckers2, M Rietschel6 and GA Rappold1,7 Recent genetic data on schizophrenia (SCZ) have suggested that proteins of the postsynaptic density of excitatory synapses have a role in its etiology. Mutations in the three SHANK genes encoding for postsynaptic scaffolding proteins have been shown to represent risk factors for autism spectrum disorders and other neurodevelopmental disorders. To address if SHANK2 variants are associated with SCZ, we sequenced SHANK2 in 481 patients and 659 unaffected individuals. We identified a significant increase in the number of rare (minor allele frequencyo1%) SHANK2 missense variants in SCZ individuals (6.9%) compared with controls (3.9%, P = 0.039). Four out of fifteen non-synonymous variants identified in the SCZ cohort (S610Y, R958S, P1119T and A1731S) were selected for functional analysis. Overexpression and knockdown-rescue experiments were carried out in cultured primary hippocampal neurons with a major focus on the analysis of morphological changes. Furthermore, the effect on actin polymerization in fibroblast cell lines was investigated. All four variants revealed functional impairment to various degrees, as a consequence of alterations in spine volume and clustering at synapses and an overall loss of presynaptic contacts. The A1731S variant was identified in four unrelated SCZ patients (0.83%) but not in any of the sequenced controls and public databases (P = 4.6 × 10 − 5).
    [Show full text]
  • Lysine-Specific Demethylase 1 Is Strongly Expressed in Poorly Differentiated Neuroblastoma: Implications for Therapy
    Published OnlineFirst February 17, 2009; DOI: 10.1158/0008-5472.CAN-08-1735 Research Article Lysine-Specific Demethylase 1 Is Strongly Expressed in Poorly Differentiated Neuroblastoma: Implications for Therapy Johannes H. Schulte,1 Soyoung Lim,3 Alexander Schramm,1 Nicolaus Friedrichs,3 Jan Koster,4 Rogier Versteeg,4 Ingrid Ora,4,5 Kristian Pajtler,1 Ludger Klein-Hitpass,2 Steffi Kuhfittig-Kulle,1 Eric Metzger,6 Roland Schu¨le,6 Angelika Eggert,1 Reinhard Buettner,3 and Jutta Kirfel3 1Department of Paediatric Oncology and Hematology, University Children’s Hospital Essen; 2Institute of Cell Biology, University Hospital of Essen, Essen, Germany; 3Institute of Pathology, University of Bonn, Bonn, Germany; 4Department of Human Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands; 5Department of Pediatric Oncology and Hematology, Lund University Hospital, Lund, Sweden; 6Center for Clinical Research, Freiburg University Medical Center, Freiburg, Germany Abstract often fatally progresses regardless of multimodal therapy (1, 2). Aberrant epigenetic changes in DNA methylation and histone Therefore, the identification of novel drug targets and development acetylation are hallmarks of most cancers, whereas histone of new therapeutic options are urgently needed. Patterns methylation was previously considered to be irreversible and characteristic of aggressive neuroblastoma have been identified less versatile. Recently, several histone demethylases were via high-throughput analysis, including expression profiling (3, 4) identified catalyzing the removal of methyl groups from histone and array CGH (5–7), with NMYC amplification, 1p36 and 11q H3 lysine residues and thereby influencing gene expression. deletion (8), and 17q gain being the most prominent chromosomal Neuroblastomas continue to remain a clinical challenge alterations.
    [Show full text]
  • Structural Variation Targets Neurodevelopmental Genes and Identifies SHANK2 As a Tumor
    bioRxiv preprint doi: https://doi.org/10.1101/572248; this version posted March 13, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Structural Variation in Neuroblastoma Lopez, Conkrite, et al. Structural variation targets neurodevelopmental genes and identifies SHANK2 as a tumor suppressor in neuroblastoma Gonzalo Lopez1,2+, Karina L. Conkrite1,2+, Miriam Doepner1,2, Komal S. Rathi3, Apexa Modi1,2,10, Zalman Vaksman1-3, Lance M. Farra1,2, Eric Hyson1,2, Moataz Noureddine1,2, Jun S. Wei4, Malcolm A. Smith9, Shahab Asgharzadeh5,6, Robert C. Seeger5,6, Javed Khan4, Jaime Guidry Auvil8, Daniela S. Gerhard8, John M. Maris1-2,10,11, Sharon J. Diskin1-3,10,11* 1Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA. 2Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA. 3Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA. 4Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA 5Division of Hematology, Oncology and Blood and Marrow Transplantation, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA. 6The Saban Research Institute, Children’s Hospital of Los Angeles, Los Angeles, CA, USA. 7Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. 8Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA. 9Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, MD, USA. 10Genomics and Computational Biology, Biomedical Graduate Studies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
    [Show full text]
  • Homer1 Promotes Dendritic Spine Growth Through Ankyrin-G and Its Loss Reshapes the Synaptic Proteome
    Molecular Psychiatry (2021) 26:1775–1789 https://doi.org/10.1038/s41380-020-00991-1 ARTICLE Homer1 promotes dendritic spine growth through ankyrin-G and its loss reshapes the synaptic proteome 1 1 2 1,5 2 Sehyoun Yoon ● Nicolas H. Piguel ● Natalia Khalatyan ● Leonardo E. Dionisio ● Jeffrey N. Savas ● Peter Penzes 1,3,4 Received: 22 February 2020 / Revised: 24 November 2020 / Accepted: 7 December 2020 / Published online: 4 January 2021 © The Author(s), under exclusive licence to Springer Nature Limited part of Springer Nature 2021. This article is published with open access Abstract Homer1 is a synaptic scaffold protein that regulates glutamatergic synapses and spine morphogenesis. HOMER1 knockout (KO) mice show behavioral abnormalities related to psychiatric disorders, and HOMER1 has been associated with psychiatric disorders such as addiction, autism disorder (ASD), schizophrenia (SZ), and depression. However, the mechanisms by which it promotes spine stability and its global function in maintaining the synaptic proteome has not yet been fully investigated. Here, we used computational approaches to identify global functions for proteins containing the Homer1-interacting PPXXF motif within the postsynaptic compartment. Ankyrin-G was one of the most topologically important nodes in the postsynaptic peripheral 1234567890();,: 1234567890();,: membrane subnetwork, and we show that one of the PPXXF motifs, present in the postsynaptically-enriched 190 kDa isoform of ankyrin-G (ankyrin-G 190), is recognized by the EVH1 domain of Homer1. We use proximity ligation combined with super- resolution microscopy to map the interaction of ankyrin-G and Homer1 to distinct nanodomains within the spine head and correlate them with spine head size.
    [Show full text]
  • 8P23.2-Pter Microdeletions: Seven New Cases Narrowing the Candidate Region and Review of the Literature
    G C A T T A C G G C A T genes Article 8p23.2-pter Microdeletions: Seven New Cases Narrowing the Candidate Region and Review of the Literature Ilaria Catusi 1,* , Maria Garzo 1 , Anna Paola Capra 2 , Silvana Briuglia 2 , Chiara Baldo 3 , Maria Paola Canevini 4 , Rachele Cantone 5, Flaviana Elia 6, Francesca Forzano 7, Ornella Galesi 8, Enrico Grosso 5, Michela Malacarne 3, Angela Peron 4,9,10 , Corrado Romano 11 , Monica Saccani 4 , Lidia Larizza 1 and Maria Paola Recalcati 1 1 Istituto Auxologico Italiano, IRCCS, Laboratory of Medical Cytogenetics and Molecular Genetics, 20145 Milan, Italy; [email protected] (M.G.); [email protected] (L.L.); [email protected] (M.P.R.) 2 Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, 98100 Messina, Italy; [email protected] (A.P.C.); [email protected] (S.B.) 3 UOC Laboratorio di Genetica Umana, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy; [email protected] (C.B.); [email protected] (M.M.) 4 Child Neuropsychiatry Unit—Epilepsy Center, Department of Health Sciences, ASST Santi Paolo e Carlo, San Paolo Hospital, Università Degli Studi di Milano, 20142 Milan, Italy; [email protected] (M.P.C.); [email protected] (A.P.); [email protected] (M.S.) 5 Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; [email protected] (R.C.); [email protected] (E.G.) 6 Unit of Psychology, Oasi Research Institute-IRCCS,
    [Show full text]
  • LGI1–ADAM22–MAGUK Configures Transsynaptic Nanoalignment for Synaptic Transmission and Epilepsy Prevention
    LGI1–ADAM22–MAGUK configures transsynaptic nanoalignment for synaptic transmission and epilepsy prevention Yuko Fukataa,b,1, Xiumin Chenc,d,1, Satomi Chikenb,e, Yoko Hiranoa,f, Atsushi Yamagatag, Hiroki Inahashia, Makoto Sanboh, Hiromi Sanob,e, Teppei Gotoh, Masumi Hirabayashib,h, Hans-Christian Kornaui,j, Harald Prüssi,k, Atsushi Nambub,e, Shuya Fukail, Roger A. Nicollc,d,2, and Masaki Fukataa,b,2 aDivision of Membrane Physiology, Department of Molecular and Cellular Physiology, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Aichi 444-8787, Japan; bDepartment of Physiological Sciences, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Aichi 444-8585, Japan; cDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158; dDepartment of Physiology, University of California, San Francisco, CA 94158; eDivision of System Neurophysiology, Department of System Neuroscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Aichi 444-8585, Japan; fDepartment of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan; gLaboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Kanagawa 230-0045, Japan; hCenter for Genetic Analysis of Behavior, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki 444-8787, Japan; iGerman Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany; jNeuroscience Research Center, Cluster NeuroCure, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; kDepartment of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany; and lDepartment of Chemistry, Graduate School of Science, Kyoto University, 606-8502 Kyoto, Japan Contributed by Roger A. Nicoll, December 1, 2020 (sent for review October 29, 2020; reviewed by David S.
    [Show full text]
  • An Overview of the Main Genetic, Epigenetic and Environmental Factors Involved in Autism Spectrum Disorder Focusing on Synaptic Activity
    International Journal of Molecular Sciences Review An Overview of the Main Genetic, Epigenetic and Environmental Factors Involved in Autism Spectrum Disorder Focusing on Synaptic Activity 1, 1, 1 2 Elena Masini y, Eleonora Loi y, Ana Florencia Vega-Benedetti , Marinella Carta , Giuseppe Doneddu 3, Roberta Fadda 4 and Patrizia Zavattari 1,* 1 Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042 Cagliari, Italy; [email protected] (E.M.); [email protected] (E.L.); [email protected] (A.F.V.-B.) 2 Center for Pervasive Developmental Disorders, Azienda Ospedaliera Brotzu, 09121 Cagliari, Italy; [email protected] 3 Centro per l’Autismo e Disturbi correlati (CADc), Nuovo Centro Fisioterapico Sardo, 09131 Cagliari, Italy; [email protected] 4 Department of Pedagogy, Psychology, Philosophy, University of Cagliari, 09123 Cagliari, Italy; [email protected] * Correspondence: [email protected] The authors contributed equally to this work. y Received: 30 September 2020; Accepted: 30 October 2020; Published: 5 November 2020 Abstract: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects social interaction and communication, with restricted interests, activity and behaviors. ASD is highly familial, indicating that genetic background strongly contributes to the development of this condition. However, only a fraction of the total number of genes thought to be associated with the condition have been discovered. Moreover, other factors may play an important role in ASD onset. In fact, it has been shown that parental conditions and in utero and perinatal factors may contribute to ASD etiology. More recently, epigenetic changes, including DNA methylation and micro RNA alterations, have been associated with ASD and proposed as potential biomarkers.
    [Show full text]
  • The Human Gene Connectome As a Map of Short Cuts for Morbid Allele Discovery
    The human gene connectome as a map of short cuts for morbid allele discovery Yuval Itana,1, Shen-Ying Zhanga,b, Guillaume Vogta,b, Avinash Abhyankara, Melina Hermana, Patrick Nitschkec, Dror Friedd, Lluis Quintana-Murcie, Laurent Abela,b, and Jean-Laurent Casanovaa,b,f aSt. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065; bLaboratory of Human Genetics of Infectious Diseases, Necker Branch, Paris Descartes University, Institut National de la Santé et de la Recherche Médicale U980, Necker Medical School, 75015 Paris, France; cPlateforme Bioinformatique, Université Paris Descartes, 75116 Paris, France; dDepartment of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; eUnit of Human Evolutionary Genetics, Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Institut Pasteur, F-75015 Paris, France; and fPediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, 75015 Paris, France Edited* by Bruce Beutler, University of Texas Southwestern Medical Center, Dallas, TX, and approved February 15, 2013 (received for review October 19, 2012) High-throughput genomic data reveal thousands of gene variants to detect a single mutated gene, with the other polymorphic genes per patient, and it is often difficult to determine which of these being of less interest. This goes some way to explaining why, variants underlies disease in a given individual. However, at the despite the abundance of NGS data, the discovery of disease- population level, there may be some degree of phenotypic homo- causing alleles from such data remains somewhat limited. geneity, with alterations of specific physiological pathways under- We developed the human gene connectome (HGC) to over- come this problem.
    [Show full text]
  • Dlgap1 Knockout Mice Exhibit Alterations of the Postsynaptic
    www.nature.com/scientificreports OPEN Dlgap1 knockout mice exhibit alterations of the postsynaptic density and selective reductions in Received: 11 October 2017 Accepted: 16 January 2018 sociability Published: xx xx xxxx M. P. Coba 3, M. J. Ramaker1, E. V. Ho1, S. L. Thompson1,2, N. H. Komiyama4, S. G. N. Grant 4, J. A. Knowles3 & S. C. Dulawa1 The scafold protein DLGAP1 is localized at the post-synaptic density (PSD) of glutamatergic neurons and is a component of supramolecular protein complexes organized by PSD95. Gain-of-function variants of DLGAP1 have been associated with obsessive-compulsive disorder (OCD), while haploinsufcient variants have been linked to autism spectrum disorder (ASD) and schizophrenia in human genetic studies. We tested male and female Dlgap1 wild type (WT), heterozygous (HT), and knockout (KO) mice in a battery of behavioral tests: open feld, dig, splash, prepulse inhibition, forced swim, nest building, social approach, and sucrose preference. We also used biochemical approaches to examine the role of DLGAP1 in the organization of PSD protein complexes. Dlgap1 KO mice were most notable for disruption of protein interactions in the PSD, and defcits in sociability. Other behavioral measures were largely unafected. Our data suggest that Dlgap1 knockout leads to PSD disruption and reduced sociability, consistent with reports of DLGAP1 haploinsufcient variants in schizophrenia and ASD. Te Disks Large Associated Protein 1 gene encodes the protein DLGAP1 (also known as GKAP or SAPAP1), which localizes at the postsynaptic density (PSD)1–7. Genetic variants of DLGAP1 and abnormalities of the PSD have been associated with neuropsychiatric disorders including schizophrenia8, autism spectrum disorder (ASD)9, and obsessive-compulsive disorder (OCD)10.
    [Show full text]
  • Supplementary Material for Spatio-Temporal Gene Discovery for Autism Spectrum Disorder
    Supplementary Material for Spatio-temporal Gene Discovery for Autism Spectrum Disorder Utku Norman and A. Ercument Cicek 1 Supplementary Tables Supplementary Table 1: MAGI genes found by running MAGI on de novo counts of De Rubeis et al. 2014 as case data and the control data provided in Hormozdiari et al. 2015 only. MAGI Best1 (M1_Best in MAGI’s terminology) is a module with maximum score and contains 47 genes (highlighted with *). MAGI Ext1 (M1_Extended) is the union of high-scoring suboptimal modules and includes 104 genes. See Hormozdiari et al. 2015 for details. Algorithm is run for 310,000+ iterations. The genes included in both Best1 and Ext1 are in bold. Note that MAGI Best1 ⊂ MAGI Ext1. ACTB* CBX5* CUL1* GTPBP4 MAP2K6* PPP1R8 RPL12 SMAD2* SNW1 UBE2I ACTL6A CCT4 DHX15* HDAC2 MAPK14 PRPF6* RSF1 SMAD4 SP1 UBE2N ADNP* CCT5 DMAP1* HNRNPK MDM2 PSMD3 RTF1 SMARCA5 SRC WDR5* AKT1 CDC73* DVL2 HNRNPR* MECP2 PSMD9 RUVBL1 SMARCB1 SRPK2 YWHAG ARID1B* CHD8* DYNC1H1 ILF2 MLL* PTEN SF3A2* SMARCC1* SRRM2* ZFAND5 ATF2 CHMP1A DYRK1A* JUP MLL3* RB1 SF3B1* SMARCC2* STRN3 AXIN1* CREB1 EP300* KAT5 MSH2 RBBP5* SF3B2* SMARCD1 TAF4* BAZ1B* CSNK1E* FAM40A KIAA1967* MYC* RELA* SFRS4 SMARCE1* TCF3* BCL11A* CSNK2A1 FBXW11* LDB1 NCOR1* REST SIN3A* SMURF1* TCF4* BRAF CSNK2A2 GORAB LEO1* NFKB1 RLIM SIRT1* SMURF2 TEX10 CASP2 CTNNB1* GSK3B* LRP5* PIAS1* RPL11 SKI* SNIP1 TRAF6 Supplementary Table 2: MAGI genes found by running MAGI on de novo counts of De Rubeis et al. 2014 as case data and the control data provided in Hormozdiari et al. 2015. only, after removing the genes in MAGI Best1.
    [Show full text]
  • Deletion of 11Q in Neuroblastomas Drives Sensitivity to PARP Inhibition Elena Sanmartín1,2, Lisandra Munoz~ 1,2, Marta Piqueras3, J
    Published OnlineFirst August 22, 2017; DOI: 10.1158/1078-0432.CCR-17-0593 Personalized Medicine and Imaging Clinical Cancer Research Deletion of 11q in Neuroblastomas Drives Sensitivity to PARP Inhibition Elena Sanmartín1,2, Lisandra Munoz~ 1,2, Marta Piqueras3, J. Antoni Sirerol1,2, Pablo Berlanga2,4, Adela Canete~ 2,4, Victoria Castel2,4, and Jaime Font de Mora1,2 Abstract Purpose: Despite advances in multimodal therapy, neuroblas- define a subgroup of neuroblastomas with higher sensitivity to tomas with hemizygous deletion in chromosome 11q (20%– PARP inhibitors. Noteworthy, concomitant treatment with ola- 30%) undergo consecutive recurrences with poor outcome. We parib and DNA alkylating agent temozolomide potently inhibited hypothesized that patients with 11q-loss may share a druggable growth of cell lines harboring 11q-loss. This drug synergism was molecular target(s) that can be exploited for a precision medicine less potent when temozolomide was exchanged for cisplatin or strategy to improve treatment outcome. irinotecan. Intact 11q cells concomitantly treated with ATM Experimental Design: SNP arrays were combined with next- inhibitor displayed growth arrest and enhanced apoptosis, reveal- generation sequencing (NGS) to precisely define the deleted ing a role for ATM in the mechanism that mediates sensitivity to region in 17 primary 11q-loss neuroblastomas and identify allelic temozolomide–olaparib. Interestingly, functional TP53 is variants in genes relevant for neuroblastoma etiology. We required for efficacy of this treatment. In an in vivo model, assessed PARP inhibitor olaparib in combination with other coadministration of temozolomide–olaparib resulted in sus- chemotherapy medications using both in vitro and in vivo models. tained xenograft regression.
    [Show full text]