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Zaki ZMM, Ali SA, Ghazali MM, Jam FA. Genetic Modifications of Developmental Dyslexia and Its Representation Using In Vivo, In Vitro Model. Glob Med Genet 2024; 11:76-85. [PMID: 38414980 PMCID: PMC10898997 DOI: 10.1055/s-0044-1781456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024] Open
Abstract
Dyslexia is a genetic and heritable disorder that has yet to discover the treatment of it, especially at the molecular and drug intervention levels. This review provides an overview of the current findings on the environmental and genetic factors involved in developmental dyslexia. The latest techniques used in diagnosing the disease and macromolecular factors findings may contribute to a higher degree of development in detangling the proper management and treatment for dyslexic individuals. Furthermore, this review tried to put together all the models used in the current dyslexia research for references in future studies that include animal models as well as in vitro models and how the previous research has provided consistent data across many years and regions. Thus, we suggest furthering the studies using an organoid model based on the existing gene polymorphism, pathways, and neuronal function input.
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Affiliation(s)
- Zakiyyah M M Zaki
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Siti A Ali
- Department of Electronic Engineering, Faculty of Engineering and Green Technology, Universiti Tunku Abdul Rahman, Kampar, Perak, Malaysia
- Centre for Healthcare Science and Technology, Universiti Tunku Abdul Rahman, Kampar, Perak, Malaysia
| | - Mazira M Ghazali
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Faculty of Medicine, Universiti Sultan Zainal Abidin, Terengganu, Malaysia
| | - Faidruz A Jam
- Department of Biochemistry, Faculty of Medicine, Manipal University College Malaysia, Melaka, Malaysia
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2
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Bieder A, Chandrasekar G, Wason A, Erkelenz S, Gopalakrishnan J, Kere J, Tapia-Páez I. Genetic and protein interaction studies between the ciliary dyslexia candidate genes DYX1C1 and DCDC2. BMC Mol Cell Biol 2023; 24:20. [PMID: 37237337 DOI: 10.1186/s12860-023-00483-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND DYX1C1 (DNAAF4) and DCDC2 are two of the most replicated dyslexia candidate genes in genetic studies. They both have demonstrated roles in neuronal migration, in cilia growth and function and they both are cytoskeletal interactors. In addition, they both have been characterized as ciliopathy genes. However, their exact molecular functions are still incompletely described. Based on these known roles, we asked whether DYX1C1 and DCDC2 interact on the genetic and the protein level. RESULTS Here, we report the physical protein-protein interaction of DYX1C1 and DCDC2 as well as their respective interactions with the centrosomal protein CPAP (CENPJ) on exogenous and endogenous levels in different cell models including brain organoids. In addition, we show a synergistic genetic interaction between dyx1c1 and dcdc2b in zebrafish exacerbating the ciliary phenotype. Finally, we show a mutual effect on transcriptional regulation among DYX1C1 and DCDC2 in a cellular model. CONCLUSIONS In summary, we describe the physical and functional interaction between the two genes DYX1C1 and DCDC2. These results contribute to the growing understanding of the molecular roles of DYX1C1 and DCDC2 and set the stage for future functional studies.
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Affiliation(s)
- Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Arpit Wason
- Center for Molecular Medicine, Institute for Biochemistry I of the University of Cologne, Cologne, Germany
| | - Steffen Erkelenz
- Institute of Human Genetics, Universitätsklinikum, Heinrich Heine University, Düsseldorf, Germany
| | - Jay Gopalakrishnan
- Institute of Human Genetics, Universitätsklinikum, Heinrich Heine University, Düsseldorf, Germany
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Molecular Neurology Research Program, University of Helsinki, Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Isabel Tapia-Páez
- Department of Medicine, Solna, Karolinska Institutet, Solnavägen 30, SE-171 76, Solna, Sweden.
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3
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Guo T, Lu C, Yang D, Lei C, Liu Y, Xu Y, Yang B, Wang R, Luo H. Case Report: DNAAF4 Variants Cause Primary Ciliary Dyskinesia and Infertility in Two Han Chinese Families. Front Genet 2022; 13:934920. [PMID: 35903363 PMCID: PMC9315306 DOI: 10.3389/fgene.2022.934920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Primary ciliary dyskinesia (PCD) is a rare genetic disorder, predominantly autosomal recessive. The dynein axonemal assembly factor 4 (DNAAF4) is mainly involved in the preassembly of multisubunit dynein protein, which is fundamental to the proper functioning of cilia and flagella. There are few reports of PCD-related pathogenic variants of DNAAF4, and almost no DNAAF4-related articles focused on sperm phenotype. Moreover, the association between DNAAF4 and scoliosis has never been reported, to the best of our knowledge.Materials and Methods: We recruited two patients with a clinical diagnosis of PCD. One came from a consanguineous and another from a non-consanguineous family. Clinical data, laboratory test results, and imaging data were analyzed. Through whole exome sequencing, immunofluorescence, electron microscopy, high-speed video microscopy analysis, and hematoxylin–eosin (HE) staining, we identified the disease-associated variants and validated the pathogenicity.Results: Proband 1 (P1, F1: II-1), a 19-year-old man, comes from a non-consanguineous family-I, and proband 2 (P2, F2: II-1), a 37-year-old woman, comes from a consanguineous family-II. Both had sinusitis, bronchiectasis, situs inversus, and scoliosis. P1 also had asthenoteratozoospermia, and P2 had an immature uterus. Two homozygous pathogenic variants in DNAAF4 (NM_130810.4), c.988C > T, p.(Arg330Trp), and DNAAF4 (NM_130810.4), c.733 C > T, p.(Arg245*), were identified through whole exome sequencing. High-speed microscopy analysis showed that most of the cilia were static in P1, with complete static of the respiratory cilia in P2. Immunofluorescence showed that the outer dynein arms (ODA) and inner dynein arms (IDA) were absent in the respiratory cilia of both probands, as well as in the sperm flagellum of P1. Transmission electron microscopy revealed the absence of ODA and IDA of respiratory cilia of P2, and HE staining showed irregular, short, absent, coiled, and bent flagella.Conclusion: Our study identified a novel variant c.733C > T, which expanded the spectrum of DNAAF4 variants. Furthermore, we linked DNAAF4 to asthenoteratozoospermia and likely scoliosis in patients with PCD. This study will contribute to a better understanding of PCD.
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Affiliation(s)
- Ting Guo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Chenyang Lu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Danhui Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Cheng Lei
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Ying Liu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Yingjie Xu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Binyi Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
| | - Rongchun Wang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
- *Correspondence: Hong Luo, ; Rongchun Wang,
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital, Central South University, Changsha, China
- Research Unit of Respiratory Disease, Central South University, Changsha, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, China
- *Correspondence: Hong Luo, ; Rongchun Wang,
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4
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Drozd MM, Capovilla M, Previderé C, Grossi M, Askenazy F, Bardoni B, Fernandez A. A Pilot Study on Early-Onset Schizophrenia Reveals the Implication of Wnt, Cadherin and Cholecystokinin Receptor Signaling in Its Pathophysiology. Front Genet 2021; 12:792218. [PMID: 34976023 PMCID: PMC8719199 DOI: 10.3389/fgene.2021.792218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
Early-Onset Schizophrenia (EOS) is a very rare mental disorder that is a form of schizophrenia occurring before the age of 18. EOS is a brain disease marked by an early onset of positive and negative symptoms of psychosis that impact development and cognitive functioning. Clinical manifestations commonly include premorbid features of Autism Spectrum Disorder (ASD), attention deficits, Intellectual Disability (ID), neurodevelopmental delay, and behavioral disturbances. After the onset of psychotic symptoms, other neuropsychiatric comorbidities are also common, including obsessive-compulsive disorder, major depressive disorder, expressive and receptive language disorders, auditory processing, and executive functioning deficits. With the purpose to better gain insight into the genetic bases of this disorder, we developed a pilot project performing whole exome sequencing of nine trios affected by EOS, ASD, and mild ID. We carried out gene prioritization by combining multiple bioinformatic tools allowing us to identify the main pathways that could underpin the neurodevelopmental phenotypes of these patients. We identified the presence of variants in genes belonging to the Wnt, cadherin and cholecystokinin receptor signaling pathways.
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Affiliation(s)
- Malgorzata Marta Drozd
- Université Côte d’Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Maria Capovilla
- Université Côte d’Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Carlo Previderé
- Laboratorio di Genetica Forense, Unità di Medicina Legale e Scienze Forensi Antonio Fornari, Dipartimento di Sanità Pubblica, Medicina Sperimentale e Forense, Università di Pavia, Pavia, Italy
| | - Mauro Grossi
- Université Côte d’Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Florence Askenazy
- Département de Psychiatrie de l’Enfant et de l’Adolescent, Hôpitaux Pédiatriques de Nice, CHU-Lenval, Nice, France
- CoBTek, EA7276, Université Côte d’Azur, Valbonne, France
| | - Barbara Bardoni
- Université Côte d’Azur, Inserm, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
| | - Arnaud Fernandez
- Université Côte d’Azur, CNRS UMR7275, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France
- Département de Psychiatrie de l’Enfant et de l’Adolescent, Hôpitaux Pédiatriques de Nice, CHU-Lenval, Nice, France
- CoBTek, EA7276, Université Côte d’Azur, Valbonne, France
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5
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Manti PG, Trattaro S, Castaldi D, Pezzali M, Spaggiari L, Testa G. Thymic stroma and TFII-I: towards new targeted therapies. Trends Mol Med 2021; 28:67-78. [PMID: 34865984 DOI: 10.1016/j.molmed.2021.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/25/2021] [Accepted: 10/29/2021] [Indexed: 12/23/2022]
Abstract
Thymic epithelial tumors (TETs) have been characterized at the molecular level through bioptic sections and cell lines. Despite these advances, there is a need for a more thorough characterization of the thymic stroma in thymoma, particularly because of the diversity of cell types that populate the tumor and the absence of a healthy thymic counterpart. Recent work on healthy pediatric thymi - both in vitro and at the single-cell level - now sets the stage for new studies on their neoplastic counterparts. Furthermore, general transcription factor IIi (GTF2I), a thymoma-specific oncogene, as well as some of its SNPs, are increasingly associated with autoimmune disease, a significant feature of thymomas. We summarize recent discoveries in the field and discuss the development of new targeted therapies.
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Affiliation(s)
- Pierluigi Giuseppe Manti
- Department of Experimental Oncology, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Via Adamello 16, 20139, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy.
| | - Sebastiano Trattaro
- Department of Experimental Oncology, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Via Adamello 16, 20139, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy
| | - Davide Castaldi
- Department of Experimental Oncology, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Via Adamello 16, 20139, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy; Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Martina Pezzali
- Department of Experimental Oncology, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Via Adamello 16, 20139, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy; Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Lorenzo Spaggiari
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy; Division of Thoracic Surgery, European Institute of Oncology-IRCSS, Via Ripamonti 435, 20141 Milan, Italy
| | - Giuseppe Testa
- Department of Experimental Oncology, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Via Adamello 16, 20139, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20122 Milan, Italy.
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6
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Nelson MM, Hoff JD, Zeese ML, Corfas G. Poly (ADP-Ribose) Polymerase 1 Regulates Cajal-Retzius Cell Development and Neural Precursor Cell Adhesion. Front Cell Dev Biol 2021; 9:693595. [PMID: 34708032 PMCID: PMC8542860 DOI: 10.3389/fcell.2021.693595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is a ubiquitously expressed enzyme that regulates DNA damage repair, cell death, inflammation, and transcription. PARP1 functions by adding ADP-ribose polymers (PAR) to proteins including itself, using NAD+ as a donor. This post-translational modification known as PARylation results in changes in the activity of PARP1 and its substrate proteins and has been linked to the pathogenesis of various neurological diseases. PARP1 KO mice display schizophrenia-like behaviors, have impaired memory formation, and have defects in neuronal proliferation and survival, while mutations in genes that affect PARylation have been associated with intellectual disability, psychosis, neurodegeneration, and stroke in humans. Yet, the roles of PARP1 in brain development have not been extensively studied. We now find that loss of PARP1 leads to defects in brain development and increased neuronal density at birth. We further demonstrate that PARP1 loss increases the expression levels of genes associated with neuronal migration and adhesion in the E15.5 cerebral cortex, including Reln. This correlates with an increased number of Cajal–Retzius (CR) cells in vivo and in cultures of embryonic neural progenitor cells (NPCs) derived from the PARP1 KO cortex. Furthermore, PARP1 loss leads to increased NPC adhesion to N-cadherin, like that induced by experimental exposure to Reelin. Taken together, these results uncover a novel role for PARP1 in brain development, i.e., regulation of CR cells, neuronal density, and cell adhesion.
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Affiliation(s)
- Megan M Nelson
- Kresge Hearing Research Institute and Department of Otolaryngology - Head and Neck Surgery, University of Michigan, Ann Arbor, MI, United States.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
| | - J Damon Hoff
- Single Molecule Analysis in Real-Time Center, Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
| | - Mya L Zeese
- Kresge Hearing Research Institute and Department of Otolaryngology - Head and Neck Surgery, University of Michigan, Ann Arbor, MI, United States.,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Gabriel Corfas
- Kresge Hearing Research Institute and Department of Otolaryngology - Head and Neck Surgery, University of Michigan, Ann Arbor, MI, United States.,Neuroscience Graduate Program, University of Michigan, Ann Arbor, MI, United States
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7
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Wang HL, Yeh TH, Huang YZ, Weng YH, Chen RS, Lu CS, Wei KC, Liu YC, Chen YL, Chen CL, Chen YJ, Lin YW, Hsu CC, Chiu CH, Chiu CC. Functional variant rs17525453 within RAB35 gene promoter is possibly associated with increased risk of Parkinson's disease in Taiwanese population. Neurobiol Aging 2021; 107:189-196. [PMID: 34275689 DOI: 10.1016/j.neurobiolaging.2021.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 05/19/2021] [Accepted: 06/13/2021] [Indexed: 11/17/2022]
Abstract
Our previous study suggests that upregulated RAB35 is implicated in etiology of Parkinson's disease (PD). We hypothesized that upregulated RAB35 results from single nucleotide polymorphisms (SNPs) in RAB35 gene promoter. We identified SNPs within RAB35 gene promoter by analyzing DNA samples of discovery cohort and validation cohort. SNP rs17525453 within RAB35 gene promoter (T>C at position of -66) was significantly associated with idiopathic PD patients. Compared to normal controls, sporadic PD patients had higher C allele frequency. CC and CT genotype significantly increased risk of PD compared with TT genotype. SNP rs17525453 within RAB35 gene promoter leads to formation of transcription factor TFII-I binding site. Results of EMSA and supershift assay indicated that TFII-I binds to rs17525453 sequence of RAB35 gene promoter. Luciferase reporter assays showed that rs17525453 variant of RAB35 gene promoter possesses an augmented transcriptional activity. Our results suggest that functional variant rs17525453 within RAB35 gene promoter is likely to enhance transcriptional activity and upregulate RAB35 protein, which could lead to increased risk of PD in Taiwanese population.
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Affiliation(s)
- Hung-Li Wang
- Department of Physiology and Pharmacology, Chang Gung University College of Medicine, Taoyuan, Taiwan; Healthy Aging Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Movement Disorders, Department of Neurology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Tu-Hsueh Yeh
- Department of Neurology, Taipei Medical University Hospital, Taiwan
| | - Ying-Zu Huang
- Healthy Aging Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Movement Disorders, Department of Neurology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yi-Hsin Weng
- Healthy Aging Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Movement Disorders, Department of Neurology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Rou-Shayn Chen
- Healthy Aging Research Center, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Movement Disorders, Department of Neurology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chin-Song Lu
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Division of Movement Disorders, Department of Neurology, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Kuo-Chen Wei
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Neurosurgery, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Yu-Chuan Liu
- Landseed Sports Medicine Center, Landseed International Hospital, Taoyuan, Taiwan
| | - Ying-Ling Chen
- Department of Nursing, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Chao-Lang Chen
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Yu-Jie Chen
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Yan-Wei Lin
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Chia-Chen Hsu
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Chi-Han Chiu
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Ching-Chi Chiu
- Neuroscience Research Center, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan; Department of Nursing, Chang Gung University of Science and Technology, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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8
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Feng Z, Duren Z, Xiong Z, Wang S, Liu F, Wong WH, Wang Y. hReg-CNCC reconstructs a regulatory network in human cranial neural crest cells and annotates variants in a developmental context. Commun Biol 2021; 4:442. [PMID: 33824393 PMCID: PMC8024315 DOI: 10.1038/s42003-021-01970-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 03/09/2021] [Indexed: 12/19/2022] Open
Abstract
Cranial Neural Crest Cells (CNCC) originate at the cephalic region from forebrain, midbrain and hindbrain, migrate into the developing craniofacial region, and subsequently differentiate into multiple cell types. The entire specification, delamination, migration, and differentiation process is highly regulated and abnormalities during this craniofacial development cause birth defects. To better understand the molecular networks underlying CNCC, we integrate paired gene expression & chromatin accessibility data and reconstruct the genome-wide human Regulatory network of CNCC (hReg-CNCC). Consensus optimization predicts high-quality regulations and reveals the architecture of upstream, core, and downstream transcription factors that are associated with functions of neural plate border, specification, and migration. hReg-CNCC allows us to annotate genetic variants of human facial GWAS and disease traits with associated cis-regulatory modules, transcription factors, and target genes. For example, we reveal the distal and combinatorial regulation of multiple SNPs to core TF ALX1 and associations to facial distances and cranial rare disease. In addition, hReg-CNCC connects the DNA sequence differences in evolution, such as ultra-conserved elements and human accelerated regions, with gene expression and phenotype. hReg-CNCC provides a valuable resource to interpret genetic variants as early as gastrulation during embryonic development. The network resources are available at https://github.com/AMSSwanglab/hReg-CNCC .
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Affiliation(s)
- Zhanying Feng
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, China.,School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Zhana Duren
- Center for Human Genetics, Department of Genetics and Biochemistry, Clemson University, Greenwood, SC, USA.,Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA, USA
| | - Ziyi Xiong
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Sijia Wang
- Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Fan Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,China National Center for Bioinformation, Chinese Academy of Sciences, Beijing, China.
| | - Wing Hung Wong
- Department of Statistics, Department of Biomedical Data Science, Bio-X Program, Stanford University, Stanford, CA, USA.
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing, China. .,School of Mathematics, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. .,Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China.
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9
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Sahlén P, Spalinskas R, Asad S, Mahapatra KD, Höjer P, Anil A, Eisfeldt J, Srivastava A, Nikamo P, Mukherjee A, Kim KH, Bergman O, Ståhle M, Sonkoly E, Pivarcsi A, Wahlgren CF, Nordenskjöld M, Taylan F, Bradley M, Tapia-Páez I. Chromatin interactions in differentiating keratinocytes reveal novel atopic dermatitis- and psoriasis-associated genes. J Allergy Clin Immunol 2020; 147:1742-1752. [PMID: 33069716 DOI: 10.1016/j.jaci.2020.09.035] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/14/2020] [Accepted: 09/17/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Hundreds of variants associated with atopic dermatitis (AD) and psoriasis, 2 common inflammatory skin disorders, have previously been discovered through genome-wide association studies (GWASs). The majority of these variants are in noncoding regions, and their target genes remain largely unclear. OBJECTIVE We sought to understand the effects of these noncoding variants on the development of AD and psoriasis by linking them to the genes that they regulate. METHODS We constructed genomic 3-dimensional maps of human keratinocytes during differentiation by using targeted chromosome conformation capture (Capture Hi-C) targeting more than 20,000 promoters and 214 GWAS variants and combined these data with transcriptome and epigenomic data sets. We validated our results with reporter assays, clustered regularly interspaced short palindromic repeats activation, and examination of patient gene expression from previous studies. RESULTS We identified 118 target genes of 82 AD and psoriasis GWAS variants. Differential expression of 58 of the 118 target genes (49%) occurred in either AD or psoriatic lesions, many of which were not previously linked to any skin disease. We highlighted the genes AFG1L, CLINT1, ADO, LINC00302, and RP1-140J1.1 and provided further evidence for their potential roles in AD and psoriasis. CONCLUSIONS Our work focused on skin barrier pathology through investigation of the interaction profile of GWAS variants during keratinocyte differentiation. We have provided a catalogue of candidate genes that could modulate the risk of AD and psoriasis. Given that only 35% of the target genes are the gene nearest to the known GWAS variants, we expect that our work will contribute to the discovery of novel pathways involved in AD and psoriasis.
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Affiliation(s)
- Pelin Sahlén
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden.
| | - Rapolas Spalinskas
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Samina Asad
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kunal Das Mahapatra
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Pontus Höjer
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Anandashankar Anil
- KTH Royal Institute of Technology, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ankit Srivastava
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Pernilla Nikamo
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anaya Mukherjee
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Kyu-Han Kim
- Basic Research and Innovation Division, Research and Development Unit, AmorePacific Corporation, Yongin-si, Korea
| | - Otto Bergman
- Division of Cardiovascular Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Karolinska University Hospital, Solna, Sweden
| | - Mona Ståhle
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Enikö Sonkoly
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Dermatology Unit, Karolinska University Hospital, Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andor Pivarcsi
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Carl-Fredrik Wahlgren
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Bradley
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Dermatology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Isabel Tapia-Páez
- Dermatology and Venereology Division, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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10
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Benítez-Burraco A. Differences in the Neanderthal BRCA2 gene might be related to their distinctive cognitive profile. Hereditas 2018; 155:38. [PMID: 30564067 PMCID: PMC6291940 DOI: 10.1186/s41065-018-0076-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 11/28/2018] [Indexed: 11/23/2022] Open
Abstract
The unique divergence of the BRCA2 gene in Neanderthals compared to modern humans has been hypothesized to account for a differential susceptibility to cancer. However, the role of the gene in brain development and its connection with autism suggest that these differences might be (also) related to the more encapsulated nature of the Neanderthal cognition and their (inferred) autistic-like features.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), University of Seville, Seville, Spain
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11
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Müller B, Boltze J, Czepezauer I, Hesse V, Wilcke A, Kirsten H. Dyslexia risk variant rs600753 is linked with dyslexia-specific differential allelic expression of DYX1C1. Genet Mol Biol 2018; 41:41-49. [PMID: 29473935 PMCID: PMC5901500 DOI: 10.1590/1678-4685-gmb-2017-0165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/28/2017] [Indexed: 11/22/2022] Open
Abstract
An increasing number of genetic variants involved in dyslexia development were
discovered during the last years, yet little is known about the molecular
functional mechanisms of these SNPs. In this study we investigated whether
dyslexia candidate SNPs have a direct, disease-specific effect on local
expression levels of the assumed target gene by using a differential allelic
expression assay. In total, 12 SNPs previously associated with dyslexia and
related phenotypes were suitable for analysis. Transcripts corresponding to four
SNPs were sufficiently expressed in 28 cell lines originating from controls and
a family affected by dyslexia. We observed a significant effect of rs600753 on
expression levels of DYX1C1 in forward and reverse sequencing
approaches. The expression level of the rs600753 risk allele was increased in
the respective seven cell lines from members of the dyslexia family which might
be due to a disturbed transcription factor binding sites. When considering our
results in the context of neuroanatomical dyslexia-specific findings, we
speculate that this mechanism may be part of the pathomechanisms underlying the
dyslexia-specific brain phenotype. Our results suggest that allele-specific
DYX1C1 expression levels depend on genetic variants of
rs600753 and contribute to dyslexia. However, these results are preliminary and
need replication.
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Affiliation(s)
- Bent Müller
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Johannes Boltze
- Fraunhofer Research Institution for Marine Biotechnology, Department of Medical Cell Technology, Lübeck, Germany.,Institute for Medical and Marine Biotechnology, University of Lübeck, Lübeck, Germany
| | - Ivonne Czepezauer
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Volker Hesse
- German Center for Growth, Development and Health Encouragement in Childhood and Adolescence, Berlin, Germany.,Charité-University Medicine Berlin, Institute for Experimental Paediatric Endocrinolgy, Berlin
| | | | - Arndt Wilcke
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Holger Kirsten
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.,LIFE - Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
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12
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Ancestral Variations of the PCDHG Gene Cluster Predispose to Dyslexia in a Multiplex Family. EBioMedicine 2018; 28:168-179. [PMID: 29409727 PMCID: PMC5835549 DOI: 10.1016/j.ebiom.2017.12.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 12/22/2017] [Accepted: 12/28/2017] [Indexed: 12/15/2022] Open
Abstract
Dyslexia is a heritable neurodevelopmental disorder characterized by difficulties in reading and writing. In this study, we describe the identification of a set of 17 polymorphisms located across 1.9 Mb region on chromosome 5q31.3, encompassing genes of the PCDHG cluster, TAF7, PCDH1 and ARHGAP26, dominantly inherited with dyslexia in a multi-incident family. Strikingly, the non-risk form of seven variations of the PCDHG cluster, are preponderant in the human lineage, while risk alleles are ancestral and conserved across Neanderthals to non-human primates. Four of these seven ancestral variations (c.460A > C [p.Ile154Leu], c.541G > A [p.Ala181Thr], c.2036G > C [p.Arg679Pro] and c.2059A > G [p.Lys687Glu]) result in amino acid alterations. p.Ile154Leu and p.Ala181Thr are present at EC2: EC3 interacting interface of γA3-PCDH and γA4-PCDH respectively might affect trans-homophilic interaction and hence neuronal connectivity. p.Arg679Pro and p.Lys687Glu are present within the linker region connecting trans-membrane to extracellular domain. Sequence analysis indicated the importance of p.Ile154, p.Arg679 and p.Lys687 in maintaining class specificity. Thus the observed association of PCDHG genes encoding neural adhesion proteins reinforces the hypothesis of aberrant neuronal connectivity in the pathophysiology of dyslexia. Additionally, the striking conservation of the identified variants indicates a role of PCDHG in the evolution of highly specialized cognitive skills critical to reading. A set of seventeen common variations on chr5q31.3 co-segregate with dyslexia Ancestral risk forms are conserved throughoutNeanderthals to primates while non-risks are preponderant in modern humans p.Ile154Leu and p.Ala181Thr, present in interacting interface of EC2: EC3 Species specific isoform identity of p.Ile154Leu, p.Arg679Pro and p.Lys687Glu
Worldwide epidemiological data suggests that one in every ten children is affected with dyslexia which is an alarming number and possesses a serious burden on mental health. We identified single nucleotide variations on protocadherin gamma (PCDHG) gene cluster co-segregate with dyslexia in a multiincident family. The described variants present on the interacting domain of protocadherin gamma reiterates the underlying dysregulated functional connectivity in dyslexia pathophysiology. This finding may help toward understanding the basic molecular mechanisms of dyslexia, and may help in identifying points of therapeutic intervention.
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13
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Benítez-Burraco A, Barcos-Martínez M, Espejo-Portero I, Fernández-Urquiza M, Torres-Ruiz R, Rodríguez-Perales S, Jiménez-Romero MS. Narrowing the Genetic Causes of Language Dysfunction in the 1q21.1 Microduplication Syndrome. Front Pediatr 2018; 6:163. [PMID: 29922639 PMCID: PMC5996825 DOI: 10.3389/fped.2018.00163] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/15/2018] [Indexed: 12/22/2022] Open
Abstract
The chromosome 1q21.1 duplication syndrome (OMIM# 612475) is characterized by head anomalies, mild facial dysmorphisms, and cognitive problems, including autistic features, mental retardation, developmental delay, and learning disabilities. Speech and language development are sometimes impaired, but no detailed characterization of language problems in this condition has been provided to date. We report in detail on the cognitive and language phenotype of a child who presents with a duplication in 1q21.1 (arr[hg19] 1q21.1q21.2(145,764,455-147,824,207) × 3), and who exhibits cognitive delay and behavioral disturbances. Language is significantly perturbed, being the expressive domain the most impaired area (with significant dysphemic features in absence of pure motor speech deficits), although language comprehension and use (pragmatics) are also affected. Among the genes found duplicated in the child, CDH1L is upregulated in the blood of the proband. ROBO1, a candidate for dyslexia, is also highly upregulated, whereas, TLE3, a target of FOXP2, is significantly downregulated. These changes might explain language, and particularly speech dysfunction in the proband.
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Affiliation(s)
- Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, University of Seville, Seville, Spain
| | - Montserrat Barcos-Martínez
- Laboratory of Molecular Genetics, University Hospital "Reina Sofía", Córdoba, Spain.,Maimónides Institute of Biomedical Research, Córdoba, Spain
| | - Isabel Espejo-Portero
- Laboratory of Molecular Genetics, University Hospital "Reina Sofía", Córdoba, Spain.,Maimónides Institute of Biomedical Research, Córdoba, Spain
| | | | - Raúl Torres-Ruiz
- Molecular Cytogenetics Group, Centro Nacional Investigaciones Oncológicas, Madrid, Spain
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14
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Abbott RD, Raskind WH, Matsushita M, Price ND, Richards T, Berninger VW. Patterns of biomarkers for three phenotype profiles of persisting specific learning disabilities during middle childhood and early adolescence: A preliminary study. BIOMARKERS AND GENES 2017; 1:103. [PMID: 30854516 PMCID: PMC6407889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Students without specific learning disabilities [SLDs] [n=18] and with one of three persisting SLDs in written language despite early and current specialized instruction-Dysgraphia [n=21], Dyslexia [n=40], or oral and written language learning disability OWL LD [n=14]- in grades 4 to 9 [N=56 boys, 38 girls] completed behavioral phenotyping assessment and gave a small blood or saliva sample. Molecular analyses informed by current cross-site research on gene candidates for learning disabilities identified associations between molecular genetic markers and the two defining behavioral phenotypes for each SLDs-WL; dysgraphia [impaired writing alphabet from memory for rs3743204 and sentence copying in best handwriting for rs79382 both in DYX1C1], dyslexia [impaired silent word reading/decoding rate for rs4535189 in DCDC2 and impaired spelling/encoding for rs374205 in DYX1C1], and OWL LD [impaired aural syntax comprehension for rs807701 and oral syntax construction for rs807701 both in DYX1C1]. Implications of these identified associations between molecular markers for alleles for different sites within two gene candidates [and mostly one] and hallmark phenotypes are discussed for translation science [application to practice] and neuroimaging that has identified contrasting brain bases for each of the three SLDs.
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Affiliation(s)
- Robert D. Abbott
- University of Washington, Quantitative Studies and Measurement, USA
| | - Wendy H. Raskind
- University of Washington, Medicine, USA,University of Washington, Psychiatry and Behavioral Sciences, USA
| | | | - Nathan D. Price
- Institute for Systems Biology, USA,University of Washington, Bioengineering, Computer Science & Engineering, Molecular & Cellular Biology, USA
| | - Todd Richards
- University of Washington, Integrated Brain Imaging Center and Radiology, USA
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15
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Thomas-Jinu S, Gordon PM, Fielding T, Taylor R, Smith BN, Snowden V, Blanc E, Vance C, Topp S, Wong CH, Bielen H, Williams KL, McCann EP, Nicholson GA, Pan-Vazquez A, Fox AH, Bond CS, Talbot WS, Blair IP, Shaw CE, Houart C. Non-nuclear Pool of Splicing Factor SFPQ Regulates Axonal Transcripts Required for Normal Motor Development. Neuron 2017; 94:322-336.e5. [PMID: 28392072 PMCID: PMC5405110 DOI: 10.1016/j.neuron.2017.03.026] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/02/2017] [Accepted: 03/17/2017] [Indexed: 12/12/2022]
Abstract
Recent progress revealed the complexity of RNA processing and its association to human disorders. Here, we unveil a new facet of this complexity. Complete loss of function of the ubiquitous splicing factor SFPQ affects zebrafish motoneuron differentiation cell autonomously. In addition to its nuclear localization, the protein unexpectedly localizes to motor axons. The cytosolic version of SFPQ abolishes motor axonal defects, rescuing key transcripts, and restores motility in the paralyzed sfpq null mutants, indicating a non-nuclear processing role in motor axons. Novel variants affecting the conserved coiled-coil domain, so far exclusively found in fALS exomes, specifically affect the ability of SFPQ to localize in axons. They broadly rescue morphology and motility in the zebrafish mutant, but alter motor axon morphology, demonstrating functional requirement for axonal SFPQ. Altogether, we uncover the axonal function of the splicing factor SFPQ in motor development and highlight the importance of the coiled-coil domain in this process. Video Abstract
SFPQ splicing factor is present in motor axons Non-nuclear SFPQ is able to drive axon maturation and connectivity Loss of axonal SFPQ affects axonal morphology Coiled-coil domain of the protein is important for non-nuclear localization
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Affiliation(s)
- Swapna Thomas-Jinu
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Patricia M Gordon
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Triona Fielding
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Richard Taylor
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Bradley N Smith
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Victoria Snowden
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Eric Blanc
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Caroline Vance
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Simon Topp
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Chun-Hao Wong
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Holger Bielen
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Kelly L Williams
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Emily P McCann
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Garth A Nicholson
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia; ANZAC Research Institute, University of Sydney, Concord Hospital, Sydney, NSW 2139, Australia
| | - Alejandro Pan-Vazquez
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK
| | - Archa H Fox
- School of Anatomy, Physiology, and Human Biology, University of Western Australia, Crawley, WA 6009, Australia; Harry Perkins Institute for Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia; Centre for Medical Research, University of Western Australia, Crawley, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, University of Western Australia, Crawley, WA 6009, Australia
| | - William S Talbot
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ian P Blair
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London SE5 8AF, UK
| | - Corinne Houart
- Centre for Developmental Neurobiology and MRC CNDD, IoPPN, Guy's Campus, King's College London, London SE1 1UL, UK.
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16
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Jubin T, Kadam A, Gani AR, Singh M, Dwivedi M, Begum R. Poly ADP-ribose polymerase-1: Beyond transcription and towards differentiation. Semin Cell Dev Biol 2017; 63:167-179. [PMID: 27476447 DOI: 10.1016/j.semcdb.2016.07.027] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 07/27/2016] [Indexed: 02/07/2023]
Abstract
Gene regulation mediates the processes of cellular development and differentiation leading to the origin of different cell types each having their own signature gene expression profile. However, the compact chromatin structure and the timely recruitment of molecules involved in various signaling pathways are of prime importance for temporal and spatial gene regulation that eventually contribute towards cell type and specificity. Poly (ADP-ribose) polymerase-1 (PARP-1), a 116-kDa nuclear multitasking protein is involved in modulation of chromatin condensation leading to altered gene expression. In response to activation signals, it adds ADP-ribose units to various target proteins including itself, thus regulating various key cellular processes like DNA repair, cell death, transcription, mRNA splicing etc. This review provides insights into the role of PARP-1 in gene regulation, cell differentiation and multicellular morphogenesis. In addition, the review also explores involvement of PARP-1 in immune cells development and therapeutic possibilities to treat various human diseases.
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Affiliation(s)
- Tina Jubin
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India
| | - Ashlesha Kadam
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India
| | - Amina Rafath Gani
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India; Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046 Telangana, India
| | - Mala Singh
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India
| | - Mitesh Dwivedi
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India; C.G. Bhakta Institute of Biotechnology, Faculty of Science, Uka Tarsadia University, Surat, Gujarat 394350, India
| | - Rasheedunnisa Begum
- Department of Biochemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat 390002, India.
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17
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Genes, Gender, Environment, and Novel Functions of Estrogen Receptor Beta in the Susceptibility to Neurodevelopmental Disorders. Brain Sci 2017; 7:brainsci7030024. [PMID: 28241485 PMCID: PMC5366823 DOI: 10.3390/brainsci7030024] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 12/30/2022] Open
Abstract
Many neurological disorders affect men and women differently regarding prevalence, progression, and severity. It is clear that many of these disorders may originate from defective signaling during fetal or perinatal brain development, which may affect males and females differently. Such sex-specific differences may originate from chromosomal or sex-hormone specific effects. This short review will focus on the estrogen receptor beta (ERβ) signaling during perinatal brain development and put it in the context of sex-specific differences in neurodevelopmental disorders. We will discuss ERβ’s recent discovery in directing DNA de-methylation to specific sites, of which one such site may bear consequences for the susceptibility to the neurological reading disorder dyslexia. We will also discuss how dysregulations in sex-hormone signaling, like those evoked by endocrine disruptive chemicals, may affect this and other neurodevelopmental disorders in a sex-specific manner through ERβ.
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18
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Role of Splice Variants of Gtf2i, a Transcription Factor Localizing at Postsynaptic Sites, and Its Relation to Neuropsychiatric Diseases. Int J Mol Sci 2017; 18:ijms18020411. [PMID: 28212274 PMCID: PMC5343945 DOI: 10.3390/ijms18020411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/01/2017] [Accepted: 02/09/2017] [Indexed: 12/17/2022] Open
Abstract
We previously reported that various mRNAs were associated with postsynaptic density (PSD) purified from rat forebrain. Among the thousands of PSD-associated mRNAs, we highlight the biology of the general transcription factor II-I (Gtf2i) mRNA, focusing on the significance of its versatile splicing for targeting its own mRNA into dendrites, regulation of translation, and the effects of Gtf2i expression level as well as its relationship with neuropsychiatric disorders.
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19
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Garcez PP, Nascimento JM, de Vasconcelos JM, Madeiro da Costa R, Delvecchio R, Trindade P, Loiola EC, Higa LM, Cassoli JS, Vitória G, Sequeira PC, Sochacki J, Aguiar RS, Fuzii HT, de Filippis AMB, da Silva Gonçalves Vianez Júnior JL, Tanuri A, Martins-de-Souza D, Rehen SK. Zika virus disrupts molecular fingerprinting of human neurospheres. Sci Rep 2017; 7:40780. [PMID: 28112162 PMCID: PMC5256095 DOI: 10.1038/srep40780] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/09/2016] [Indexed: 11/08/2022] Open
Abstract
Zika virus (ZIKV) has been associated with microcephaly and other brain abnormalities; however, the molecular consequences of ZIKV to human brain development are still not fully understood. Here we describe alterations in human neurospheres derived from induced pluripotent stem (iPS) cells infected with the strain of Zika virus that is circulating in Brazil. Combining proteomics and mRNA transcriptional profiling, over 500 proteins and genes associated with the Brazilian ZIKV infection were found to be differentially expressed. These genes and proteins provide an interactome map, which indicates that ZIKV controls the expression of RNA processing bodies, miRNA biogenesis and splicing factors required for self-replication. It also suggests that impairments in the molecular pathways underpinning cell cycle and neuronal differentiation are caused by ZIKV. These results point to biological mechanisms implicated in brain malformations, which are important to further the understanding of ZIKV infection and can be exploited as therapeutic potential targets to mitigate it.
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Affiliation(s)
- Patricia P. Garcez
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Minardi Nascimento
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
- Institute of Biology, Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | | | | | - Rodrigo Delvecchio
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pablo Trindade
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | | | - Luiza M. Higa
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana S. Cassoli
- Institute of Biology, Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Gabriela Vitória
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | | | - Jaroslaw Sochacki
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Renato S. Aguiar
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | | | - Amilcar Tanuri
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Daniel Martins-de-Souza
- Institute of Biology, Department of Biochemistry and Tissue Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Stevens K. Rehen
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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20
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SFPQ associates to LSD1 and regulates the migration of newborn pyramidal neurons in the developing cerebral cortex. Int J Dev Neurosci 2016; 57:1-11. [PMID: 28034769 DOI: 10.1016/j.ijdevneu.2016.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/16/2016] [Accepted: 12/20/2016] [Indexed: 12/24/2022] Open
Abstract
The development of the cerebral cortex requires the coordination of multiple processes ranging from the proliferation of progenitors to the migration and establishment of connectivity of the newborn neurons. Epigenetic regulation carried out by the COREST/LSD1 complex has been identified as a mechanism that regulates the development of pyramidal neurons of the cerebral cortex. We now identify the association of the multifunctional RNA-binding protein SFPQ to LSD1 during the development of the cerebral cortex. In vivo reduction of SFPQ dosage by in utero electroporation of a shRNA results in impaired radial migration of newborn pyramidal neurons, in a similar way to that observed when COREST or LSD1 expressions are decreased. Diminished SFPQ expression also associates to decreased proliferation of progenitor cells, while it does not affect the acquisition of neuronal fate. These results are compatible with the idea that SFPQ, plays an important role regulating proliferation and migration during the development of the cerebral cortex.
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Tammimies K, Bieder A, Lauter G, Sugiaman-Trapman D, Torchet R, Hokkanen ME, Burghoorn J, Castrén E, Kere J, Tapia-Páez I, Swoboda P. Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs. FASEB J 2016; 30:3578-3587. [PMID: 27451412 PMCID: PMC5024701 DOI: 10.1096/fj.201500124rr] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 07/05/2016] [Indexed: 11/11/2022]
Abstract
DYX1C1, DCDC2, and KIAA0319 are
three of the most replicated dyslexia candidate genes (DCGs). Recently, these DCGs
were implicated in functions at the cilium. Here, we investigate the regulation of
these DCGs by Regulatory Factor X transcription factors (RFX TFs), a gene family
known for transcriptionally regulating ciliary genes. We identify conserved X-box
motifs in the promoter regions of DYX1C1, DCDC2, and
KIAA0319 and demonstrate their functionality, as well as the
ability to recruit RFX TFs using reporter gene and electrophoretic mobility shift
assays. Furthermore, we uncover a complex regulation pattern between
RFX1, RFX2, and RFX3 and their
significant effect on modifying the endogenous expression of DYX1C1
and DCDC2 in a human retinal pigmented epithelial cell line
immortalized with hTERT (hTERT-RPE1). In addition, induction of ciliogenesis
increases the expression of RFX TFs and DCGs. At the protein level, we show that
endogenous DYX1C1 localizes to the base of the cilium, whereas DCDC2 localizes along
the entire axoneme of the cilium, thereby validating earlier localization studies
using overexpression models. Our results corroborate the emerging role of DCGs in
ciliary function and characterize functional noncoding elements, X-box promoter
motifs, in DCG promoter regions, which thus can be targeted for mutation screening in
dyslexia and ciliopathies associated with these genes.—Tammimies, K., Bieder,
A., Lauter, G., Sugiaman-Trapman, D., Torchet, R., Hokkanen, M.-E., Burghoorn, J.,
Castrén, E., Kere, J., Tapia-Páez, I., Swoboda, P. Ciliary dyslexia
candidate genes DYX1C1 and DCDC2 are regulated by
Regulatory Factor (RF) X transcription factors through X-box promoter motifs.
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Affiliation(s)
- Kristiina Tammimies
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Center of Neurodevelopmental Disorders (KIND), Pediatric Neuropsychiatry Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Rachel Torchet
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Jan Burghoorn
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Eero Castrén
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland; and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Isabel Tapia-Páez
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden;
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden;
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22
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Cosker KE, Fenstermacher SJ, Pazyra-Murphy MF, Elliott HL, Segal RA. The RNA-binding protein SFPQ orchestrates an RNA regulon to promote axon viability. Nat Neurosci 2016; 19:690-696. [PMID: 27019013 PMCID: PMC5505173 DOI: 10.1038/nn.4280] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/01/2016] [Indexed: 12/20/2022]
Abstract
To achieve accurate spatiotemporal patterns of gene expression, RNA-binding proteins (RBPs) guide nuclear processing, intracellular trafficking and local translation of target mRNAs. In neurons, RBPs direct transport of target mRNAs to sites of translation in remote axons and dendrites. However, it is not known whether an individual RBP coordinately regulates multiple mRNAs within these morphologically complex cells. Here we identify SFPQ (splicing factor, poly-glutamine rich) as an RBP that binds and regulates multiple mRNAs in dorsal root ganglion sensory neurons and thereby promotes neurotrophin-dependent axonal viability. SFPQ acts in nuclei, cytoplasm and axons to regulate functionally related mRNAs essential for axon survival. Notably, SFPQ is required for coassembly of LaminB2 (Lmnb2) and Bclw (Bcl2l2) mRNAs in RNA granules and for axonal trafficking of these mRNAs. Together these data demonstrate that SFPQ orchestrates spatial gene expression of a newly identified RNA regulon essential for axonal viability.
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Affiliation(s)
- Katharina E Cosker
- Department of Neurobiology, Harvard Medical School, Department of Cancer
Biology, Dana-Farber Cancer Institute, Boston MA 02215, USA
| | - Sara J Fenstermacher
- Department of Neurobiology, Harvard Medical School, Department of Cancer
Biology, Dana-Farber Cancer Institute, Boston MA 02215, USA
| | - Maria F Pazyra-Murphy
- Department of Neurobiology, Harvard Medical School, Department of Cancer
Biology, Dana-Farber Cancer Institute, Boston MA 02215, USA
| | - Hunter L Elliott
- Image and Data Analysis Core, Harvard Medical School, Boston, MA 02115,
USA
| | - Rosalind A Segal
- Department of Neurobiology, Harvard Medical School, Department of Cancer
Biology, Dana-Farber Cancer Institute, Boston MA 02215, USA
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Knott GJ, Bond CS, Fox AH. The DBHS proteins SFPQ, NONO and PSPC1: a multipurpose molecular scaffold. Nucleic Acids Res 2016; 44:3989-4004. [PMID: 27084935 PMCID: PMC4872119 DOI: 10.1093/nar/gkw271] [Citation(s) in RCA: 199] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/05/2016] [Indexed: 12/23/2022] Open
Abstract
Nuclear proteins are often given a concise title that captures their function, such as 'transcription factor,' 'polymerase' or 'nuclear-receptor.' However, for members of the Drosophila behavior/human splicing (DBHS) protein family, no such clean-cut title exists. DBHS proteins are frequently identified engaging in almost every step of gene regulation, including but not limited to, transcriptional regulation, RNA processing and transport, and DNA repair. Herein, we present a coherent picture of DBHS proteins, integrating recent structural insights on dimerization, nucleic acid binding modalities and oligomerization propensity with biological function. The emerging paradigm describes a family of dynamic proteins mediating a wide range of protein-protein and protein-nucleic acid interactions, on the whole acting as a multipurpose molecular scaffold. Overall, significant steps toward appreciating the role of DBHS proteins have been made, but we are only beginning to understand the complexity and broader importance of this family in cellular biology.
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Affiliation(s)
- Gavin J Knott
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Charles S Bond
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia
| | - Archa H Fox
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, Crawley, Western Australia, WA 6009, Australia Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
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Wang G, Yang H, Yan S, Wang CE, Liu X, Zhao B, Ouyang Z, Yin P, Liu Z, Zhao Y, Liu T, Fan N, Guo L, Li S, Li XJ, Lai L. Cytoplasmic mislocalization of RNA splicing factors and aberrant neuronal gene splicing in TDP-43 transgenic pig brain. Mol Neurodegener 2015; 10:42. [PMID: 26334913 PMCID: PMC4557629 DOI: 10.1186/s13024-015-0036-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 08/10/2015] [Indexed: 12/13/2022] Open
Abstract
Background TAR DNA-binding protein 43 (TDP-43) is a nuclear protein, but it is redistributed in the neuronal cytoplasm in both amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Because small transgenic animal models often lack cytoplasmic TDP-43, how the cytoplasmic accumulation of TDP-43 contributes to these diseases remains unclear. The current study is aimed at studying the mechanism of cytoplasmic pathology of TDP-43. Results We established transgenic pigs expressing mutant TDP-43 (M337V). This pig model shows severe phenotypes and early death. We found that transgenic TDP-43 is also distributed in the cytoplasm of neuronal cells in the spinal cord and brain. Transgenic TDP-43 interacts with PSF, an RNA splicing factor that associates with NeuN to regulate neuronal RNA splicing. The interaction of TDP-43, PSF and NeuN causes PSF and NeuN mislocalize into the neuronal cytoplasm in transgenic pigs. Consistently, abnormal PSF-related neuronal RNA splicing is seen in TDP-43 transgenic pigs. The cytoplasmic localization of PSF and NeuN as well as abnormal PSF-related neuronal RNA splicing was also found in ALS patient brains. Conclusion Our findings from a large mammalian model suggest that cytoplasmic mutant TDP-43 could reduce the nuclear function of RNA splicing factors, contributing to neuropathology.
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Affiliation(s)
- Guohao Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Huaqiang Yang
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Sen Yan
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Chuan-En Wang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Xudong Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Bentian Zhao
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Zhen Ouyang
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Peng Yin
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhaoming Liu
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Yu Zhao
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Tao Liu
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Nana Fan
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Lin Guo
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Shihua Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Xiao-Jiang Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China. .,Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Liangxue Lai
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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25
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Shirai Y, Watanabe M, Sakagami H, Suzuki T. Novel splice variants in the 5'UTR of Gtf2i expressed in the rat brain: alternative 5'UTRs and differential expression in the neuronal dendrites. J Neurochem 2015; 134:578-89. [PMID: 25913238 DOI: 10.1111/jnc.13136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Revised: 04/15/2015] [Accepted: 04/16/2015] [Indexed: 11/29/2022]
Abstract
General transcription factor II-I (Gtf2i) is a transcription factor and one of the genes implicated in Willams-Beuren syndrome, an autism spectrum disorder. In this study, we investigated splice variants of the Gtf2i gene in both the 5'untranslated region (5'UTR) and the coding region. To search for novel 5'UTRs of Gtf2i, we utilized the cap analysis gene expression database of the mouse. We identified seven novel Gtf2i transcripts with alternatively spliced 5'UTRs in the rat brain. We also identified four novel splice variants in the coding sequence of Gtf2i. Furthermore, we identified a selective usage of certain types of 5'UTR by coding variants. In situ hybridization demonstrated a differential pattern of expression of Gtf2i mRNAs with alternatively spliced 5'UTRs among neuronal cells, and the localization of one of the variants in neuronal dendrites in the rat brain. Immunohistochemistry also demonstrated a distribution of Gtf2i-immunoreactivity in the dendrites. These results suggest multiple pathways of expression of Gtf2i gene in the brain. The expression patterns may be under the control of alternative promoters coupled to the alternative splicing in the coding region. Differential localization of mRNA to neuronal dendrites suggests spatiotemporal-specific translation at the post-synaptic sites that is involved in transfer of synaptic activity to expression of specific sets of genes in the nucleus. Gtf2i is a transcription factor and implicated in Willams-Beuren syndrome. We identified seven novel Gtf2i transcripts with alternatively spliced 5'UTRs in the rat brain. In situ hybridization demonstrated a differential expression of Gtf2i mRNAs with different 5'UTRs in somas and dendrites of neuronal cells. Differential localization of mRNA to neuronal dendrites suggests spatiotemporal-specific translation at the postsynaptic sites. The scheme shows genomic structure showing the positions of the potential transcription start tags (rDEC695, rDEC3D7, rDEC1D3, rDEC104, rDEC072 and rDEBE25). Newly identified exons (1.1-1.6) are shown with the white boxes. The distances from rDEC695-5'end are indicated in bp.
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Affiliation(s)
- Yoshinori Shirai
- Department of Neuroplasticity, Institute of Pathogenesis and Disease Prevention, Shinshu University Graduate School of Medicine, Matsumoto, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hiroyuki Sakagami
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan
| | - Tatsuo Suzuki
- Department of Neuroplasticity, Institute of Pathogenesis and Disease Prevention, Shinshu University Graduate School of Medicine, Matsumoto, Japan.,Department of Biological Sciences for Intractable Neurological Diseases, Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Japan
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26
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Mills JD, Chen J, Kim WS, Waters PD, Prabowo AS, Aronica E, Halliday GM, Janitz M. Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter. Neurogenetics 2015; 16:201-13. [PMID: 25819921 DOI: 10.1007/s10048-015-0445-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/14/2015] [Indexed: 12/30/2022]
Abstract
Pervasive transcription of the genome produces a diverse array of functional non-coding RNAs (ncRNAs). One particular class of ncRNAs, long intervening non-coding RNAs (lincRNAs) are thought to play a role in regulating gene expression and may be a major contributor to organism and tissue complexity. The human brain with its heterogeneous cellular make-up is a rich source of lincRNAs; however, the functions of the majority of lincRNAs are unknown. Recently, by completing RNA sequencing (RNA-Seq) of the human frontal cortex, we identified linc00320 as being highly expressed in the white matter compared to grey matter in multiple system atrophy (MSA) brain. Here, we further investigate the expression patterns of linc00320 and conclude that it is involved in specific brain regions rather than having involvement in the MSA disease process. We also show that the full-length linc00320 is only expressed in human brain tissue and not in other primates, suggesting that it may be involved in improved functional connectivity for higher human brain cognition.
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Affiliation(s)
- James D Mills
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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27
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Boeckx C, Benítez-Burraco A. Globularity and language-readiness: generating new predictions by expanding the set of genes of interest. Front Psychol 2014; 5:1324. [PMID: 25505436 PMCID: PMC4243498 DOI: 10.3389/fpsyg.2014.01324] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022] Open
Abstract
This study builds on the hypothesis put forth in Boeckx and Benítez-Burraco (2014), according to which the developmental changes expressed at the levels of brain morphology and neural connectivity that resulted in a more globular braincase in our species were crucial to understand the origins of our language-ready brain. Specifically, this paper explores the links between two well-known 'language-related' genes like FOXP2 and ROBO1 implicated in vocal learning and the initial set of genes of interest put forth in Boeckx and Benítez-Burraco (2014), with RUNX2 as focal point. Relying on the existing literature, we uncover potential molecular links that could be of interest to future experimental inquiries into the biological foundations of language and the testing of our initial hypothesis. Our discussion could also be relevant for clinical linguistics and for the interpretation of results from paleogenomics.
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Affiliation(s)
- Cedric Boeckx
- Catalan Institute for Advanced Studies and Research (ICREA)Barcelona, Spain
- Department of Linguistics, Universitat de BarcelonaBarcelona, Spain
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28
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Kere J. The molecular genetics and neurobiology of developmental dyslexia as model of a complex phenotype. Biochem Biophys Res Commun 2014; 452:236-43. [PMID: 25078623 DOI: 10.1016/j.bbrc.2014.07.102] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 07/22/2014] [Indexed: 10/25/2022]
Abstract
Among complex disorders, those concerning neuropsychiatric phenotypes involve particular challenges compared to disorders with more easily distinguished clinical signs and measures. One such common and unusually challenging phenotype to disentangle genetically is developmental dyslexia (DD), or reading disability, defined as the inability to learn to read and write for an otherwise normally intelligent child with normal senses and educational opportunity. There is presently ample evidence for the strongly biological etiology for DD, and a dozen susceptibility genes have been suggested. Many of these genes point to common but previously unsuspected biological mechanisms, such as neuronal migration and cilia functions. I discuss here the state-of-the-art in genomic and neurobiological aspects of DD research, starting with short general background to its history.
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Affiliation(s)
- Juha Kere
- Department of Biosciences and Nutrition, Centre for Innovative Medicine, Karolinska Institutet, Stockholm, Sweden; Molecular Neurology Research Program, University of Helsinki, Folkhälsan Institute of Genetics, Helsinki, Finland.
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29
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Association of SNPs of DYX1C1 with developmental dyslexia in an Indian population. Psychiatr Genet 2014; 24:10-20. [PMID: 24362368 DOI: 10.1097/ypg.0000000000000009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE DYX1C1 has been identified as a susceptible candidate gene for developmental dyslexia (DD); studies in various populations have yielded inconclusive results and the causal allele is unknown in the Indian population. On the basis of the initial association studies and the role of DYX1C1 in neuronal migration, we investigated the role of DYX1C1 in causing DD in an Indian population. MATERIALS AND METHODS Ten single-nucleotide polymorphisms (SNPs) of DYX1C1 were genotyped in 210 cases with DD and 256 age-matched nondyslexic controls. Genotyping of these SNPs was carried with the MassARRAY technique using SpectroCHIP and analysed with MALDI-TOF MS. Single-marker and two-marker haplotype analyses were carried out and the χ-test, odds ratios, 95% confidence intervals and Yates correction were applied to identify the significance of the genotyped SNPs. RESULTS A significant association was observed for the homozygous genotype (GG) of the SNP rs12899331 (3.12%) and individual allele frequency (P=0.039). Psycholinguistic tests showed an association between rs12899331 with dyslexic phenotypes such as word and nonword reading, syllable reversal task, spoonerism task and spelling. Two-marker haplotype analysis also showed a significant association for the markers G/C at rs12899331/rs1075938 (P=0.039) with the phenotypes rapid naming ability and phonological awareness, as well as with word reading, spelling and sentence repetition. CONCLUSION The promoter SNP rs12899331 of DYX1C1 may contribute towards the manifestation of DD. This study supports the association of DYX1C1 with DD in an Indian population.
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Carrion-Castillo A, Franke B, Fisher SE. Molecular genetics of dyslexia: an overview. DYSLEXIA (CHICHESTER, ENGLAND) 2013; 19:214-240. [PMID: 24133036 DOI: 10.1002/dys.1464] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 09/02/2013] [Indexed: 05/28/2023]
Abstract
Dyslexia is a highly heritable learning disorder with a complex underlying genetic architecture. Over the past decade, researchers have pinpointed a number of candidate genes that may contribute to dyslexia susceptibility. Here, we provide an overview of the state of the art, describing how studies have moved from mapping potential risk loci, through identification of associated gene variants, to characterization of gene function in cellular and animal model systems. Work thus far has highlighted some intriguing mechanistic pathways, such as neuronal migration, axon guidance, and ciliary biology, but it is clear that we still have much to learn about the molecular networks that are involved. We end the review by highlighting the past, present, and future contributions of the Dutch Dyslexia Programme to studies of genetic factors. In particular, we emphasize the importance of relating genetic information to intermediate neurobiological measures, as well as the value of incorporating longitudinal and developmental data into molecular designs.
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Affiliation(s)
- Amaia Carrion-Castillo
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, Netherlands
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31
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Genetic analysis of dyslexia candidate genes in the European cross-linguistic NeuroDys cohort. Eur J Hum Genet 2013; 22:675-80. [PMID: 24022301 DOI: 10.1038/ejhg.2013.199] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 08/02/2013] [Accepted: 08/07/2013] [Indexed: 02/02/2023] Open
Abstract
Dyslexia is one of the most common childhood disorders with a prevalence of around 5-10% in school-age children. Although an important genetic component is known to have a role in the aetiology of dyslexia, we are far from understanding the molecular mechanisms leading to the disorder. Several candidate genes have been implicated in dyslexia, including DYX1C1, DCDC2, KIAA0319, and the MRPL19/C2ORF3 locus, each with reports of both positive and no replications. We generated a European cross-linguistic sample of school-age children - the NeuroDys cohort - that includes more than 900 individuals with dyslexia, sampled with homogenous inclusion criteria across eight European countries, and a comparable number of controls. Here, we describe association analysis of the dyslexia candidate genes/locus in the NeuroDys cohort. We performed both case-control and quantitative association analyses of single markers and haplotypes previously reported to be dyslexia-associated. Although we observed association signals in samples from single countries, we did not find any marker or haplotype that was significantly associated with either case-control status or quantitative measurements of word-reading or spelling in the meta-analysis of all eight countries combined. Like in other neurocognitive disorders, our findings underline the need for larger sample sizes to validate possibly weak genetic effects.
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Tammimies K, Vitezic M, Matsson H, Le Guyader S, Bürglin TR, Ohman T, Strömblad S, Daub CO, Nyman TA, Kere J, Tapia-Páez I. Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins. Biol Psychiatry 2013; 73:583-90. [PMID: 23036959 DOI: 10.1016/j.biopsych.2012.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 08/07/2012] [Accepted: 08/08/2012] [Indexed: 11/28/2022]
Abstract
BACKGROUND The dyslexia susceptibility 1 candidate 1 (DYX1C1) gene has recently been associated with dyslexia and reading scores in several population samples. The DYX1C1 has also been shown to affect neuronal migration and modulate estrogen receptor signaling. METHODS We have analyzed the molecular networks of DYX1C1 by gene expression and protein interaction profiling in a human neuroblastoma cell line. RESULTS We find that DYX1C1 can modulate the expression of nervous system development and neuronal migration genes such as RELN and associate with a number of cytoskeletal proteins. We also show by live cell imaging that DYX1C1 regulates cell migration of the human neuroblastoma cell line dependent on its tetratricopeptide repeat and DYX1 protein domains. The DYX1 domain is a novel highly conserved domain identified in this study by multiple sequence alignment of DYX1C1 proteins recovered from a wide range of eukaryotic species. CONCLUSIONS Our results contribute to the hypothesis that dyslexia has a developmental neurobiological basis by linking DYX1C1 with many genes involved in neuronal migration disorders.
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Affiliation(s)
- Kristiina Tammimies
- Center for Biosciences, Department of Biosciences and Nutrition, Novum, Karolinska Institutet, Huddinge, Sweden
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Tran C, Gagnon F, Wigg K, Feng Y, Gomez L, Cate-Carter T, Kerr E, Field L, Kaplan B, Lovett M, Barr C. A family-based association analysis and meta-analysis of the reading disabilities candidate gene DYX1C1. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:146-56. [PMID: 23341075 PMCID: PMC5381964 DOI: 10.1002/ajmg.b.32123] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 11/07/2012] [Indexed: 11/11/2022]
Abstract
Reading disabilities (RD) have a significant genetic basis and have shown linkage to multiple regions including chromosome 15q. Dyslexia susceptibility 1 candidate gene 1 (DYX1C1) on chromosome 15q21 was originally proposed as a candidate gene with two potentially functional polymorphisms at the -3G/A and 1249G/T positions showing association with RD. However, subsequent studies have yielded mixed results. We performed a literature review and meta-analysis of the -3G/A and 1249G/T polymorphisms, including new unpublished data from two family-based samples. Ten markers in DYX1C1 were genotyped in the two independently ascertained samples. Single marker and -3G/A:1249G/T haplotype analyses were performed for RD in both samples, and quantitative trait analyses using standardized reading-related measures was performed in one of the samples. For the meta-analysis, we used a random-effects model to summarize studies that tested for association between -3G/A or 1249G/T and RD. No significant association was found between the DYX1C1 SNPs and RD or any of the reading-related measures tested after correction for the number of tests performed. The previously reported risk haplotype (-3A:1249T) was not biased in transmission. A total of 9 and 10 study samples were included in the meta-analysis of the -3G/A and 1249G/T polymorphisms, respectively. Neither polymorphism reached statistical significance, but the heterogeneity for the 1249G/T polymorphism was high. The results of this study do not provide evidence for association between the putatively functional SNPs -3G/A and 1249G/T and RD.
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Affiliation(s)
- C. Tran
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - F. Gagnon
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - K.G. Wigg
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - Y. Feng
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - L. Gomez
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada
| | - T.D. Cate-Carter
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - E.N. Kerr
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - L.L. Field
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - B.J. Kaplan
- Alberta Children’s Hospital and Department of Paediatrics, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - M.W. Lovett
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - C.L. Barr
- Genetics and Development Division, Toronto Western Research Institute, Toronto Western Hospital, University Health Network, Toronto, Ontario, Canada,Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, Ontario, Canada,Correspondence to: Dr. C.L. Barr, Genetics and Development Division, The Toronto Western Hospital, 399 Bathurst St., Room MP14-302, Toronto, ON, Canada M5T 2S8.
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A polymorphic microsatellite repeat within the ECE-1c promoter is involved in transcriptional start site determination, human evolution, and Alzheimer's disease. J Neurosci 2013; 32:16807-20. [PMID: 23175834 DOI: 10.1523/jneurosci.2636-12.2012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Genetic factors strongly contribute to the pathogenesis of sporadic Alzheimer's disease (AD). Nevertheless, genome-wide association studies only yielded single nucleotide polymorphism loci of moderate importance. In contrast, microsatellite repeats are functionally less characterized structures within our genomes. Previous work has shown that endothelin-converting enzyme-1 (ECE-1) is able to reduce amyloid β content. Here we demonstrate that a CpG-CA repeat within the human ECE-1c promoter is highly polymorphic, harbors transcriptional start sites, is able to recruit the transcription factors poly(ADP-ribose) polymerase-1 and splicing factor proline and glutamine-rich, and is functional regarding haplotype-specific promoter activity. Furthermore, genotyping of 403 AD patients and 444 controls for CpG-CA repeat length indicated shifted allelic frequency distributions. Sequencing of 245 haplotype clones demonstrated that the overall CpG-CA repeat composition of AD patients and controls is distinct. Finally, we show that human and chimpanzee [CpG](m)-[CA](n) ECE-1c promoter repeats are genetically and functionally distinct. Our data indicate that a short genomic repeat structure constitutes a novel core promoter element, coincides with human evolution, and contributes to the pathogenesis of AD.
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Raskind WH, Peter B, Richards T, Eckert MM, Berninger VW. The genetics of reading disabilities: from phenotypes to candidate genes. Front Psychol 2013; 3:601. [PMID: 23308072 PMCID: PMC3538356 DOI: 10.3389/fpsyg.2012.00601] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 12/18/2012] [Indexed: 12/19/2022] Open
Abstract
This article provides an overview of (a) issues in definition and diagnosis of specific reading disabilities at the behavioral level that may occur in different constellations of developmental and phenotypic profiles (patterns); (b) rapidly expanding research on genetic heterogeneity and gene candidates for dyslexia and other reading disabilities; (c) emerging research on gene-brain relationships; and (d) current understanding of epigenetic mechanisms whereby environmental events may alter behavioral expression of genetic variations. A glossary of genetic terms (denoted by bold font) is provided for readers not familiar with the technical terms.
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Affiliation(s)
- Wendy H Raskind
- Department of Medicine, University of Washington Seattle, WA, USA ; Department of Psychiatry and Behavioral Sciences, University of Washington Seattle, WA, USA
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Abstract
Three genes GTF2IRD1, GTF2I, and GTF2IRD2, which encode members of the GTF2I (or TFII-I) family of so-called general transcription factors, were discovered and studied during the last two decades. Chromosome location and similarity of exon-intron structures suggest that the family evolved by duplications. The initial duplication of ancestral proto-GTF2IRD1 gene likely occurred in early vertebrates prior to origin of cartilaginous fish and led to formation of GTF2I (>450 MYA), which was later lost in bony fish but successfully evolved in the land vertebrates. The second duplication event, which created GTF2IRD2, occurred prior to major radiation events of eutherian mammalian evolution (>100 MYA). During recent steps of primate evolution there was another duplication which led to formation of GTF2IRD2B (<4 MYA). Two latest duplications were coupled with inversions. Genes belonging to the family have several highly conservative repeats which are implicated in DNA binding. Phylogenetic analysis of the repeats revealed a pattern of intragenic duplications, deletions and substitutions which led to diversification of the genes and proteins. Distribution of statistically rare atypical substitutions (p ≤ 0.01) sheds some light on structural differentiation of repeats and hence evolution of the genes. The atypical substitutions are often located on secondary structures joining α-helices and affect 3D arrangement of the protein globule. Such substitutions are commonly traced at the early stages of evolution in Tetrapoda, Amniota, and Mammalia.
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Zou L, Chen W, Shao S, Sun Z, Zhong R, Shi J, Miao X, Song R. Genetic variant in KIAA0319, but not in DYX1C1, is associated with risk of dyslexia: an integrated meta-analysis. Am J Med Genet B Neuropsychiatr Genet 2012; 159B:970-6. [PMID: 23065966 DOI: 10.1002/ajmg.b.32102] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/14/2012] [Indexed: 01/13/2023]
Abstract
DYX1C1 and KIAA0319 have been two of the most extensively studied candidate genes for dyslexia given their important roles in the neuronal migration and neurite growth. The -3G > A in DYX1C1 and the 931C > T in KIAA0319 were of special interest for dyslexia but with inconsistent results. We performed a meta-analysis integrating case-control and transmission/disequilibrium test (TDT) studies to clearly discern the effect of these two variants in dyslexia. Data from case-control and TDT studies were analyzed in an allelic model using the Catmap software. In overall meta-analysis, the pooled OR for the -3A allele and the 931T allele was 0.68 (95% CI = 0.25-1.87, P(heterogeneity) = 0.000) and 0.87 (95% CI = 0.78-0.98, P(heterogeneity)= 0.125), respectively. The stratified analysis showed that the between-study heterogeneity regarding the -3G > A polymorphism might be accounted by the publication year. Additionally, the sensitivity analysis of -3G > A polymorphism indicated the stability of the result. In conclusion, our results suggested that the 931C > T variant in KIAA0319, but not the -3G > A in DYX1C1, was significantly associated with the risk of dyslexia.
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Affiliation(s)
- Li Zou
- Department of Maternal and Child Health, School of Public Health, Tongji Medical College, Huangzhong University of Science and Technology, Wuhan, China
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Palmer SJ, Taylor KM, Santucci N, Widagdo J, Chan YKA, Yeo JL, Adams M, Gunning PW, Hardeman EC. GTF2IRD2 from the Williams-Beuren critical region encodes a mobile-element-derived fusion protein that antagonizes the action of its related family members. J Cell Sci 2012; 125:5040-50. [PMID: 22899722 DOI: 10.1242/jcs.102798] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
GTF2IRD2 belongs to a family of transcriptional regulators (including TFII-I and GTF2IRD1) that are responsible for many of the key features of Williams-Beuren syndrome (WBS). Sequence evidence suggests that GTF2IRD2 arose in eutherian mammals by duplication and divergence from the gene encoding TFII-I. However, in GTF2IRD2, most of the C-terminal domain has been lost and replaced by the domesticated remnant of an in-frame hAT-transposon mobile element. In this first experimental analysis of function, we show that transgenic expression of each of the three family members in skeletal muscle causes significant fiber type shifts, but the GTF2IRD2 protein causes an extreme shift in the opposite direction to the two other family members. Mating of GTF2IRD1 and GTF2IRD2 mice restores the fiber type balance, indicating an antagonistic relationship between these two paralogs. In cells, GTF2IRD2 localizes to cytoplasmic microtubules and discrete speckles in the nuclear periphery. We show that it can interact directly with TFII-Iβ and GTF2IRD1, and upon co-transfection changes the normal distribution of these two proteins into a punctate nuclear pattern typical of GTF2IRD2. These data suggest that GTF2IRD2 has evolved as a regulator of GTF2IRD1 and TFII-I; inhibiting their function by direct interaction and sequestration into inactive nuclear zones.
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Affiliation(s)
- Stephen J Palmer
- Neuromuscular and Regenerative Medicine Unit, School of Medical Sciences, The University of New South Wales, Sydney 2052, Australia.
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Anthoni H, Sucheston LE, Lewis BA, Tapia-Páez I, Fan X, Zucchelli M, Taipale M, Stein CM, Hokkanen ME, Castrén E, Pennington BF, Smith SD, Olson RK, Tomblin JB, Schulte-Körne G, Nöthen M, Schumacher J, Müller-Myhsok B, Hoffmann P, Gilger JW, Hynd GW, Nopola-Hemmi J, Leppanen PHT, Lyytinen H, Schoumans J, Nordenskjöld M, Spencer J, Stanic D, Boon WC, Simpson E, Mäkelä S, Gustafsson JÅ, Peyrard-Janvid M, Iyengar S, Kere J. The aromatase gene CYP19A1: several genetic and functional lines of evidence supporting a role in reading, speech and language. Behav Genet 2012; 42:509-27. [PMID: 22426781 PMCID: PMC3375077 DOI: 10.1007/s10519-012-9532-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Accepted: 02/11/2012] [Indexed: 02/06/2023]
Abstract
Inspired by the localization, on 15q21.2 of the CYP19A1 gene in the linkage region of speech and language disorders, and a rare translocation in a dyslexic individual that was brought to our attention, we conducted a series of studies on the properties of CYP19A1 as a candidate gene for dyslexia and related conditions. The aromatase enzyme is a member of the cytochrome P450 super family, and it serves several key functions: it catalyzes the conversion of androgens into estrogens; during early mammalian development it controls the differentiation of specific brain areas (e.g. local estrogen synthesis in the hippocampus regulates synaptic plasticity and axonal growth); it is involved in sexual differentiation of the brain; and in songbirds and teleost fishes, it regulates vocalization. Our results suggest that variations in CYP19A1 are associated with dyslexia as a categorical trait and with quantitative measures of language and speech, such as reading, vocabulary, phonological processing and oral motor skills. Variations near the vicinity of its brain promoter region altered transcription factor binding, suggesting a regulatory role in CYP19A1 expression. CYP19A1 expression in human brain correlated with the expression of dyslexia susceptibility genes such as DYX1C1 and ROBO1. Aromatase-deficient mice displayed increased cortical neuronal density and occasional cortical heterotopias, also observed in Robo1-/- mice and human dyslexic brains, respectively. An aromatase inhibitor reduced dendritic growth in cultured rat neurons. From this broad set of evidence, we propose CYP19A1 as a candidate gene for human cognitive functions implicated in reading, speech and language.
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Affiliation(s)
- Heidi Anthoni
- Department of Medical Genetics, Biomedicum, University of Helsinki, 00014 Helsinki, Finland
- Neuroscience Center, University of Helsinki, 00014 Helsinki, Finland
| | - Lara E. Sucheston
- Department of Biostatistics, State University of New York at Buffalo, Buffalo, NY 14214-3000 USA
| | - Barbara A. Lewis
- Department of Psychological Sciences, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Isabel Tapia-Páez
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Xiaotang Fan
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Marco Zucchelli
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Mikko Taipale
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142-1479 USA
| | - Catherine M. Stein
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106 USA
| | | | - Eero Castrén
- Neuroscience Center, University of Helsinki, 00014 Helsinki, Finland
| | | | - Shelley D. Smith
- Munroe Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198-5450 USA
| | - Richard K. Olson
- Department of Psychology, University of Colorado, Boulder, CO USA
| | - J. Bruce Tomblin
- Department of Communication Sciences and Disorders, University of Iowa, Iowa City, IA 52242 USA
| | - Gerd Schulte-Körne
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany
| | - Markus Nöthen
- Department of Genomics, Life and Brain Centre, University of Bonn, 53127 Bonn, Germany
- Institute of Human Genetics, Biomedical Centre, University of Bonn, 53127 Bonn, Germany
| | - Johannes Schumacher
- Institute of Human Genetics, Biomedical Centre, University of Bonn, 53127 Bonn, Germany
| | | | - Per Hoffmann
- Department of Genomics, Life and Brain Centre, University of Bonn, 53127 Bonn, Germany
- Institute of Human Genetics, Biomedical Centre, University of Bonn, 53127 Bonn, Germany
| | - Jeffrey W. Gilger
- Psychological Sciences, University of California, Merced, CA 95343 USA
| | - George W. Hynd
- Department of Psychology, College of Charleston, 66 George Street, Charleston, SC 29424 USA
| | - Jaana Nopola-Hemmi
- Division of Child Neurology, Department of Gynecology and Pediatrics, HUCH, University of Helsinki, 00014 Helsinki, Finland
| | | | - Heikki Lyytinen
- Department of Psychology, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Jacqueline Schoumans
- Department of Molecular Medicine and Surgery, Karolinska Institutet at Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet at Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Jason Spencer
- Howard Florey Institute, Parkville, VIC 3010 Australia
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800 Australia
| | - Davor Stanic
- Howard Florey Institute, Parkville, VIC 3010 Australia
- Centre for Neuroscience, University of Melbourne, Parkville, VIC 3010 Australia
| | - Wah Chin Boon
- Howard Florey Institute, Parkville, VIC 3010 Australia
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800 Australia
- Centre for Neuroscience, University of Melbourne, Parkville, VIC 3010 Australia
- Prince Henry’s Institute of Medical Research, Clayton, VIC 3168 Australia
| | - Evan Simpson
- Prince Henry’s Institute of Medical Research, Clayton, VIC 3168 Australia
| | - Sari Mäkelä
- Institute of Biomedicine, University of Turku, 20014 Turku, Finland
| | - Jan-Åke Gustafsson
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, TX 77204-5056 USA
| | - Myriam Peyrard-Janvid
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Sudha Iyengar
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Juha Kere
- Department of Medical Genetics, Biomedicum, University of Helsinki, 00014 Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
- Department of Clinical Research Center, Karolinska Institutet, 141 83 Huddinge, Sweden
- Science for Life Laboratory, Karolinska Institutet, 171 65 Solna, Sweden
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Ke Y, Dramiga J, Schütz U, Kril JJ, Ittner LM, Schröder H, Götz J. Tau-mediated nuclear depletion and cytoplasmic accumulation of SFPQ in Alzheimer's and Pick's disease. PLoS One 2012; 7:e35678. [PMID: 22558197 PMCID: PMC3338448 DOI: 10.1371/journal.pone.0035678] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 03/20/2012] [Indexed: 11/19/2022] Open
Abstract
Tau dysfunction characterizes neurodegenerative diseases such as Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD). Here, we performed an unbiased SAGE (serial analysis of gene expression) of differentially expressed mRNAs in the amygdala of transgenic pR5 mice that express human tau carrying the P301L mutation previously identified in familial cases of FTLD. SAGE identified 29 deregulated transcripts including Sfpq that encodes a nuclear factor implicated in the splicing and regulation of gene expression. To assess the relevance for human disease we analyzed brains from AD, Pick's disease (PiD, a form of FTLD), and control cases. Strikingly, in AD and PiD, both dementias with a tau pathology, affected brain areas showed a virtually complete nuclear depletion of SFPQ in both neurons and astrocytes, along with cytoplasmic accumulation. Accordingly, neurons harboring either AD tangles or Pick bodies were also depleted of SFPQ. Immunoblot analysis of human entorhinal cortex samples revealed reduced SFPQ levels with advanced Braak stages suggesting that the SFPQ pathology may progress together with the tau pathology in AD. To determine a causal role for tau, we stably expressed both wild-type and P301L human tau in human SH-SY5Y neuroblastoma cells, an established cell culture model of tau pathology. The cells were differentiated by two independent methods, mitomycin C-mediated cell cycle arrest or neuronal differentiation with retinoic acid. Confocal microscopy revealed that SFPQ was confined to nuclei in non-transfected wild-type cells, whereas in wild-type and P301L tau over-expressing cells, irrespective of the differentiation method, it formed aggregates in the cytoplasm, suggesting that pathogenic tau drives SFPQ pathology in post-mitotic cells. Our findings add SFPQ to a growing list of transcription factors with an altered nucleo-cytoplasmic distribution under neurodegenerative conditions.
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Affiliation(s)
- Yazi Ke
- Alzheimer's and Parkinson's Disease Laboratory, Brain & Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - Joe Dramiga
- Department II of Anatomy and Neuroanatomy, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, CMMC, University of Cologne, Cologne, Germany
| | - Ulrich Schütz
- Department II of Anatomy and Neuroanatomy, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, CMMC, University of Cologne, Cologne, Germany
| | - Jillian J. Kril
- Disciplines of Medicine and Pathology, University of Sydney, Sydney, New South Wales, Australia
| | - Lars M. Ittner
- Alzheimer's and Parkinson's Disease Laboratory, Brain & Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia
| | - Hannsjörg Schröder
- Department II of Anatomy and Neuroanatomy, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, CMMC, University of Cologne, Cologne, Germany
- * E-mail: (HS); (JG)
| | - Jürgen Götz
- Alzheimer's and Parkinson's Disease Laboratory, Brain & Mind Research Institute, University of Sydney, Camperdown, New South Wales, Australia
- * E-mail: (HS); (JG)
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Tammimies K, Tapia-Páez I, Rüegg J, Rosin G, Kere J, Gustafsson JÅ, Nalvarte I. The rs3743205 SNP is important for the regulation of the dyslexia candidate gene DYX1C1 by estrogen receptor β and DNA methylation. Mol Endocrinol 2012; 26:619-29. [PMID: 22383464 DOI: 10.1210/me.2011-1376] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Estrogen is involved in numerous physiological processes such as growth, differentiation, and function of the male and female reproductive tissues. In the developing brain, estrogen signaling has been linked to cognitive functions, such as learning and memory; however, the molecular mechanisms underlying this phenomenon are poorly understood. We have previously shown a link between developmental dyslexia and estrogen signaling, when we studied the functional interactions between the dyslexia candidate protein DYX1C1 and the estrogen receptors α (ERα) and β (ERβ). Here, we investigate the 17β-estradiol (E2)-dependent regulation of dyslexia susceptibility 1 candidate 1 (DYX1C1) expression. We demonstrate that ERβ, not ERα, binds to a transcriptionally active cis-regulatory region upstream of DYX1C1 transcriptional start site and that DYX1C1 expression is enhanced by E2 in a neuroblastoma cell line. This regulation is dependent on transcription factor II-I and liganded ERβ recruitment to this region. In addition, we describe that a single nucleotide polymorphism previously shown to be associated with dyslexia and located in the cis-regulatory region of DYX1C1 may alter the epigenetic and endocrine regulation of this gene. Our data provide important molecular insights into the relationship between developmental dyslexia susceptibility and estrogen signaling.
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Affiliation(s)
- Kristiina Tammimies
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14183 Huddinge, Sweden
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Rosin G, Hannelius U, Lindström L, Hall P, Bergh J, Hartman J, Kere J. The dyslexia candidate gene DYX1C1 is a potential marker of poor survival in breast cancer. BMC Cancer 2012; 12:79. [PMID: 22375924 PMCID: PMC3337251 DOI: 10.1186/1471-2407-12-79] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 02/29/2012] [Indexed: 01/20/2023] Open
Abstract
Background The dyslexia candidate gene, DYX1C1, shown to regulate and interact with estrogen receptors and involved in the regulation of neuronal migration, has recently been proposed as a putative cancer biomarker. This study was undertaken to assess the prognostic value and therapy-predictive potential of DYX1C1 mRNA and protein expression in breast cancer. Methods DYX1C1 mRNA expression was assessed at the mRNA level in three independent population-derived patient cohorts. An association to estrogen/progesterone receptor status, Elston grade, gene expression subtype and lymph node status was analyzed within these cohorts. DYX1C1 protein expression was examined using immunohistochemistry in cancer and normal breast tissue. The statistical analyses were performed using the non-parametric Wilcoxon rank-sum test, ANOVA, Fisher's exact test and a multivariate proportional hazard (Cox) model. Results DYX1C1 mRNA is significantly more highly expressed in tumors that have been classified as estrogen receptor α and progesterone receptor-positive. The expression of DYX1C1 among the molecular subtypes shows the lowest median expression within the basal type tumors, which are considered to have the worst prognosis. The expression of DYX1C1 is significantly lower in tumors graded as Elston grade 3 compared with grades 1 and 2. DYX1C1 protein is expressed in 88% of tumors and in all 10 normal breast tissues examined. Positive protein expression was significantly correlated to overall survival (Hazard ratio 3.44 [CI 1.84-6.42]) of the patients but not to any of the variables linked with mRNA expression. Conclusion We show that the expression of DYX1C1 in breast cancer is associated with several clinicopathological parameters and that loss of DYX1C1 correlates with a more aggressive disease, in turn indicating that DYX1C1 is a potential prognostic biomarker in breast cancer.
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Affiliation(s)
- Gustaf Rosin
- Department of Biosciences and Nutrition, Novum, and Science for Life Laboratory, Karolinska Institutet, Hälsovägen 7, Huddinge, Sweden.
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Abstract
Language and learning disorders such as reading disability and language impairment are recognized to be subject to substantial genetic influences, but few causal mutations have been identified in the coding regions of candidate genes. Association analyses of single nucleotide polymorphisms have suggested the involvement of regulatory regions of these genes, and a few mutations affecting gene expression levels have been identified, indicating that the quantity rather than the quality of the gene product may be most relevant for these disorders. In addition, several of the candidate genes appear to be involved in neuronal migration, confirming the importance of early developmental processes. Accordingly, alterations in epigenetic processes such as DNA methylation and histone modification are likely to be important in the causes of language and learning disorders based on their functions in gene regulation. Epigenetic processes direct the differentiation of cells in early development when neurological pathways are set down, and mutations in genes involved in epigenetic regulation are known to cause cognitive disorders in humans. Epigenetic processes also regulate the changes in gene expression in response to learning, and alterations in histone modification are associated with learning and memory deficits in animals. Genetic defects in histone modification have been reversed in animals through therapeutic interventions resulting in rescue of these deficits, making it particularly important to investigate their potential contribution to learning disorders in humans.
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Roy AL. Biochemistry and biology of the inducible multifunctional transcription factor TFII-I: 10 years later. Gene 2011; 492:32-41. [PMID: 22037610 DOI: 10.1016/j.gene.2011.10.030] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 10/08/2011] [Accepted: 10/11/2011] [Indexed: 12/12/2022]
Abstract
Exactly twenty years ago TFII-I was discovered as a biochemical entity that was able to bind to and function via a core promoter element called the Initiator (Inr). Since then several different properties of this signal-induced multifunctional factor were discovered. Here I update these ever expanding functions of TFII-I--focusing primarily on the last ten years since the first review appeared in this journal.
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Affiliation(s)
- Ananda L Roy
- Department of Pathology, Sackler School of Biomedical Sciences, Tufts University School of Medicine, 150 Harrison Avenue, Boston, MA 02111, USA.
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Lim CKP, Ho CSH, Chou CHN, Waye MMY. Association of the rs3743205 variant of DYX1C1 with dyslexia in Chinese children. Behav Brain Funct 2011; 7:16. [PMID: 21599957 PMCID: PMC3123182 DOI: 10.1186/1744-9081-7-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 05/20/2011] [Indexed: 11/10/2022] Open
Abstract
Background Dyslexia is a learning disability that is characterized by difficulties in the acquisition of reading and spelling skills independent of intelligence, motivation or schooling. Studies of western populations have suggested that DYX1C1 is a candidate gene for dyslexia. In view of the different languages used in Caucasian and Chinese populations, it is therefore worthwhile to investigate whether there is an association of DYX1C1 in Chinese children with dyslexia. Method and Results Eight single nucleotide polymorphisms (SNPs) were genotyped from three hundred and ninety three individuals from 131 Chinese families with two which have been reported in the literature and six tag SNPs at DYX1C1. Analysis for allelic and haplotypic associations was performed with the UNPHASED program and multiple testing was corrected using false discovery rates. We replicated the previously reported association of rs3743205 in Chinese children with dyslexia (pcorrected = 0.0072). This SNP was also associated with rapid naming, phonological memory and orthographic skills in quantitative trait analysis. Conclusion Our findings suggest that DYX1C1 is associated with dyslexia in people of Chinese ethnicity in Hong Kong.
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Affiliation(s)
- Cadmon K P Lim
- Croucher Laboratory for Human Genomics, School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong
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Poelmans G, Buitelaar JK, Pauls DL, Franke B. A theoretical molecular network for dyslexia: integrating available genetic findings. Mol Psychiatry 2011; 16:365-82. [PMID: 20956978 DOI: 10.1038/mp.2010.105] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Developmental dyslexia is a common specific childhood learning disorder with a strong heritable component. Previous studies using different genetic approaches have identified several genetic loci and candidate genes for dyslexia. In this article, we have integrated the current knowledge on 14 dyslexia candidate genes suggested by cytogenetic findings, linkage and association studies. We found that 10 of the 14 dyslexia candidate genes (ROBO1, KIAA0319, KIAA0319L, S100B, DOCK4, FMR1, DIP2A, GTF2I, DYX1C1 and DCDC2) fit into a theoretical molecular network involved in neuronal migration and neurite outgrowth. Based on this, we also propose three novel dyslexia candidate genes (SLIT2, HMGB1 and VAPA) from known linkage regions, and we discuss the possible involvement of genes emerging from the two reported genome-wide association studies for reading impairment-related phenotypes in the identified network.
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Affiliation(s)
- G Poelmans
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
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Kere J. Molecular genetics and molecular biology of dyslexia. WILEY INTERDISCIPLINARY REVIEWS. COGNITIVE SCIENCE 2011; 2:441-448. [PMID: 26302203 DOI: 10.1002/wcs.138] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Developmental dyslexia has been recognized as a distinct entity among learning disabilities as early as the late 1800s and its partially genetic nature has been firmly established by family and twin studies. The application of genetic mapping and molecular cloning methods has revealed specific genes that contribute to the genetic risk, but those known now do not yet suffice for explaining all of it. More importantly, the first genes, some of them found by the study of rare families, have indicated specific neurodevelopmental processes important for the development of dyslexia, including control of neuronal migration for the DYX1C1, DCDC2, and KIAA0319 genes, and a role of axonal and dendritic guidance suggested by the ROBO1 gene. I anticipate that forthcoming research within only a few years will yield molecular networks with fundamental roles in the molecular biology of dyslexia, and may aid in resolving relationships between comorbid disorders. WIREs Cogni Sci 2011 2 441-448 DOI: 10.1002/wcs.138 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Juha Kere
- Department of Biosciences and Nutrition, and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Department of Medical Genetics, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
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The effects of embryonic knockdown of the candidate dyslexia susceptibility gene homologue Dyx1c1 on the distribution of GABAergic neurons in the cerebral cortex. Neuroscience 2010; 172:535-46. [PMID: 21070838 DOI: 10.1016/j.neuroscience.2010.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Revised: 11/01/2010] [Accepted: 11/02/2010] [Indexed: 01/30/2023]
Abstract
Developmental dyslexia is a language-based learning disability, and a number of candidate dyslexia susceptibility genes have been identified, including DYX1C1, KIAA0319, and DCDC2. Knockdown of function by embryonic transfection of small hairpin RNA (shRNA) of rat homologues of these genes dramatically disrupts neuronal migration to the cerebral cortex by both cell autonomous and non-cell autonomous effects. Here we sought to investigate the extent of non-cell autonomous effects following in utero disruption of the candidate dyslexia susceptibility gene homolog Dyx1c1 by assessing the effects of this disruption on GABAergic neurons. We transfected the ventricular zone of embryonic day (E) 15.5 rat pups with either Dyx1c1 shRNA, DYX1C1 expression construct, both Dyx1c1 shRNA and DYX1C1 expression construct, or a scrambled version of Dyx1c1 shRNA, and sacrificed them at postnatal day 21. The mothers of these rats were injected with BrdU at either E13.5, E15.5, or E17.5. Neurons transfected with Dyx1c1 shRNA were bi-modally distributed in the cerebral cortex with one population in heterotopic locations at the white matter border and another migrating beyond their expected location in the cerebral cortex. In contrast, there was no disruption of migration following transfection with the DYX1C1 expression construct. We found untransfected GABAergic neurons (parvalbumin, calretinin, and neuropeptide Y) in the heterotopic collections of neurons in Dyx1c1 shRNA treated animals, supporting the hypothesis of non-cell autonomous effects. In contrast, we found no evidence that the position of the GABAergic neurons that made it to the cerebral cortex was disrupted by the embryonic transfection with any of the constructs. Taken together, these results support the notion that neurons within heterotopias caused by transfection with Dyx1c1 shRNA result from both cell autonomous and non-cell autonomous effects, but there is no evidence to support non-cell autonomous disruption of neuronal position in the cerebral cortex itself.
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Benítez-Burraco A. Neurobiología y neurogenética de la dislexia. Neurologia 2010; 25:563-81. [DOI: 10.1016/j.nrl.2009.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 12/22/2009] [Indexed: 01/12/2023] Open
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Paracchini S, Ang QW, Stanley FJ, Monaco AP, Pennell CE, Whitehouse AJO. Analysis of dyslexia candidate genes in the Raine cohort representing the general Australian population. GENES BRAIN AND BEHAVIOR 2010; 10:158-65. [PMID: 20846247 PMCID: PMC3084500 DOI: 10.1111/j.1601-183x.2010.00651.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Several genes have been suggested as dyslexia candidates. Some of these candidate genes have been recently shown to be associated with literacy measures in sample cohorts derived from the general population. Here, we have conducted an association study in a novel sample derived from the Australian population (the Raine cohort) to further investigate the role of dyslexia candidate genes. We analysed markers, previously reported to be associated with dyslexia, located within the MRPL19/C2ORF3, KIAA0319, DCDC2 and DYX1C1 genes in a sample of 520 individuals and tested them for association with reading and spelling measures. Association signals were detected for several single nucleotide polymorphisms (SNPs) within DYX1C1 with both the reading and spelling tests. The high linkage disequilibrium (LD) we observed across the DYX1C1 gene suggests that the association signal might not be refined by further genetic mapping.
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Affiliation(s)
- S Paracchini
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom.
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