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Dewa KI, Arimura N, Kakegawa W, Itoh M, Adachi T, Miyashita S, Inoue YU, Hizawa K, Hori K, Honjoya N, Yagishita H, Taya S, Miyazaki T, Usui C, Tatsumoto S, Tsuzuki A, Uetake H, Sakai K, Yamakawa K, Sasaki T, Nagai J, Kawaguchi Y, Sone M, Inoue T, Go Y, Ichinohe N, Kaibuchi K, Watanabe M, Koizumi S, Yuzaki M, Hoshino M. Neuronal DSCAM regulates the peri-synaptic localization of GLAST in Bergmann glia for functional synapse formation. Nat Commun 2024; 15:458. [PMID: 38302444 PMCID: PMC10834496 DOI: 10.1038/s41467-023-44579-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 12/19/2023] [Indexed: 02/03/2024] Open
Abstract
In the central nervous system, astrocytes enable appropriate synapse function through glutamate clearance from the synaptic cleft; however, it remains unclear how astrocytic glutamate transporters function at peri-synaptic contact. Here, we report that Down syndrome cell adhesion molecule (DSCAM) in Purkinje cells controls synapse formation and function in the developing cerebellum. Dscam-mutant mice show defects in CF synapse translocation as is observed in loss of function mutations in the astrocytic glutamate transporter GLAST expressed in Bergmann glia. These mice show impaired glutamate clearance and the delocalization of GLAST away from the cleft of parallel fibre (PF) synapse. GLAST complexes with the extracellular domain of DSCAM. Riluzole, as an activator of GLAST-mediated uptake, rescues the proximal impairment in CF synapse formation in Purkinje cell-selective Dscam-deficient mice. DSCAM is required for motor learning, but not gross motor coordination. In conclusion, the intercellular association of synaptic and astrocyte proteins is important for synapse formation and function in neural transmission.
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Affiliation(s)
- Ken-Ichi Dewa
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
- Department of Neuropharmacology, Interdisciplinary Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
- Laboratory for Glia-Neuron Circuit Dynamics, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Nariko Arimura
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan.
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 980-8578, Tohoku, Japan.
| | - Wataru Kakegawa
- Department of Physiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Masayuki Itoh
- Department of Physiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Toma Adachi
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
| | - Satoshi Miyashita
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, 951-8585, Japan
| | - Yukiko U Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
| | - Kento Hizawa
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 980-8578, Tohoku, Japan
| | - Kei Hori
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
| | - Natsumi Honjoya
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 980-8578, Tohoku, Japan
| | - Haruya Yagishita
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 980-8578, Tohoku, Japan
| | - Shinichiro Taya
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
- Division of Behavioural Neuropharmacology, International Center for Brain Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Taisuke Miyazaki
- Department of Health Sciences, School of Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0812, Japan
| | - Chika Usui
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Shoji Tatsumoto
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan
| | - Akiko Tsuzuki
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
| | - Hirotomo Uetake
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
- Department of Biomolecular Science, Faculty of Science, Toho University, Funabashi, Saitama, 274-8510, Japan
| | - Kazuhisa Sakai
- Department of Ultrastructural Research, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
| | - Kazuhiro Yamakawa
- Department of Neurodevelopmental Disorder Genetics, Nagoya City University Graduate School of Medicine, Nagoya, Aichi, 467-8601, Japan
| | - Takuya Sasaki
- Department of Pharmacology, Graduate School of Pharmaceutical Sciences, Tohoku University, 980-8578, Tohoku, Japan
| | - Jun Nagai
- Laboratory for Glia-Neuron Circuit Dynamics, RIKEN Center for Brain Science, Wako, Saitama, 351-0198, Japan
| | - Yoshiya Kawaguchi
- Department of Life Science Frontiers, Center for iPS cell Research and Application (CiRA), Kyoto University, Kyoto, 606-8507, Japan
| | - Masaki Sone
- Department of Biomolecular Science, Faculty of Science, Toho University, Funabashi, Saitama, 274-8510, Japan
| | - Takayoshi Inoue
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
| | - Yasuhiro Go
- Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan
- Department of System Neuroscience, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, 444-8585, Japan
- Graduate School of Information Science, University of Hyogo, Kobe, Hyogo, 650-0047, Japan
| | - Noritaka Ichinohe
- Department of Ultrastructural Research, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan
| | - Kozo Kaibuchi
- Division of Cell Biology, International Center for Brain Science, Fujita Health University, Toyoake, Aichi, 470-1192, Japan
| | - Masahiko Watanabe
- Department of Anatomy, Faculty of Medicine, Hokkaido University, Sapporo, Hokkaido, 060-8638, Japan
- The University of Texas at Austin, Austin, Texas, 78712-0805, USA
| | - Schuichi Koizumi
- Department of Neuropharmacology, Interdisciplinary Graduate School of Medicine, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
| | - Michisuke Yuzaki
- Department of Physiology, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, 187-8502, Japan.
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2
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Hergenreder T, Yang T, Ye B. The role of Down syndrome cell adhesion molecule in Down syndrome. MEDICAL REVIEW (2021) 2024; 4:31-41. [PMID: 38515781 PMCID: PMC10954295 DOI: 10.1515/mr-2023-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/18/2024] [Indexed: 03/23/2024]
Abstract
Down syndrome (DS) is caused by the presence of an extra copy of the entire or a portion of human chromosome 21 (HSA21). This genomic alteration leads to elevated expression of numerous HSA21 genes, resulting in a variety of health issues in individuals with DS. Among the genes located in the DS "critical region" of HSA21, Down syndrome cell adhesion molecule (DSCAM) plays an important role in neuronal development. There is a growing body of evidence underscoring DSCAM's involvement in various DS-related disorders. This review aims to provide a concise overview of the established functions of DSCAM, with a particular focus on its implications in DS. We delve into the roles that DSCAM plays in DS-associated diseases. In the concluding section of this review, we explore prospective avenues for future research to further unravel DSCAM's role in DS and opportunities for therapeutic treatments.
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Affiliation(s)
- Ty Hergenreder
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Tao Yang
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Bing Ye
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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Liu H, Caballero-Florán RN, Hergenreder T, Yang T, Hull JM, Pan G, Li R, Veling MW, Isom LL, Kwan KY, Huang ZJ, Fuerst PG, Jenkins PM, Ye B. DSCAM gene triplication causes excessive GABAergic synapses in the neocortex in Down syndrome mouse models. PLoS Biol 2023; 21:e3002078. [PMID: 37079499 PMCID: PMC10118173 DOI: 10.1371/journal.pbio.3002078] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/14/2023] [Indexed: 04/21/2023] Open
Abstract
Down syndrome (DS) is caused by the trisomy of human chromosome 21 (HSA21). A major challenge in DS research is to identify the HSA21 genes that cause specific symptoms. Down syndrome cell adhesion molecule (DSCAM) is encoded by a HSA21 gene. Previous studies have shown that the protein level of the Drosophila homolog of DSCAM determines the size of presynaptic terminals. However, whether the triplication of DSCAM contributes to presynaptic development in DS remains unknown. Here, we show that DSCAM levels regulate GABAergic synapses formed on neocortical pyramidal neurons (PyNs). In the Ts65Dn mouse model for DS, where DSCAM is overexpressed due to DSCAM triplication, GABAergic innervation of PyNs by basket and chandelier interneurons is increased. Genetic normalization of DSCAM expression rescues the excessive GABAergic innervations and the increased inhibition of PyNs. Conversely, loss of DSCAM impairs GABAergic synapse development and function. These findings demonstrate excessive GABAergic innervation and synaptic transmission in the neocortex of DS mouse models and identify DSCAM overexpression as the cause. They also implicate dysregulated DSCAM levels as a potential pathogenic driver in related neurological disorders.
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Affiliation(s)
- Hao Liu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - René N. Caballero-Florán
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Ty Hergenreder
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Tao Yang
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jacob M. Hull
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Geng Pan
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ruonan Li
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Macy W. Veling
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lori L. Isom
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Kenneth Y. Kwan
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Z. Josh Huang
- Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Biomedical Engineering, Duke University Pratt School of Engineering, Durham, North Carolina, United States of America
| | - Peter G. Fuerst
- University of Idaho, Department of Biological Sciences, Moscow, Idaho, United States of America
| | - Paul M. Jenkins
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Psychiatry, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Bing Ye
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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Hasina Z, Wang N, Wang CC. Developmental Neuropathology and Neurodegeneration of Down Syndrome: Current Knowledge in Humans. Front Cell Dev Biol 2022; 10:877711. [PMID: 35676933 PMCID: PMC9168127 DOI: 10.3389/fcell.2022.877711] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/18/2022] [Indexed: 12/25/2022] Open
Abstract
Individuals with Down syndrome (DS) suffer from developmental delay, intellectual disability, and an early-onset of neurodegeneration, Alzheimer’s-like disease, or precocious dementia due to an extra chromosome 21. Studying the changes in anatomical, cellular, and molecular levels involved may help to understand the pathogenesis and develop target treatments, not just medical, but also surgical, cell and gene therapy, etc., for individuals with DS. Here we aim to identify key neurodevelopmental manifestations, locate knowledge gaps, and try to build molecular networks to better understand the mechanisms and clinical importance. We summarize current information about the neuropathology and neurodegeneration of the brain from conception to adulthood of foetuses and individuals with DS at anatomical, cellular, and molecular levels in humans. Understanding the alterations and characteristics of developing Down syndrome will help target treatment to improve the clinical outcomes. Early targeted intervention/therapy for the manifestations associated with DS in either the prenatal or postnatal period may be useful to rescue the neuropathology and neurodegeneration in DS.
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Affiliation(s)
- Zinnat Hasina
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Nicole Wang
- School of Veterinary Medicine, Glasgow University, Glasgow, United Kingdom
| | - Chi Chiu Wang
- Department of Obstetrics & Gynaecology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, School of Biomedical Sciences, Chinese University of Hong Kong -Sichuan University Joint Laboratory in Reproductive Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- *Correspondence: Chi Chiu Wang,
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5
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Mitsogiannis MD, Pancho A, Aerts T, Sachse SM, Vanlaer R, Noterdaeme L, Schmucker D, Seuntjens E. Subtle Roles of Down Syndrome Cell Adhesion Molecules in Embryonic Forebrain Development and Neuronal Migration. Front Cell Dev Biol 2021; 8:624181. [PMID: 33585465 PMCID: PMC7876293 DOI: 10.3389/fcell.2020.624181] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/22/2020] [Indexed: 12/26/2022] Open
Abstract
Down Syndrome (DS) Cell Adhesion Molecules (DSCAMs) are transmembrane proteins of the immunoglobulin superfamily. Human DSCAM is located within the DS critical region of chromosome 21 (duplicated in Down Syndrome patients), and mutations or copy-number variations of this gene have also been associated to Fragile X syndrome, intellectual disability, autism, and bipolar disorder. The DSCAM paralogue DSCAM-like 1 (DSCAML1) maps to chromosome 11q23, implicated in the development of Jacobsen and Tourette syndromes. Additionally, a spontaneous mouse DSCAM deletion leads to motor coordination defects and seizures. Previous research has revealed roles for DSCAMs in several neurodevelopmental processes, including synaptogenesis, dendritic self-avoidance, cell sorting, axon growth and branching. However, their functions in embryonic mammalian forebrain development have yet to be completely elucidated. In this study, we revealed highly dynamic spatiotemporal patterns of Dscam and Dscaml1 expression in definite cortical layers of the embryonic mouse brain, as well as in structures and ganglionic eminence-derived neural populations within the embryonic subpallium. However, an in-depth histological analysis of cortical development, ventral forebrain morphogenesis, cortical interneuron migration, and cortical-subcortical connectivity formation processes in Dscam and Dscaml1 knockout mice (Dscam del17 and Dscaml1 GT ) at several embryonic stages indicated that constitutive loss of Dscam and Dscaml1 does not affect these developmental events in a significant manner. Given that several Dscam- and Dscaml1-linked neurodevelopmental disorders are associated to chromosomal region duplication events, we furthermore sought to examine the neurodevelopmental effects of Dscam and Dscaml1 gain of function (GOF). In vitro, ex vivo, and in vivo GOF negatively impacted neural migration processes important to cortical development, and affected the morphology of maturing neurons. Overall, these findings contribute to existing knowledge on the molecular etiology of human neurodevelopmental disorders by elucidating how dosage variations of genes encoding adhesive cues can disrupt cell-cell or cell-environment interactions crucial for neuronal migration.
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Affiliation(s)
- Manuela D. Mitsogiannis
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Anna Pancho
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Tania Aerts
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sonja M. Sachse
- Neuronal Wiring Laboratory, Department of Neurosciences, VIB-KU Leuven Center for Brain & Disease Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ria Vanlaer
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lut Noterdaeme
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Dietmar Schmucker
- Neuronal Wiring Laboratory, Department of Neurosciences, VIB-KU Leuven Center for Brain & Disease Research, Katholieke Universiteit Leuven, Leuven, Belgium
- Neuronal Wiring Group, Life & Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Eve Seuntjens
- Developmental Neurobiology Group, Animal Physiology and Neurobiology Division, Department of Biology, Katholieke Universiteit Leuven, Leuven, Belgium
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6
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Stachowicz K. The role of DSCAM in the regulation of synaptic plasticity: possible involvement in neuropsychiatric disorders. Acta Neurobiol Exp (Wars) 2018. [DOI: 10.21307/ane-2018-019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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7
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O'Shea KS, McInnis MG. Neurodevelopmental origins of bipolar disorder: iPSC models. Mol Cell Neurosci 2015; 73:63-83. [PMID: 26608002 DOI: 10.1016/j.mcn.2015.11.006] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 10/14/2015] [Accepted: 11/18/2015] [Indexed: 12/22/2022] Open
Abstract
Bipolar disorder (BP) is a chronic neuropsychiatric condition characterized by pathological fluctuations in mood from mania to depression. Adoption, twin and family studies have consistently identified a significant hereditary component to BP, yet there is no clear genetic event or consistent neuropathology. BP has been suggested to have a developmental origin, although this hypothesis has been difficult to test since there are no viable neurons or glial cells to analyze, and research has relied largely on postmortem brain, behavioral and imaging studies, or has examined proxy tissues including saliva, olfactory epithelium and blood cells. Neurodevelopmental factors, particularly pathways related to nervous system development, cell migration, extracellular matrix, H3K4 methylation, and calcium signaling have been identified in large gene expression and GWAS studies as altered in BP. Recent advances in stem cell biology, particularly the ability to reprogram adult somatic tissues to a pluripotent state, now make it possible to interrogate these pathways in viable cell models. A number of induced pluripotent stem cell (iPSC) lines from BP patient and healthy control (C) individuals have been derived in several laboratories, and their ability to form cortical neurons examined. Early studies suggest differences in activity, calcium signaling, blocks to neuronal differentiation, and changes in neuronal, and possibly glial, lineage specification. Initial observations suggest that differentiation of BP patient-derived neurons to dorsal telencephalic derivatives may be impaired, possibly due to alterations in WNT, Hedgehog or Nodal pathway signaling. These investigations strongly support a developmental contribution to BP and identify novel pathways, mechanisms and opportunities for improved treatments.
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Affiliation(s)
- K Sue O'Shea
- Department of Cell and Developmental Biology, University of Michigan, 3051 BSRB, 109 Zina Pitcher PL, Ann Arbor, MI 48109-2200, United States; Department of Psychiatry, University of Michigan, 4250 Plymouth Rd, Ann Arbor, MI 48109-5765, United States.
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, 4250 Plymouth Rd, Ann Arbor, MI 48109-5765, United States
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8
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Roles for DSCAM and DSCAML1 in central nervous system development and disease. ADVANCES IN NEUROBIOLOGY 2014; 8:249-70. [PMID: 25300140 DOI: 10.1007/978-1-4614-8090-7_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DSCAMs (Down syndrome cell adhesion molecules) are a group of immunoglobulin-like transmembrane proteins that contain fibronectin III domains. The founding member of the family was isolated in a positional cloning study that sought to identify genes located on chromosome 21 at the locus 21q22.2-q22.3 that is implicated in the neurological and cardiac phenotypes associated with Down's syndrome. In Drosophila, Dscam proteins are involved in neuronal wiring, while in vertebrates, the role of these cell adhesion molecules in neurogenesis, dendritogenesis, axonal outgrowth, synaptogenesis, and synaptic plasticity is only just beginning to be understood. In this chapter, we will review the functions ascribed to the two paralogous proteins found in humans, DSCAM and DSCAML1 (DSCAM-like 1), based on findings in knockout mice. The signaling pathways downstream of DSCAM activation and the role of DSCAM miss-expression in disease will be also discussed, particularly with regard to the intellectual disability in Down's syndrome.
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9
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Dolejsi E, Bodenstorfer B, Frommlet F. Analyzing genome-wide association studies with an FDR controlling modification of the Bayesian Information Criterion. PLoS One 2014; 9:e103322. [PMID: 25061809 PMCID: PMC4111553 DOI: 10.1371/journal.pone.0103322] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 07/01/2014] [Indexed: 01/24/2023] Open
Abstract
The prevailing method of analyzing GWAS data is still to test each marker individually, although from a statistical point of view it is quite obvious that in case of complex traits such single marker tests are not ideal. Recently several model selection approaches for GWAS have been suggested, most of them based on LASSO-type procedures. Here we will discuss an alternative model selection approach which is based on a modification of the Bayesian Information Criterion (mBIC2) which was previously shown to have certain asymptotic optimality properties in terms of minimizing the misclassification error. Heuristic search strategies are introduced which attempt to find the model which minimizes mBIC2, and which are efficient enough to allow the analysis of GWAS data. Our approach is implemented in a software package called MOSGWA. Its performance in case control GWAS is compared with the two algorithms HLASSO and d-GWASelect, as well as with single marker tests, where we performed a simulation study based on real SNP data from the POPRES sample. Our results show that MOSGWA performs slightly better than HLASSO, where specifically for more complex models MOSGWA is more powerful with only a slight increase in Type I error. On the other hand according to our simulations GWASelect does not at all control the type I error when used to automatically determine the number of important SNPs. We also reanalyze the GWAS data from the Wellcome Trust Case-Control Consortium and compare the findings of the different procedures, where MOSGWA detects for complex diseases a number of interesting SNPs which are not found by other methods.
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Affiliation(s)
- Erich Dolejsi
- Center for Medical Statistics, Informatics, and Intelligent Systems/Section of Medical Statistics, Medical University Vienna, Vienna, Austria
| | | | - Florian Frommlet
- Center for Medical Statistics, Informatics, and Intelligent Systems/Section of Medical Statistics, Medical University Vienna, Vienna, Austria
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10
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Kim JH, Wang X, Coolon R, Ye B. Dscam expression levels determine presynaptic arbor sizes in Drosophila sensory neurons. Neuron 2013; 78:827-38. [PMID: 23764288 DOI: 10.1016/j.neuron.2013.05.020] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2013] [Indexed: 11/19/2022]
Abstract
Expression of the Down syndrome cell-adhesion molecule (Dscam) is increased in the brains of patients with several neurological disorders. Although Dscam is critically involved in many aspects of neuronal development, little is known about either the mechanism that regulates its expression or the functional consequences of dysregulated Dscam expression. Here, we show that Dscam expression levels serve as an instructive code for the size control of presynaptic arbor. Two convergent pathways, involving dual leucine zipper kinase (DLK) and fragile X mental retardation protein (FMRP), control Dscam expression through protein translation. Defects in this regulation of Dscam translation lead to exuberant presynaptic arbor growth in Drosophila somatosensory neurons. Our findings uncover a function of Dscam in presynaptic size control and provide insights into how dysregulated Dscam may contribute to the pathogenesis of neurological disorders.
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Affiliation(s)
- Jung Hwan Kim
- Life Sciences Institute and Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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11
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Wen B, Wu H, Loh YH, Briem E, Daley GQ, Feinberg AP. Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions. BMC Genomics 2012; 13:566. [PMID: 23102236 PMCID: PMC3507770 DOI: 10.1186/1471-2164-13-566] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 10/19/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The organization of higher order chromatin is an emerging epigenetic mechanism for understanding development and disease. We and others have previously observed dynamic changes during differentiation and oncogenesis in large heterochromatin domains such as Large Organized Chromatin K (lysine) modifications (LOCKs), of histone H3 lysine-9 dimethylation (H3K9me2) or other repressive histone posttranslational modifications. The microstructure of these regions has not previously been explored. RESULTS We analyzed the genome-wide distribution of H3K9me2 in two human pluripotent stem cell lines and three differentiated cells lines. We identified > 2,500 small regions with very low H3K9me2 signals in the body of LOCKs, which were termed as euchromatin islands (EIs). EIs are 6.5-fold enriched for DNase I Hypersensitive Sites and 8-fold enriched for the binding of CTCF, the major organizer of higher-order chromatin. Furthermore, EIs are 2-6 fold enriched for differentially DNA-methylated regions associated with tissue types (T-DMRs), reprogramming (R-DMRs) and cancer (C-DMRs). Gene ontology (GO) analysis suggests that EI-associated genes are functionally related to organ system development, cell adhesion and cell differentiation. CONCLUSIONS We identify the existence of EIs as a finer layer of epigenomic architecture within large heterochromatin domains. Their enrichment for CTCF sites and DNAse hypersensitive sites, as well as association with DMRs, suggest that EIs play an important role in normal epigenomic architecture and its disruption in disease.
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Affiliation(s)
- Bo Wen
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Graae L, Karlsson R, Paddock S. Significant association of estrogen receptor binding site variation with bipolar disorder in females. PLoS One 2012; 7:e32304. [PMID: 22389694 PMCID: PMC3289647 DOI: 10.1371/journal.pone.0032304] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/26/2012] [Indexed: 12/22/2022] Open
Abstract
Major depression is nearly twice as prevalent in women compared to men. In bipolar disorder, depressive episodes have been reported to be more common amongst female patients. Furthermore, periods of depression often correlate with periods of hormonal fluctuations. A link between hormone signaling and these mood disorders has, therefore, been suggested to exist in many studies. Estrogen, one of the primary female sex hormones, mediates its effect mostly by binding to estrogen receptors (ERs). Nuclear ERs function as transcription factors and regulate gene transcription by binding to specific DNA sequences. A nucleotide change in the binding sequence might alter the binding efficiency, which could affect transcription levels of nearby genes. In order to investigate if variation in ER DNA-binding sequences may be involved in mood disorders, we conducted a genome-wide study of ER DNA-binding in patients diagnosed with major depression or bipolar disorder. Association studies were performed within each gender separately and the results were corrected for multiple testing by the Bonferroni method. In the female bipolar disorder material a significant association result was found for rs6023059 (corrected p-value = 0.023; odds ratio (OR) 0.681, 95% confidence interval (CI) 0.570–0.814), a single nucleotide polymorphism (SNP) placed downstream of the gene coding for transglutaminase 2 (TGM2). Thus, females with a specific genotype at this SNP may be more vulnerable to fluctuating estrogen levels, which may then act as a triggering factor for bipolar disorder.
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Affiliation(s)
- Lisette Graae
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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Patel SD, Le-Niculescu H, Koller DL, Green SD, Lahiri DK, McMahon FJ, Nurnberger JI, Niculescu AB. Coming to grips with complex disorders: genetic risk prediction in bipolar disorder using panels of genes identified through convergent functional genomics. Am J Med Genet B Neuropsychiatr Genet 2010; 153B:850-77. [PMID: 20468069 DOI: 10.1002/ajmg.b.31087] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We previously proposed and provided proof of principle for the use of a complementary approach, convergent functional genomics (CFG), combining gene expression and genetic data, from human and animal model studies, as a way of mining the existing GWAS datasets for signals that are there already, but did not reach significance using a genetics-only approach [Le-Niculescu et al., 2009b]. CFG provides a fit-to-disease prioritization of genes that leads to generalizability in independent cohorts, and counterbalances the fit-to-cohort prioritization inherent in classic genetic-only approaches, which have been plagued by poor reproducibility across cohorts. We have now extended our previous work to include more datasets of GWAS, and more recent evidence from other lines of work. In essence our analysis is the most comprehensive integration of genetics and functional genomics to date in the field of bipolar disorder. Biological pathway analyses identified top canonical pathways, and epistatic interaction testing inside these pathways has identified genes that merit future follow-up as direct interactors (intra-pathway epistasis, INPEP). Moreover, we have put together a panel of best P-value single nucleotide polymorphisms (SNPs), based on the top candidate genes we identified. We have developed a genetic risk prediction score (GRPS) based on our panel, and demonstrate how in two independent test cohorts the GRPS differentiates between subjects with bipolar disorder and normal controls, in both European-American and African-American populations. Lastly, we describe a prototype of how such testing could be used to categorize disease risk in individuals and aid personalized medicine approaches, in psychiatry and beyond.
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Affiliation(s)
- S D Patel
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, Indiana, USA
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