1
|
Tan WJ, Hawley HR, Wilson SJ, Fitzsimons HL. Deciphering the roles of subcellular distribution and interactions involving the MEF2 binding region, the ankyrin repeat binding motif and the catalytic site of HDAC4 in Drosophila neuronal morphogenesis. BMC Biol 2024; 22:2. [PMID: 38167120 PMCID: PMC10763444 DOI: 10.1186/s12915-023-01800-1] [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: 02/14/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Dysregulation of nucleocytoplasmic shuttling of histone deacetylase 4 (HDAC4) is associated with several neurodevelopmental and neurodegenerative disorders. Consequently, understanding the roles of nuclear and cytoplasmic HDAC4 along with the mechanisms that regulate nuclear entry and exit is an area of concerted effort. Efficient nuclear entry is dependent on binding of the transcription factor MEF2, as mutations in the MEF2 binding region result in cytoplasmic accumulation of HDAC4. It is well established that nuclear exit and cytoplasmic retention are dependent on 14-3-3-binding, and mutations that affect binding are widely used to induce nuclear accumulation of HDAC4. While regulation of HDAC4 shuttling is clearly important, there is a gap in understanding of how the nuclear and cytoplasmic distribution of HDAC4 impacts its function. Furthermore, it is unclear whether other features of the protein including the catalytic site, the MEF2-binding region and/or the ankyrin repeat binding motif influence the distribution and/or activity of HDAC4 in neurons. Since HDAC4 functions are conserved in Drosophila, and increased nuclear accumulation of HDAC4 also results in impaired neurodevelopment, we used Drosophila as a genetic model for investigation of HDAC4 function. RESULTS Here we have generated a series of mutants for functional dissection of HDAC4 via in-depth examination of the resulting subcellular distribution and nuclear aggregation, and correlate these with developmental phenotypes resulting from their expression in well-established models of neuronal morphogenesis of the Drosophila mushroom body and eye. We found that in the mushroom body, forced sequestration of HDAC4 in the nucleus or the cytoplasm resulted in defects in axon morphogenesis. The actions of HDAC4 that resulted in impaired development were dependent on the MEF2 binding region, modulated by the ankyrin repeat binding motif, and largely independent of an intact catalytic site. In contrast, disruption to eye development was largely independent of MEF2 binding but mutation of the catalytic site significantly reduced the phenotype, indicating that HDAC4 acts in a neuronal-subtype-specific manner. CONCLUSIONS We found that the impairments to mushroom body and eye development resulting from nuclear accumulation of HDAC4 were exacerbated by mutation of the ankyrin repeat binding motif, whereas there was a differing requirement for the MEF2 binding site and an intact catalytic site. It will be of importance to determine the binding partners of HDAC4 in nuclear aggregates and in the cytoplasm of these tissues to further understand its mechanisms of action.
Collapse
Affiliation(s)
- Wei Jun Tan
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Hannah R Hawley
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Sarah J Wilson
- School of Natural Sciences, Massey University, Palmerston North, New Zealand
| | - Helen L Fitzsimons
- School of Natural Sciences, Massey University, Palmerston North, New Zealand.
| |
Collapse
|
2
|
Cabana-Domínguez J, Antón-Galindo E, Fernàndez-Castillo N, Singgih EL, O'Leary A, Norton WH, Strekalova T, Schenck A, Reif A, Lesch KP, Slattery D, Cormand B. The translational genetics of ADHD and related phenotypes in model organisms. Neurosci Biobehav Rev 2023; 144:104949. [PMID: 36368527 DOI: 10.1016/j.neubiorev.2022.104949] [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: 07/01/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a highly prevalent neurodevelopmental disorder resulting from the interaction between genetic and environmental risk factors. It is well known that ADHD co-occurs frequently with other psychiatric disorders due, in part, to shared genetics factors. Although many studies have contributed to delineate the genetic landscape of psychiatric disorders, their specific molecular underpinnings are still not fully understood. The use of animal models can help us to understand the role of specific genes and environmental stimuli-induced epigenetic modifications in the pathogenesis of ADHD and its comorbidities. The aim of this review is to provide an overview on the functional work performed in rodents, zebrafish and fruit fly and highlight the generated insights into the biology of ADHD, with a special focus on genetics and epigenetics. We also describe the behavioral tests that are available to study ADHD-relevant phenotypes and comorbid traits in these models. Furthermore, we have searched for new models to study ADHD and its comorbidities, which can be useful to test potential pharmacological treatments.
Collapse
Affiliation(s)
- Judit Cabana-Domínguez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
| | - Ester Antón-Galindo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain
| | - Euginia L Singgih
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Aet O'Leary
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany; Division of Neuropsychopharmacology, Department of Psychology, University of Tartu, Tartu, Estonia
| | - William Hg Norton
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Tatyana Strekalova
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany, and Department of Neuropsychology and Psychiatry, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany
| | - Klaus-Peter Lesch
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany, and Department of Neuropsychology and Psychiatry, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - David Slattery
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
| |
Collapse
|
3
|
Rounds JC, Corgiat EB, Ye C, Behnke JA, Kelly SM, Corbett AH, Moberg KH. The disease-associated proteins Drosophila Nab2 and Ataxin-2 interact with shared RNAs and coregulate neuronal morphology. Genetics 2022; 220:iyab175. [PMID: 34791182 PMCID: PMC8733473 DOI: 10.1093/genetics/iyab175] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 09/27/2021] [Indexed: 01/05/2023] Open
Abstract
Nab2 encodes the Drosophila melanogaster member of a conserved family of zinc finger polyadenosine RNA-binding proteins (RBPs) linked to multiple steps in post-transcriptional regulation. Mutation of the Nab2 human ortholog ZC3H14 gives rise to an autosomal recessive intellectual disability but understanding of Nab2/ZC3H14 function in metazoan nervous systems is limited, in part because no comprehensive identification of metazoan Nab2/ZC3H14-associated RNA transcripts has yet been conducted. Moreover, many Nab2/ZC3H14 functional protein partnerships remain unidentified. Here, we present evidence that Nab2 genetically interacts with Ataxin-2 (Atx2), which encodes a neuronal translational regulator, and that these factors coordinately regulate neuronal morphology, circadian behavior, and adult viability. We then present the first high-throughput identifications of Nab2- and Atx2-associated RNAs in Drosophila brain neurons using RNA immunoprecipitation-sequencing (RIP-Seq). Critically, the RNA interactomes of each RBP overlap, and Nab2 exhibits high specificity in its RNA associations in neurons in vivo, associating with a small fraction of all polyadenylated RNAs. The identities of shared associated transcripts (e.g., drk, me31B, stai) and of transcripts specific to Nab2 or Atx2 (e.g., Arpc2 and tea) promise insight into neuronal functions of, and genetic interactions between, each RBP. Consistent with prior biochemical studies, Nab2-associated neuronal RNAs are overrepresented for internal A-rich motifs, suggesting these sequences may partially mediate Nab2 target selection. These data support a model where Nab2 functionally opposes Atx2 in neurons, demonstrate Nab2 shares associated neuronal RNAs with Atx2, and reveal Drosophila Nab2 associates with a more specific subset of polyadenylated mRNAs than its polyadenosine affinity alone may suggest.
Collapse
Affiliation(s)
- J Christopher Rounds
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Edwin B Corgiat
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Changtian Ye
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Joseph A Behnke
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Seth M Kelly
- Department of Biology, The College of Wooster, Wooster, OH 44691, USA
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Kenneth H Moberg
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| |
Collapse
|
4
|
Dissecting the complexity of CNV pathogenicity: insights from Drosophila and zebrafish models. Curr Opin Genet Dev 2021; 68:79-87. [PMID: 33812298 DOI: 10.1016/j.gde.2021.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/21/2021] [Accepted: 02/26/2021] [Indexed: 11/20/2022]
Abstract
Genetic architecture predisposes regions of the human genome to copy-number variants, which confer substantial disease risk, most prominently towards neurodevelopmental disorders. These variants typically contain multiple genes and are often associated with extensive pleiotropy and variable phenotypic expressivity. Despite the expansion of the fidelity of CNV detection, and the study of such lesions at the population level, understanding causal mechanisms for CNV phenotypes will require biological testing of constituent genes and their interactions. In this regard, model systems amenable to high-throughput phenotypic analysis of dosage-sensitive genes (and combinations thereof) are beginning to offer improved granularity of CNV-driven pathology. Here, we review the utility of Drosophila and zebrafish models for pathogenic CNV regions, highlight the advances made in discovery of single gene drivers and genetic interactions that determine specific CNV phenotypes, and argue for their validity in dissecting conserved developmental mechanisms associated with CNVs.
Collapse
|
5
|
Mariano V, Achsel T, Bagni C, Kanellopoulos AK. Modelling Learning and Memory in Drosophila to Understand Intellectual Disabilities. Neuroscience 2020; 445:12-30. [PMID: 32730949 DOI: 10.1016/j.neuroscience.2020.07.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022]
Abstract
Neurodevelopmental disorders (NDDs) include a large number of conditions such as Fragile X syndrome, autism spectrum disorders and Down syndrome, among others. They are characterized by limitations in adaptive and social behaviors, as well as intellectual disability (ID). Whole-exome and whole-genome sequencing studies have highlighted a large number of NDD/ID risk genes. To dissect the genetic causes and underlying biological pathways, in vivo experimental validation of the effects of these mutations is needed. The fruit fly, Drosophila melanogaster, is an ideal model to study NDDs, with highly tractable genetics, combined with simple behavioral and circuit assays, permitting rapid medium-throughput screening of NDD/ID risk genes. Here, we review studies where the use of well-established assays to study mechanisms of learning and memory in Drosophila has permitted insights into molecular mechanisms underlying IDs. We discuss how technologies in the fly model, combined with a high degree of molecular and physiological conservation between flies and mammals, highlight the Drosophila system as an ideal model to study neurodevelopmental disorders, from genetics to behavior.
Collapse
Affiliation(s)
- Vittoria Mariano
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne 1005, Switzerland; Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne 1005, Switzerland
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne 1005, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome 00133, Italy.
| | | |
Collapse
|
6
|
Proteomic mapping of Drosophila transgenic elav.L-GAL4/+ brain as a tool to illuminate neuropathology mechanisms. Sci Rep 2020; 10:5430. [PMID: 32214222 PMCID: PMC7096425 DOI: 10.1038/s41598-020-62510-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/10/2020] [Indexed: 12/13/2022] Open
Abstract
Drosophila brain has emerged as a powerful model system for the investigation of genes being related to neurological pathologies. To map the proteomic landscape of fly brain, in a high-resolution scale, we herein employed a nano liquid chromatography-tandem mass spectrometry technology, and high-content catalogues of 7,663 unique peptides and 2,335 single proteins were generated. Protein-data processing, through UniProt, DAVID, KEGG and PANTHER bioinformatics subroutines, led to fly brain-protein classification, according to sub-cellular topology, molecular function, implication in signaling and contribution to neuronal diseases. Given the importance of Ubiquitin Proteasome System (UPS) in neuropathologies and by using the almost completely reassembled UPS, we genetically targeted genes encoding components of the ubiquitination-dependent protein-degradation machinery. This analysis showed that driving RNAi toward proteasome components and regulators, using the GAL4-elav.L driver, resulted in changes to longevity and climbing-activity patterns during aging. Our proteomic map is expected to advance the existing knowledge regarding brain biology in animal species of major translational-research value and economical interest.
Collapse
|
7
|
Singh MD, Jensen M, Lasser M, Huber E, Yusuff T, Pizzo L, Lifschutz B, Desai I, Kubina A, Yennawar S, Kim S, Iyer J, Rincon-Limas DE, Lowery LA, Girirajan S. NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and Xenopus laevis models. PLoS Genet 2020; 16:e1008590. [PMID: 32053595 PMCID: PMC7043793 DOI: 10.1371/journal.pgen.1008590] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/26/2020] [Accepted: 12/30/2019] [Indexed: 12/12/2022] Open
Abstract
The 1.6 Mbp deletion on chromosome 3q29 is associated with a range of neurodevelopmental disorders, including schizophrenia, autism, microcephaly, and intellectual disability. Despite its importance towards neurodevelopment, the role of individual genes, genetic interactions, and disrupted biological mechanisms underlying the deletion have not been thoroughly characterized. Here, we used quantitative methods to assay Drosophila melanogaster and Xenopus laevis models with tissue-specific individual and pairwise knockdown of 14 homologs of genes within the 3q29 region. We identified developmental, cellular, and neuronal phenotypes for multiple homologs of 3q29 genes, potentially due to altered apoptosis and cell cycle mechanisms during development. Using the fly eye, we screened for 314 pairwise knockdowns of homologs of 3q29 genes and identified 44 interactions between pairs of homologs and 34 interactions with other neurodevelopmental genes. Interestingly, NCBP2 homologs in Drosophila (Cbp20) and X. laevis (ncbp2) enhanced the phenotypes of homologs of the other 3q29 genes, leading to significant increases in apoptosis that disrupted cellular organization and brain morphology. These cellular and neuronal defects were rescued with overexpression of the apoptosis inhibitors Diap1 and xiap in both models, suggesting that apoptosis is one of several potential biological mechanisms disrupted by the deletion. NCBP2 was also highly connected to other 3q29 genes in a human brain-specific interaction network, providing support for the relevance of our results towards the human deletion. Overall, our study suggests that NCBP2-mediated genetic interactions within the 3q29 region disrupt apoptosis and cell cycle mechanisms during development. Rare copy-number variants, or large deletions and duplications in the genome, are associated with a wide range of neurodevelopmental disorders. The 3q29 deletion confers an increased risk for schizophrenia and autism. To understand the conserved biological mechanisms that are disrupted by this deletion, we systematically tested 14 individual homologs and 314 pairwise interactions of 3q29 genes for neuronal, cellular, and developmental phenotypes in Drosophila melanogaster and Xenopus laevis models. We found that multiple homologs of genes within the deletion region contribute towards developmental defects, such as larval lethality and disrupted cellular organization. Interestingly, we found that NCBP2 acts as a key modifier gene within the region, enhancing the developmental phenotypes of each of the homologs for other 3q29 genes and leading to disruptions in apoptosis and cell cycle pathways. Our results suggest that multiple genes within the 3q29 region interact with each other through shared mechanisms and jointly contribute to neurodevelopmental defects.
Collapse
Affiliation(s)
- Mayanglambam Dhruba Singh
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Micaela Lasser
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Emily Huber
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Tanzeen Yusuff
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Brian Lifschutz
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Inshya Desai
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Alexis Kubina
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sneha Yennawar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Sydney Kim
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Janani Iyer
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America
| | - Laura Anne Lowery
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
- Department of Medicine, Boston University Medical Center, Boston, Massachusetts, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| |
Collapse
|
8
|
Straub J, Gregor A, Sauerer T, Fliedner A, Distel L, Suchy C, Ekici AB, Ferrazzi F, Zweier C. Genetic interaction screen for severe neurodevelopmental disorders reveals a functional link between Ube3a and Mef2 in Drosophila melanogaster. Sci Rep 2020; 10:1204. [PMID: 31988313 PMCID: PMC6985129 DOI: 10.1038/s41598-020-58182-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 01/13/2020] [Indexed: 11/09/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically extremely heterogeneous with shared phenotypes often associated with genes from the same networks. Mutations in TCF4, MEF2C, UBE3A, ZEB2 or ATRX cause phenotypically overlapping, syndromic forms of NDDs with severe intellectual disability, epilepsy and microcephaly. To characterize potential functional links between these genes/proteins, we screened for genetic interactions in Drosophila melanogaster. We induced ubiquitous or tissue specific knockdown or overexpression of each single orthologous gene (Da, Mef2, Ube3a, Zfh1, XNP) and in pairwise combinations. Subsequently, we assessed parameters such as lethality, wing and eye morphology, neuromuscular junction morphology, bang sensitivity and climbing behaviour in comparison between single and pairwise dosage manipulations. We found most stringent evidence for genetic interaction between Ube3a and Mef2 as simultaneous dosage manipulation in different tissues including glia, wing and eye resulted in multiple phenotype modifications. We subsequently found evidence for physical interaction between UBE3A and MEF2C also in human cells. Systematic pairwise assessment of the Drosophila orthologues of five genes implicated in clinically overlapping, severe NDDs and subsequent confirmation in a human cell line revealed interactions between UBE3A/Ube3a and MEF2C/Mef2, thus contributing to the characterization of the underlying molecular commonalities.
Collapse
Affiliation(s)
- Jonas Straub
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Anne Gregor
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Tatjana Sauerer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Anna Fliedner
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Laila Distel
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christine Suchy
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Fulvia Ferrazzi
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054, Erlangen, Germany.
| |
Collapse
|
9
|
Fenckova M, Blok LER, Asztalos L, Goodman DP, Cizek P, Singgih EL, Glennon JC, IntHout J, Zweier C, Eichler EE, von Reyn CR, Bernier RA, Asztalos Z, Schenck A. Habituation Learning Is a Widely Affected Mechanism in Drosophila Models of Intellectual Disability and Autism Spectrum Disorders. Biol Psychiatry 2019; 86:294-305. [PMID: 31272685 PMCID: PMC7053436 DOI: 10.1016/j.biopsych.2019.04.029] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Although habituation is one of the most ancient and fundamental forms of learning, its regulators and its relevance for human disease are poorly understood. METHODS We manipulated the orthologs of 286 genes implicated in intellectual disability (ID) with or without comorbid autism spectrum disorder (ASD) specifically in Drosophila neurons, and we tested these models in light-off jump habituation. We dissected neuronal substrates underlying the identified habituation deficits and integrated genotype-phenotype annotations, gene ontologies, and interaction networks to determine the clinical features and molecular processes that are associated with habituation deficits. RESULTS We identified >100 genes required for habituation learning. For 93 of these genes, a role in habituation learning was previously unknown. These genes characterize ID disorders with macrocephaly and/or overgrowth and comorbid ASD. Moreover, individuals with ASD from the Simons Simplex Collection carrying damaging de novo mutations in these genes exhibit increased aberrant behaviors associated with inappropriate, stereotypic speech. At the molecular level, ID genes required for normal habituation are enriched in synaptic function and converge on Ras/mitogen-activated protein kinase (Ras/MAPK) signaling. Both increased Ras/MAPK signaling in gamma-aminobutyric acidergic (GABAergic) neurons and decreased Ras/MAPK signaling in cholinergic neurons specifically inhibit the adaptive habituation response. CONCLUSIONS Our work supports the relevance of habituation learning to ASD, identifies an unprecedented number of novel habituation players, supports an emerging role for inhibitory neurons in habituation, and reveals an opposing, circuit-level-based mechanism for Ras/MAPK signaling. These findings establish habituation as a possible, widely applicable functional readout and target for pharmacologic intervention in ID/ASD.
Collapse
Affiliation(s)
- Michaela Fenckova
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laura E R Blok
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lenke Asztalos
- Aktogen Limited, Department of Genetics, University of Cambridge, Cambridge, United Kingdom; Aktogen Hungary Limited, Bay Zoltán Nonprofit Limited for Applied Research, Institute for Biotechnology, Szeged, Hungary
| | - David P Goodman
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania
| | - Pavel Cizek
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Euginia L Singgih
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeffrey C Glennon
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joanna IntHout
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington; Howard Hughes Medical Institute, University of Washington, Seattle, Washington
| | - Catherine R von Reyn
- School of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, Pennsylvania; Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington
| | - Zoltan Asztalos
- Aktogen Limited, Department of Genetics, University of Cambridge, Cambridge, United Kingdom; Aktogen Hungary Limited, Bay Zoltán Nonprofit Limited for Applied Research, Institute for Biotechnology, Szeged, Hungary; Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.
| |
Collapse
|
10
|
Zamurrad S, Hatch HAM, Drelon C, Belalcazar HM, Secombe J. A Drosophila Model of Intellectual Disability Caused by Mutations in the Histone Demethylase KDM5. Cell Rep 2019; 22:2359-2369. [PMID: 29490272 DOI: 10.1016/j.celrep.2018.02.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 12/08/2017] [Accepted: 02/05/2018] [Indexed: 10/17/2022] Open
Abstract
Mutations in KDM5 family histone demethylases cause intellectual disability in humans. However, the molecular mechanisms linking KDM5-regulated transcription and cognition remain unknown. Here, we establish Drosophila as a model to understand this connection by generating a fly strain harboring an allele analogous to a disease-causing missense mutation in human KDM5C (kdm5A512P). Transcriptome analysis of kdm5A512P flies revealed a striking downregulation of genes required for ribosomal assembly and function and a concomitant reduction in translation. kdm5A512P flies also showed impaired learning and/or memory. Significantly, the behavioral and transcriptional changes in kdm5A512P flies were similar to those specifically lacking demethylase activity. These data suggest that the primary defect of the KDM5A512P mutation is a loss of histone demethylase activity and reveal an unexpected role for this enzymatic function in gene activation. Because translation is critical for neuronal function, we propose that this defect contributes to the cognitive defects of kdm5A512P flies.
Collapse
Affiliation(s)
- Sumaira Zamurrad
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461, USA
| | - Coralie Drelon
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Helen M Belalcazar
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Julie Secombe
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, 1410 Pelham Parkway South, Bronx, NY 10461, USA.
| |
Collapse
|
11
|
Coll-Tané M, Krebbers A, Castells-Nobau A, Zweier C, Schenck A. Intellectual disability and autism spectrum disorders 'on the fly': insights from Drosophila. Dis Model Mech 2019; 12:dmm039180. [PMID: 31088981 PMCID: PMC6550041 DOI: 10.1242/dmm.039180] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Intellectual disability (ID) and autism spectrum disorders (ASD) are frequently co-occurring neurodevelopmental disorders and affect 2-3% of the population. Rapid advances in exome and genome sequencing have increased the number of known implicated genes by threefold, to more than a thousand. The main challenges in the field are now to understand the various pathomechanisms associated with this bewildering number of genetic disorders, to identify new genes and to establish causality of variants in still-undiagnosed cases, and to work towards causal treatment options that so far are available only for a few metabolic conditions. To meet these challenges, the research community needs highly efficient model systems. With an increasing number of relevant assays and rapidly developing novel methodologies, the fruit fly Drosophila melanogaster is ideally positioned to change gear in ID and ASD research. The aim of this Review is to summarize some of the exciting work that already has drawn attention to Drosophila as a model for these disorders. We highlight well-established ID- and ASD-relevant fly phenotypes at the (sub)cellular, brain and behavioral levels, and discuss strategies of how this extraordinarily efficient and versatile model can contribute to 'next generation' medical genomics and to a better understanding of these disorders.
Collapse
Affiliation(s)
- Mireia Coll-Tané
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alina Krebbers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Anna Castells-Nobau
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| |
Collapse
|
12
|
Eidhof I, van de Warrenburg BP, Schenck A. Integrative network and brain expression analysis reveals mechanistic modules in ataxia. J Med Genet 2019; 56:283-292. [PMID: 30591515 PMCID: PMC6581079 DOI: 10.1136/jmedgenet-2018-105703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/14/2018] [Accepted: 11/30/2018] [Indexed: 01/13/2023]
Abstract
BACKGROUND Genetic forms of ataxia are a heterogenous group of degenerative diseases of the cerebellum. Many causative genes have been identified. We aimed to systematically investigate these genes to better understand ataxia pathophysiology. METHODS A manually curated catalogue of 71 genes involved in disorders with progressive ataxias as a major clinical feature was subjected to an integrated gene ontology, protein network and brain gene expression profiling analysis. RESULTS We found that genes mutated in ataxias operate in networks with significantly enriched protein connectivity, demonstrating coherence on a global level, independent of inheritance mode. Moreover, elevated expression specifically in the cerebellum predisposes to ataxia. Genes expressed in this pattern are significantly over-represented among genes mutated in ataxia and are enriched for ion homeostasis/synaptic functions. The majority of genes mutated in ataxia, however, does not show elevated cerebellar expression that could account for region-specific degeneration. For these, we identified defective cellular stress responses as a major common biological theme, suggesting that the defence pathways against stress are more critical to maintain cerebellar integrity than integrity of other brain regions. Approximately half of the genes mutated in ataxia, mostly part of the stress module, show higher expression at embryonic stages, which argues for a developmental predisposition. CONCLUSION Genetic defects in ataxia predominantly affect neuronal homeostasis, to which the cerebellum appears to be excessively susceptible. Based on the identified modules, it is conceivable to propose common therapeutic interventions that target deregulated calcium and reactive oxygen species levels, or mechanisms that can decrease the harmful downstream effects of these deleterious insults.
Collapse
Affiliation(s)
- Ilse Eidhof
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Bart P van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Centre, Nijmegen, The Netherlands
| |
Collapse
|
13
|
Deal SL, Yamamoto S. Unraveling Novel Mechanisms of Neurodegeneration Through a Large-Scale Forward Genetic Screen in Drosophila. Front Genet 2019; 9:700. [PMID: 30693015 PMCID: PMC6339878 DOI: 10.3389/fgene.2018.00700] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 12/13/2018] [Indexed: 01/04/2023] Open
Abstract
Neurodegeneration is characterized by progressive loss of neurons. Genetic and environmental factors both contribute to demise of neurons, leading to diverse devastating cognitive and motor disorders, including Alzheimer's and Parkinson's diseases in humans. Over the past few decades, the fruit fly, Drosophila melanogaster, has become an integral tool to understand the molecular, cellular and genetic mechanisms underlying neurodegeneration. Extensive tools and sophisticated technologies allow Drosophila geneticists to identify and study evolutionarily conserved genes that are essential for neural maintenance. In this review, we will focus on a large-scale mosaic forward genetic screen on the fly X-chromosome that led to the identification of a number of essential genes that exhibit neurodegenerative phenotypes when mutated. Most genes identified from this screen are evolutionarily conserved and many have been linked to human diseases with neurological presentations. Systematic electrophysiological and ultrastructural characterization of mutant tissue in the context of the Drosophila visual system, followed by a series of experiments to understand the mechanism of neurodegeneration in each mutant led to the discovery of novel molecular pathways that are required for neuronal integrity. Defects in mitochondrial function, lipid and iron metabolism, protein trafficking and autophagy are recurrent themes, suggesting that insults that eventually lead to neurodegeneration may converge on a set of evolutionarily conserved cellular processes. Insights from these studies have contributed to our understanding of known neurodegenerative diseases such as Leigh syndrome and Friedreich's ataxia and have also led to the identification of new human diseases. By discovering new genes required for neural maintenance in flies and working with clinicians to identify patients with deleterious variants in the orthologous human genes, Drosophila biologists can play an active role in personalized medicine.
Collapse
Affiliation(s)
- Samantha L Deal
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, United States
| | - Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, United States.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, United States.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States
| |
Collapse
|
14
|
Kazeminasab S, Taskiran II, Fattahi Z, Bazazzadegan N, Hosseini M, Rahimi M, Oladnabi M, Haddadi M, Celik A, Ropers HH, Najmabadi H, Kahrizi K. CNKSR1 gene defect can cause syndromic autosomal recessive intellectual disability. Am J Med Genet B Neuropsychiatr Genet 2018; 177:691-699. [PMID: 30450701 DOI: 10.1002/ajmg.b.32648] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The advent of high-throughput sequencing technologies has led to an exponential increase in the identification of novel disease-causing genes in highly heterogeneous diseases. A novel frameshift mutation in CNKSR1 gene was detected by Next-Generation Sequencing (NGS) in an Iranian family with syndromic autosomal recessive intellectual disability (ARID). CNKSR1 encodes a connector enhancer of kinase suppressor of Ras 1, which acts as a scaffold component for receptor tyrosine kinase in mitogen-activated protein kinase (MAPK) cascades. CNKSR1 interacts with proteins which have already been shown to be associated with intellectual disability (ID) in the MAPK signaling pathway and promotes cell migration through RhoA-mediated c-Jun N-terminal kinase (JNK) activation. Lack of CNKSR1 transcripts and protein was observed in lymphoblastoid cells derived from affected patients using qRT-PCR and western blot analysis, respectively. Furthermore, RNAi-mediated knockdown of cnk, the CNKSR1 orthologue in Drosophila melanogaster brain, led to defects in eye and mushroom body (MB) structures. In conclusion, our findings support the possible role of CNKSR1 in brain development which can lead to cognitive impairment.
Collapse
Affiliation(s)
- Somayeh Kazeminasab
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Niloofar Bazazzadegan
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Masoumeh Hosseini
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Rahimi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Morteza Oladnabi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Haddadi
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran
| | - Arzu Celik
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| |
Collapse
|
15
|
Linda K, Fiuza C, Nadif Kasri N. The promise of induced pluripotent stem cells for neurodevelopmental disorders. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:382-391. [PMID: 29128445 DOI: 10.1016/j.pnpbp.2017.11.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 10/30/2017] [Accepted: 11/07/2017] [Indexed: 12/19/2022]
Abstract
A major challenge in clinical genetics and medicine is represented by genetically and phenotypically highly diverse neurodevelopmental disorders, like for example intellectual disability and autism. Intellectual disability is characterized by substantial limitations in cognitive function and adaptive behaviour. At the cellular level, this is reflected by deficits in synaptic structure and plasticity and therefore has been coined as a synaptic disorder or "synaptopathy". In this review, we summarize the findings from recent studies in which iPSCs have been used to model specific neurodevelopmental syndromes, including Fragile X syndrome, Rett syndrome, Williams-Beuren syndrome and Phelan-McDermid syndrome. We discuss what we have learned from these studies and what key issues need to be addressed to move the field forward.
Collapse
Affiliation(s)
- Katrin Linda
- Department of Human Genetics, Department of Cognitive Neuroscience, Radboudumc, 6500 HB, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands
| | - Carol Fiuza
- Department of Human Genetics, Department of Cognitive Neuroscience, Radboudumc, 6500 HB, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Department of Cognitive Neuroscience, Radboudumc, 6500 HB, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ, Nijmegen, The Netherlands.
| |
Collapse
|
16
|
Ueda A, Woods S, McElree I, O'Harrow TCDG, Inman C, Thenuwara S, Aftab M, Iyengar A. Two novel forms of ERG oscillation in Drosophila: age and activity dependence. J Neurogenet 2018; 32:118-126. [PMID: 29688104 DOI: 10.1080/01677063.2018.1461866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Over an animal's lifespan, neuronal circuits and systems often decline in an inherently heterogeneous fashion. To compare the age-dependent progression of changes in visual behavior with alterations in retinal physiology, we examined phototaxis and electroretinograms (ERGs) in a wild-type D. melanogaster strain (Canton-S) across their lifespan. In aged flies (beyond 50% median lifespan), we found a marked decline in phototaxis, while motor coordination was less disrupted, as indicated by relatively stronger negative geotaxis. These aged flies displayed substantially reduced ERG transient amplitudes while the receptor potentials (RP) remained largely intact. Using a repetitive light flash protocol, we serendipitously discovered two forms of activity-dependent oscillation in the ERG waveforms of young flies: 'light-off' and 'light-on' oscillations. After repeated 500 ms light flashes, light-off oscillations appeared during the ERG off-transients (frequency: 50-120 Hz, amplitude: ∼1 mV). Light-on oscillations (100-200 Hz, ∼0.3 mV) were induced by a series of 50 ms flashes, and were evident during the ERG on-transients. Both forms of oscillation were observed in other strains of D. melanogaster (Oregon-R, Berlin), additional Drosophila species (D. funerbris, D. euronotus, D. hydei, D. americana), and were evoked by a variety of light sources. Both light-off and light-on oscillations were distinct from previously described ERG oscillations in the visual mutant rosA in terms of location within the waveform and frequency. However, within rosA mutants, light-off oscillations, but not light-on oscillations could be recruited by the repetitive light flash protocol. Importantly though, we found that both forms of oscillation were rarely observed in aged flies. Although the physiological bases of these oscillations remain to be elucidated, they may provide important clues to age-related changes in neuronal excitability and synaptic transmission.
Collapse
Affiliation(s)
- Atsushi Ueda
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | - Scott Woods
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | - Ian McElree
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | | | - Casey Inman
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | | | - Muhammad Aftab
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| | - Atulya Iyengar
- a Department of Biology , University of Iowa , Iowa City , IA , USA
| |
Collapse
|
17
|
Kelly SM, Elchert A, Kahl M. Dissection and Immunofluorescent Staining of Mushroom Body and Photoreceptor Neurons in Adult Drosophila melanogaster Brains. J Vis Exp 2017. [PMID: 29155751 PMCID: PMC5755316 DOI: 10.3791/56174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Nervous system development involves a sequential series of events that are coordinated by several signaling pathways and regulatory networks. Many of the proteins involved in these pathways are evolutionarily conserved between mammals and other eukaryotes, such as the fruit fly Drosophila melanogaster, suggesting that similar organizing principles exist during the development of these organisms. Importantly, Drosophila has been used extensively to identify cellular and molecular mechanisms regulating processes that are required in mammals including neurogenesis, differentiation, axonal guidance, and synaptogenesis. Flies have also been used successfully to model a variety of human neurodevelopmental diseases. Here we describe a protocol for the step-by-step microdissection, fixation, and immunofluorescent localization of proteins within the adult Drosophila brain. This protocol focuses on two example neuronal populations, mushroom body neurons and retinal photoreceptors, and includes optional steps to trace individual mushroom body neurons using Mosaic Analysis with a Repressible Cell Marker (MARCM) technique. Example data from both wild-type and mutant brains are shown along with a brief description of a scoring criteria for axonal guidance defects. While this protocol highlights two well-established antibodies for investigating the morphology of mushroom body and photoreceptor neurons, other Drosophila brain regions and the localization of proteins within other brain regions can also be investigated using this protocol.
Collapse
Affiliation(s)
- Seth M Kelly
- Program in Neuroscience, The College of Wooster; Department of Biology, The College of Wooster;
| | - Alexandra Elchert
- Program in Biochemistry, Cellular, and Molecular Biology, The College of Wooster
| | - Michael Kahl
- Department of Biology, The College of Wooster; Program in Biochemistry, Cellular, and Molecular Biology, The College of Wooster
| |
Collapse
|
18
|
Klein M, Onnink M, van Donkelaar M, Wolfers T, Harich B, Shi Y, Dammers J, Arias-Vásquez A, Hoogman M, Franke B. Brain imaging genetics in ADHD and beyond - Mapping pathways from gene to disorder at different levels of complexity. Neurosci Biobehav Rev 2017; 80:115-155. [PMID: 28159610 PMCID: PMC6947924 DOI: 10.1016/j.neubiorev.2017.01.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 12/08/2016] [Accepted: 01/09/2017] [Indexed: 01/03/2023]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a common and often persistent neurodevelopmental disorder. Beyond gene-finding, neurobiological parameters, such as brain structure, connectivity, and function, have been used to link genetic variation to ADHD symptomatology. We performed a systematic review of brain imaging genetics studies involving 62 ADHD candidate genes in childhood and adult ADHD cohorts. Fifty-one eligible research articles described studies of 13 ADHD candidate genes. Almost exclusively, single genetic variants were studied, mostly focussing on dopamine-related genes. While promising results have been reported, imaging genetics studies are thus far hampered by methodological differences in study design and analysis methodology, as well as limited sample sizes. Beyond reviewing imaging genetics studies, we also discuss the need for complementary approaches at multiple levels of biological complexity and emphasize the importance of combining and integrating findings across levels for a better understanding of biological pathways from gene to disease. These may include multi-modal imaging genetics studies, bioinformatic analyses, and functional analyses of cell and animal models.
Collapse
Affiliation(s)
- Marieke Klein
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Marten Onnink
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Marjolein van Donkelaar
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Thomas Wolfers
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Benjamin Harich
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Yan Shi
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Janneke Dammers
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands; Department of Psychiatry, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Alejandro Arias-Vásquez
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands; Department of Psychiatry, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands; Department of Cognitive Neuroscience, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Martine Hoogman
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Barbara Franke
- Department of Human Genetics, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands; Department of Psychiatry, Radboud university medical center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
| |
Collapse
|
19
|
Stessman HAF, Xiong B, Coe BP, Wang T, Hoekzema K, Fenckova M, Kvarnung M, Gerdts J, Trinh S, Cosemans N, Vives L, Lin J, Turner TN, Santen G, Ruivenkamp C, Kriek M, van Haeringen A, Aten E, Friend K, Liebelt J, Barnett C, Haan E, Shaw M, Gecz J, Anderlid BM, Nordgren A, Lindstrand A, Schwartz C, Kooy RF, Vandeweyer G, Helsmoortel C, Romano C, Alberti A, Vinci M, Avola E, Giusto S, Courchesne E, Pramparo T, Pierce K, Nalabolu S, Amaral D, Scheffer IE, Delatycki MB, Lockhart PJ, Hormozdiari F, Harich B, Castells-Nobau A, Xia K, Peeters H, Nordenskjöld M, Schenck A, Bernier RA, Eichler EE. Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases. Nat Genet 2017; 49:515-526. [PMID: 28191889 PMCID: PMC5374041 DOI: 10.1038/ng.3792] [Citation(s) in RCA: 411] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/22/2017] [Indexed: 12/12/2022]
Abstract
Gene-disruptive mutations contribute to the biology of neurodevelopmental disorders (NDDs), but most of the related pathogenic genes are not known. We sequenced 208 candidate genes from >11,730 cases and >2,867 controls. We identified 91 genes, including 38 new NDD genes, with an excess of de novo mutations or private disruptive mutations in 5.7% of cases. Drosophila functional assays revealed a subset with increased involvement in NDDs. We identified 25 genes showing a bias for autism versus intellectual disability and highlighted a network associated with high-functioning autism (full-scale IQ >100). Clinical follow-up for NAA15, KMT5B, and ASH1L highlighted new syndromic and nonsyndromic forms of disease.
Collapse
Affiliation(s)
| | - Bo Xiong
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of forensic medicine and Institute of Brain Research, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tianyun Wang
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michaela Fenckova
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jennifer Gerdts
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Sandy Trinh
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Nele Cosemans
- Centre for Human Genetics, KU Leuven and Leuven Autism Research (LAuRes), Leuven, Belgium
| | - Laura Vives
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Janice Lin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Tychele N. Turner
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Gijs Santen
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Marjolein Kriek
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Emmelien Aten
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Kathryn Friend
- Robinson Research Institute and the University of Adelaide at the Women’s and Children’s Hospital, North Adelaide, Australia
- SA Pathology, Adelaide, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, SA Pathology (at Women’s and Children’s Hospital), Adelaide, Australia, Australia
| | - Christopher Barnett
- South Australian Clinical Genetics Service, SA Pathology (at Women’s and Children’s Hospital), Adelaide, Australia, Australia
| | - Eric Haan
- Robinson Research Institute and the University of Adelaide at the Women’s and Children’s Hospital, North Adelaide, Australia
- South Australian Clinical Genetics Service, SA Pathology (at Women’s and Children’s Hospital), Adelaide, Australia, Australia
| | - Marie Shaw
- Robinson Research Institute and the University of Adelaide at the Women’s and Children’s Hospital, North Adelaide, Australia
| | - Jozef Gecz
- Robinson Research Institute and the University of Adelaide at the Women’s and Children’s Hospital, North Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Charles Schwartz
- Center for Molecular Studies, J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | | | | | | | | | - Stefania Giusto
- Unit of Neurology, IRCCS Associazione Oasi Maria Santissima, Troina, Italy
| | | | | | - Karen Pierce
- UCSD, Autism Center of Excellence, La Jolla, CA, USA
| | | | - David Amaral
- MIND Institute and the University of California Davis School of Medicine, Sacramento, CA, USA
| | - Ingrid E. Scheffer
- Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Australia
- The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - Martin B. Delatycki
- Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Paul J. Lockhart
- Department of Paediatrics, University of Melbourne, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children’s Research Institute, Parkville, Victoria, Australia
| | - Fereydoun Hormozdiari
- Department of Biochemistry and Molecular Medicine, University of California at Davis, Davis, CA, USA
| | - Benjamin Harich
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Anna Castells-Nobau
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Kun Xia
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Hilde Peeters
- Centre for Human Genetics, KU Leuven and Leuven Autism Research (LAuRes), Leuven, Belgium
| | - 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
| | - Annette Schenck
- Department of Human Genetics, Radboud university medical center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud university medical center, Nijmegen, The Netherlands
| | - Raphael A. Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| |
Collapse
|
20
|
Atkinson D, Nikodinovic Glumac J, Asselbergh B, Ermanoska B, Blocquel D, Steiner R, Estrada-Cuzcano A, Peeters K, Ooms T, De Vriendt E, Yang XL, Hornemann T, Milic Rasic V, Jordanova A. Sphingosine 1-phosphate lyase deficiency causes Charcot-Marie-Tooth neuropathy. Neurology 2017; 88:533-542. [PMID: 28077491 DOI: 10.1212/wnl.0000000000003595] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/16/2016] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE To identify the unknown genetic cause in a nuclear family with an axonal form of peripheral neuropathy and atypical disease course. METHODS Detailed neurologic, electrophysiologic, and neuropathologic examinations of the patients were performed. Whole exome sequencing of both affected individuals was done. The effect of the identified sequence variations was investigated at cDNA and protein level in patient-derived lymphoblasts. The plasma sphingoid base profile was analyzed. Functional consequences of neuron-specific downregulation of the gene were studied in Drosophila. RESULTS Both patients present an atypical form of axonal peripheral neuropathy, characterized by acute or subacute onset and episodes of recurrent mononeuropathy. We identified compound heterozygous mutations cosegregating with disease and absent in controls in the SGPL1 gene, encoding sphingosine 1-phosphate lyase (SPL). The p.Ser361* mutation triggers nonsense-mediated mRNA decay. The missense p.Ile184Thr mutation causes partial protein degradation. The plasma levels of sphingosine 1-phosphate and sphingosine/sphinganine ratio were increased in the patients. Neuron-specific downregulation of the Drosophila orthologue impaired the morphology of the neuromuscular junction and caused progressive degeneration of the chemosensory neurons innervating the wing margin bristles. CONCLUSIONS We suggest SPL deficiency as a cause of a distinct form of Charcot-Marie-Tooth disease in humans, thus extending the currently recognized clinical and genetic spectrum of inherited peripheral neuropathies. Our data emphasize the importance of sphingolipid metabolism for neuronal function.
Collapse
Affiliation(s)
- Derek Atkinson
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Jelena Nikodinovic Glumac
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Bob Asselbergh
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Biljana Ermanoska
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - David Blocquel
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Regula Steiner
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Alejandro Estrada-Cuzcano
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Kristien Peeters
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Tinne Ooms
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Els De Vriendt
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Xiang-Lei Yang
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Thorsten Hornemann
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland
| | - Vedrana Milic Rasic
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland.
| | - Albena Jordanova
- From the Molecular Neurogenomics Group (D.A., B.E., A.E.-C., K.P., T.O., E.D.V., A.J.), VIB Department of Molecular Genetics (B.A.), University of Antwerp, Belgium; Clinic for Neurology and Psychiatry for Children and Youth (J.N.G), Belgrade, Serbia; Faculty of Medicine (V.M.R.), Clinic for Neurology and Psychiatry for Children and Youth, University of Belgrade, Serbia; Departments of Chemical Physiology and Cell and Molecular Biology (D.B., X.-L.Y.), The Scripps Research Institute, La Jolla, CA; and Institute of Clinical Chemistry (R.S., T.H.), University Hospital Zurich, University of Zurich, Switzerland.
| |
Collapse
|
21
|
Keerthikumar S, Gangoda L, Liem M, Fonseka P, Atukorala I, Ozcitti C, Mechler A, Adda CG, Ang CS, Mathivanan S. Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes. Oncotarget 2016; 6:15375-96. [PMID: 25944692 PMCID: PMC4558158 DOI: 10.18632/oncotarget.3801] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/18/2015] [Indexed: 12/27/2022] Open
Abstract
Extracellular vesicles (EVs) include the exosomes (30-100 nm) that are produced through the endocytic pathway via the multivesicular bodies and the ectosomes (100-1000 nm) that are released through the budding of the plasma membrane. Despite the differences in the mode of biogenesis and size, reliable markers that can distinguish between exosomes and ectosomes are non-existent. Moreover, the precise functional differences between exosomes and ectosomes remains poorly characterised. Here, using label-free quantitative proteomics, we highlight proteins that could be exploited as markers to discriminate between exosomes and ectosomes. For the first time, a global proteogenomics analysis unveiled the secretion of mutant proteins that are implicated in cancer progression through tumor-derived EVs. Follow up integrated bioinformatics analysis highlighted the enrichment of oncogenic cargo in exosomes and ectosomes. Interestingly, exosomes induced significant cell proliferation and migration in recipient cells compared to ectosomes confirming the oncogenic nature of exosomes. These findings ascertain that cancer cells facilitate oncogenesis by the secretion of mutant and oncoproteins into the tumor microenvironment via exosomes and ectosomes. The integrative proteogenomics approach utilized in this study has the potential to identify disease biomarker candidates which can be later assayed in liquid biopsies obtained from cancer patients.
Collapse
Affiliation(s)
- Shivakumar Keerthikumar
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Lahiru Gangoda
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Michael Liem
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Pamali Fonseka
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ishara Atukorala
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Cemil Ozcitti
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Adam Mechler
- Department of Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Christopher G Adda
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Ching-Seng Ang
- Bio21 Institute, University of Melbourne, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| |
Collapse
|
22
|
Kochinke K, Zweier C, Nijhof B, Fenckova M, Cizek P, Honti F, Keerthikumar S, Oortveld M, Kleefstra T, Kramer J, Webber C, Huynen M, Schenck A. Systematic Phenomics Analysis Deconvolutes Genes Mutated in Intellectual Disability into Biologically Coherent Modules. Am J Hum Genet 2016; 98:149-64. [PMID: 26748517 DOI: 10.1016/j.ajhg.2015.11.024] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022] Open
Abstract
Intellectual disability (ID) disorders are genetically and phenotypically extremely heterogeneous. Can this complexity be depicted in a comprehensive way as a means of facilitating the understanding of ID disorders and their underlying biology? We provide a curated database of 746 currently known genes, mutations in which cause ID (ID-associated genes [ID-AGs]), classified according to ID manifestation and associated clinical features. Using this integrated resource, we show that ID-AGs are substantially enriched with co-expression, protein-protein interactions, and specific biological functions. Systematic identification of highly enriched functional themes and phenotypes revealed typical phenotype combinations characterizing process-defined groups of ID disorders, such as chromatin-related disorders and deficiencies in DNA repair. Strikingly, phenotype classification efficiently breaks down ID-AGs into subsets with significantly elevated biological coherence and predictive power. Custom-made functional Drosophila datasets revealed further characteristic phenotypes among ID-AGs and specific clinical classes. Our study and resource provide systematic insights into the molecular and clinical landscape of ID disorders, represent a significant step toward overcoming current limitations in ID research, and prove the utility of systematic human and cross-species phenomics analyses in highly heterogeneous genetic disorders.
Collapse
|
23
|
Abstract
Genetic factors play a major part in intellectual disability (ID), but genetic studies have been complicated for a long time by the extreme clinical and genetic heterogeneity. Recently, progress has been made using different next-generation sequencing approaches in combination with new functional readout systems. This approach has provided novel insights into the biological pathways underlying ID, improved the diagnostic process and offered new targets for therapy. In this Review, we highlight the insights obtained from recent studies on the role of genetics in ID and its impact on diagnosis, prognosis and therapy. We also discuss the future directions of genetics research for ID and related neurodevelopmental disorders.
Collapse
|
24
|
Dubos A, Castells-Nobau A, Meziane H, Oortveld MAW, Houbaert X, Iacono G, Martin C, Mittelhaeuser C, Lalanne V, Kramer JM, Bhukel A, Quentin C, Slabbert J, Verstreken P, Sigrist SJ, Messaddeq N, Birling MC, Selloum M, Stunnenberg HG, Humeau Y, Schenck A, Herault Y. Conditional depletion of intellectual disability and Parkinsonism candidate gene ATP6AP2 in fly and mouse induces cognitive impairment and neurodegeneration. Hum Mol Genet 2015; 24:6736-55. [PMID: 26376863 PMCID: PMC4634377 DOI: 10.1093/hmg/ddv380] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 09/11/2015] [Indexed: 12/20/2022] Open
Abstract
ATP6AP2, an essential accessory component of the vacuolar H+ ATPase (V-ATPase), has been associated with intellectual disability (ID) and Parkinsonism. ATP6AP2 has been implicated in several signalling pathways; however, little is known regarding its role in the nervous system. To decipher its function in behaviour and cognition, we generated and characterized conditional knockdowns of ATP6AP2 in the nervous system of Drosophila and mouse models. In Drosophila, ATP6AP2 knockdown induced defective phototaxis and vacuolated photoreceptor neurons and pigment cells when depleted in eyes and altered short- and long-term memory when depleted in the mushroom body. In mouse, conditional Atp6ap2 deletion in glutamatergic neurons (Atp6ap2Camk2aCre/0 mice) caused increased spontaneous locomotor activity and altered fear memory. Both Drosophila ATP6AP2 knockdown and Atp6ap2Camk2aCre/0 mice presented with presynaptic transmission defects, and with an abnormal number and morphology of synapses. In addition, Atp6ap2Camk2aCre/0 mice showed autophagy defects that led to axonal and neuronal degeneration in the cortex and hippocampus. Surprisingly, axon myelination was affected in our mutant mice, and axonal transport alterations were observed in Drosophila. In accordance with the identified phenotypes across species, genome-wide transcriptome profiling of Atp6ap2Camk2aCre/0 mouse hippocampi revealed dysregulation of genes involved in myelination, action potential, membrane-bound vesicles and motor behaviour. In summary, ATP6AP2 disruption in mouse and fly leads to cognitive impairment and neurodegeneration, mimicking aspects of the neuropathology associated with ATP6AP2 mutations in humans. Our results identify ATP6AP2 as an essential gene for the nervous system.
Collapse
Affiliation(s)
- Aline Dubos
- Institut Clinique de la Souris, PHENOMIN, GIE CERBM, 1 rue Laurent Fries, 67404 Illkirch, France, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France, Centre National de la Recherche Scientifique, UMR7104, Illkirch, France, Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France and Université de Strasbourg, Illkirch, France
| | - Anna Castells-Nobau
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Hamid Meziane
- Institut Clinique de la Souris, PHENOMIN, GIE CERBM, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Merel A W Oortveld
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Xander Houbaert
- Team Synapse in Cognition, Institut Interdisciplinaire de NeuroScience, Centre National de la Recherche Scientifique CNRS UMR5297, Université de Bordeaux, Bordeaux, France
| | - Giovanni Iacono
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Christelle Martin
- Team Synapse in Cognition, Institut Interdisciplinaire de NeuroScience, Centre National de la Recherche Scientifique CNRS UMR5297, Université de Bordeaux, Bordeaux, France
| | - Christophe Mittelhaeuser
- Institut Clinique de la Souris, PHENOMIN, GIE CERBM, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Valérie Lalanne
- Institut Clinique de la Souris, PHENOMIN, GIE CERBM, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Jamie M Kramer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Anuradha Bhukel
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Christine Quentin
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany, NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Slabbert
- VIB, Center for the Biology of Disease, Leuven, Belgium, KU Leuven, Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), Leuven, Belgium
| | - Patrik Verstreken
- VIB, Center for the Biology of Disease, Leuven, Belgium, KU Leuven, Center for Human Genetics and Leuven Institute for Neuroscience and Disease (LIND), Leuven, Belgium
| | - Stefan J Sigrist
- Genetics, Institute of Biology, Freie Universität Berlin, Berlin, Germany, NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nadia Messaddeq
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France, Centre National de la Recherche Scientifique, UMR7104, Illkirch, France, Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France and Université de Strasbourg, Illkirch, France
| | - Marie-Christine Birling
- Institut Clinique de la Souris, PHENOMIN, GIE CERBM, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Mohammed Selloum
- Institut Clinique de la Souris, PHENOMIN, GIE CERBM, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Henk G Stunnenberg
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Yann Humeau
- Team Synapse in Cognition, Institut Interdisciplinaire de NeuroScience, Centre National de la Recherche Scientifique CNRS UMR5297, Université de Bordeaux, Bordeaux, France
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, The Netherlands,
| | - Yann Herault
- Institut Clinique de la Souris, PHENOMIN, GIE CERBM, 1 rue Laurent Fries, 67404 Illkirch, France, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France, Centre National de la Recherche Scientifique, UMR7104, Illkirch, France, Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France and Université de Strasbourg, Illkirch, France
| |
Collapse
|
25
|
Thomas AL, Davis SM, Dierick HA. Of Fighting Flies, Mice, and Men: Are Some of the Molecular and Neuronal Mechanisms of Aggression Universal in the Animal Kingdom? PLoS Genet 2015; 11:e1005416. [PMID: 26312756 PMCID: PMC4551476 DOI: 10.1371/journal.pgen.1005416] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Aggressive behavior is widespread in the animal kingdom, but the degree of molecular conservation between distantly related species is still unclear. Recent reports suggest that at least some of the molecular mechanisms underlying this complex behavior in flies show remarkable similarities with such mechanisms in mice and even humans. Surprisingly, some aspects of neuronal control of aggression also show remarkable similarity between these distantly related species. We will review these recent findings, address the evolutionary implications, and discuss the potential impact for our understanding of human diseases characterized by excessive aggression.
Collapse
Affiliation(s)
- Amanda L. Thomas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shaun M. Davis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Herman A. Dierick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|
26
|
Guna A, Butcher NJ, Bassett AS. Comparative mapping of the 22q11.2 deletion region and the potential of simple model organisms. J Neurodev Disord 2015; 7:18. [PMID: 26137170 PMCID: PMC4487986 DOI: 10.1186/s11689-015-9113-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 05/26/2015] [Indexed: 01/18/2023] Open
Abstract
Background 22q11.2 deletion syndrome (22q11.2DS) is the most common micro-deletion syndrome. The associated 22q11.2 deletion conveys the strongest known molecular risk for schizophrenia. Neurodevelopmental phenotypes, including intellectual disability, are also prominent though variable in severity. Other developmental features include congenital cardiac and craniofacial anomalies. Whereas existing mouse models have been helpful in determining the role of some genes overlapped by the hemizygous 22q11.2 deletion in phenotypic expression, much remains unknown. Simple model organisms remain largely unexploited in exploring these genotype-phenotype relationships. Methods We first developed a comprehensive map of the human 22q11.2 deletion region, delineating gene content, and brain expression. To identify putative orthologs, standard methods were used to interrogate the proteomes of the zebrafish (D. rerio), fruit fly (D. melanogaster), and worm (C. elegans), in addition to the mouse. Spatial locations of conserved homologues were mapped to examine syntenic relationships. We systematically cataloged available knockout and knockdown models of all conserved genes across these organisms, including a comprehensive review of associated phenotypes. Results There are 90 genes overlapped by the typical 2.5 Mb deletion 22q11.2 region. Of the 46 protein-coding genes, 41 (89.1 %) have documented expression in the human brain. Identified homologues in the zebrafish (n = 37, 80.4 %) were comparable to those in the mouse (n = 40, 86.9 %) and included some conserved gene cluster structures. There were 22 (47.8 %) putative homologues in the fruit fly and 17 (37.0 %) in the worm involving multiple chromosomes. Individual gene knockdown mutants were available for the simple model organisms, but not for mouse. Although phenotypic data were relatively limited for knockout and knockdown models of the 17 genes conserved across all species, there was some evidence for roles in neurodevelopmental phenotypes, including four of the six mitochondrial genes in the 22q11.2 deletion region. Conclusions Simple model organisms represent a powerful but underutilized means of investigating the molecular mechanisms underlying the elevated risk for neurodevelopmental disorders in 22q11.2DS. This comparative multi-species study provides novel resources and support for the potential utility of non-mouse models in expression studies and high-throughput drug screening. The approach has implications for other recurrent copy number variations associated with neurodevelopmental phenotypes. Electronic supplementary material The online version of this article (doi:10.1186/s11689-015-9113-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alina Guna
- Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON Canada
| | - Nancy J Butcher
- Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON Canada ; Institute of Medical Science, University of Toronto, Toronto, ON Canada
| | - Anne S Bassett
- Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON Canada ; Institute of Medical Science, University of Toronto, Toronto, ON Canada ; Dalglish Family Hearts and Minds Clinic for Adults with 22q11.2 Deletion Syndrome, Division of Cardiology, Department of Medicine, Department of Psychiatry, and Toronto General Research Institute, University Health Network, Toronto, ON Canada ; Department of Psychiatry, University of Toronto, Toronto, ON Canada ; Centre for Addiction and Mental Health, 33 Russell Street, Room 1100, M5S 2S1 Toronto, ON Canada
| |
Collapse
|
27
|
Grice SJ, Liu JL, Webber C. Synergistic interactions between Drosophila orthologues of genes spanned by de novo human CNVs support multiple-hit models of autism. PLoS Genet 2015; 11:e1004998. [PMID: 25816101 PMCID: PMC4376901 DOI: 10.1371/journal.pgen.1004998] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 01/12/2015] [Indexed: 01/30/2023] Open
Abstract
Autism spectrum disorders (ASDs) are highly heritable and characterised by deficits in social interaction and communication, as well as restricted and repetitive behaviours. Although a number of highly penetrant ASD gene variants have been identified, there is growing evidence to support a causal role for combinatorial effects arising from the contributions of multiple loci. By examining synaptic and circadian neurological phenotypes resulting from the dosage variants of unique human:fly orthologues in Drosophila, we observe numerous synergistic interactions between pairs of informatically-identified candidate genes whose orthologues are jointly affected by large de novo copy number variants (CNVs). These CNVs were found in the genomes of individuals with autism, including a patient carrying a 22q11.2 deletion. We first demonstrate that dosage alterations of the unique Drosophila orthologues of candidate genes from de novo CNVs that harbour only a single candidate gene display neurological defects similar to those previously reported in Drosophila models of ASD-associated variants. We then considered pairwise dosage changes within the set of orthologues of candidate genes that were affected by the same single human de novo CNV. For three of four CNVs with complete orthologous relationships, we observed significant synergistic effects following the simultaneous dosage change of gene pairs drawn from a single CNV. The phenotypic variation observed at the Drosophila synapse that results from these interacting genetic variants supports a concordant phenotypic outcome across all interacting gene pairs following the direction of human gene copy number change. We observe both specificity and transitivity between interactors, both within and between CNV candidate gene sets, supporting shared and distinct genetic aetiologies. We then show that different interactions affect divergent synaptic processes, demonstrating distinct molecular aetiologies. Our study illustrates mechanisms through which synergistic effects resulting from large structural variation can contribute to human disease.
Collapse
Affiliation(s)
- Stuart J. Grice
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Caleb Webber
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
| |
Collapse
|
28
|
Jimenez-Del-Rio M, Velez-Pardo C. Alzheimer’s Disease, Drosophila melanogaster and Polyphenols. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 863:21-53. [DOI: 10.1007/978-3-319-18365-7_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
29
|
Yamamoto S, Jaiswal M, Charng WL, Gambin T, Karaca E, Mirzaa G, Wiszniewski W, Sandoval H, Haelterman NA, Xiong B, Zhang K, Bayat V, David G, Li T, Chen K, Gala U, Harel T, Pehlivan D, Penney S, Vissers LELM, de Ligt J, Jhangiani SN, Xie Y, Tsang SH, Parman Y, Sivaci M, Battaloglu E, Muzny D, Wan YW, Liu Z, Lin-Moore AT, Clark RD, Curry CJ, Link N, Schulze KL, Boerwinkle E, Dobyns WB, Allikmets R, Gibbs RA, Chen R, Lupski JR, Wangler MF, Bellen HJ. A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases. Cell 2014; 159:200-214. [PMID: 25259927 PMCID: PMC4298142 DOI: 10.1016/j.cell.2014.09.002] [Citation(s) in RCA: 278] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 06/04/2014] [Accepted: 09/02/2014] [Indexed: 12/31/2022]
Abstract
Invertebrate model systems are powerful tools for studying human disease owing to their genetic tractability and ease of screening. We conducted a mosaic genetic screen of lethal mutations on the Drosophila X chromosome to identify genes required for the development, function, and maintenance of the nervous system. We identified 165 genes, most of whose function has not been studied in vivo. In parallel, we investigated rare variant alleles in 1,929 human exomes from families with unsolved Mendelian disease. Genes that are essential in flies and have multiple human homologs were found to be likely to be associated with human diseases. Merging the human data sets with the fly genes allowed us to identify disease-associated mutations in six families and to provide insights into microcephaly associated with brain dysgenesis. This bidirectional synergism between fly genetics and human genomics facilitates the functional annotation of evolutionarily conserved genes involved in human health.
Collapse
Affiliation(s)
- Shinya Yamamoto
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA
| | - Manish Jaiswal
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Wu-Lin Charng
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Institute of Computer Science, Warsaw University of Technology, 00-661 Warsaw, Poland
| | - Ender Karaca
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Ghayda Mirzaa
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Wojciech Wiszniewski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Hector Sandoval
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Nele A Haelterman
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Bo Xiong
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Ke Zhang
- Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA
| | - Vafa Bayat
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Gabriela David
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Tongchao Li
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Kuchuan Chen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Upasana Gala
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Tamar Harel
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Samantha Penney
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Joep de Ligt
- Department of Human Genetics, Radboudumc, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | - Yajing Xie
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Yesim Parman
- Neurology Department and Neuropathology Laboratory, Istanbul University Medical School, Istanbul 34390, Turkey
| | - Merve Sivaci
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Esra Battaloglu
- Department of Molecular Biology and Genetics, Bogazici University, Istanbul 34342, Turkey
| | - Donna Muzny
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Ying-Wooi Wan
- Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Department of Obstetrics and Gynecology, BCM, Houston, TX 77030, USA
| | - Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Department of Pediatrics, BCM, Houston, TX 77030, USA
| | | | - Robin D Clark
- Division of Medical Genetics, Department of Pediatrics, Loma Linda University Medical Center, Loma Linda, CA 92354, USA
| | - Cynthia J Curry
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA; Genetic Medicine Central California, Fresno, CA 93701, USA
| | - Nichole Link
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Karen L Schulze
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA; Human Genetics Center, University of Texas, Health Science Center, Houston, TX 77030, USA
| | - William B Dobyns
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Neurology, University of Washington, Seattle WA 98195, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Rui Chen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Hugo J Bellen
- Program in Developmental Biology, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA; Program in Structural and Computational Biology and Molecular Biophysics, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA.
| |
Collapse
|
30
|
Taniguchi H, Moore AW. Chromatin regulators in neurodevelopment and disease: Analysis of fly neural circuits provides insights. Bioessays 2014; 36:872-83. [DOI: 10.1002/bies.201400087] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hiroaki Taniguchi
- Laboratory for Genetic Code; Graduate School of Life and Medical Sciences; Doshisha University; Kyotanabe Kyoto Japan
| | - Adrian W. Moore
- Laboratory for Genetic Control of Neuronal Architecture; RIKEN Brain Science Institute; Wako-shi Saitama Japan
| |
Collapse
|
31
|
Drosophila models of early onset cognitive disorders and their clinical applications. Neurosci Biobehav Rev 2014; 46 Pt 2:326-42. [PMID: 24661984 DOI: 10.1016/j.neubiorev.2014.01.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 12/28/2022]
Abstract
The number of genes known to cause human monogenic diseases is increasing rapidly. For the extremely large, genetically and phenotypically heterogeneous group of intellectual disability (ID) disorders, more than 600 causative genes have been identified to date. However, knowledge about the molecular mechanisms and networks disrupted by these genetic aberrations is lagging behind. The fruit fly Drosophila has emerged as a powerful model organism to close this knowledge gap. This review summarizes recent achievements that have been made in this model and envisions its future contribution to our understanding of ID genetics and neuropathology. The available resources and efficiency of Drosophila place it in a position to tackle the main challenges in the field: mapping functional modules of ID genes to provide conceptually novel insights into the genetic control of cognition, tailored functional studies to improve 'next-generation' diagnostics, and identification of reversible ID phenotypes and medication. Drosophila's behavioral repertoire and powerful genetics also open up perspectives for modeling genetically complex forms of ID and neuropsychiatric disorders, which overlap in their genetic etiologies. In conclusion, Drosophila provides many opportunities to advance future medical genomics of early onset cognitive disorders.
Collapse
|