1
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Yost RT, Scott AM, Kurbaj JM, Walshe-Roussel B, Dukas R, Simon AF. Recovery from social isolation requires dopamine in males, but not the autism-related gene nlg3 in either sex. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240604. [PMID: 39086833 PMCID: PMC11288677 DOI: 10.1098/rsos.240604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 08/02/2024]
Abstract
Social isolation causes profound changes in social behaviour in a variety of species. However, the genetic and molecular mechanisms modulating behavioural responses to social isolation and social recovery remain to be elucidated. Here, we quantified the behavioural response of vinegar flies to social isolation using two distinct protocols (social space preference and sociability, the spontaneous tendencies to form groups). We found that social isolation increased social space and reduced sociability. These effects of social isolation were reversible and could be reduced after 3 days of group housing. Flies with a loss of function of neuroligin3 (orthologue of autism-related neuroligin genes) with known increased social space in a socially enriched environment were still able to recover from social isolation. We also show that dopamine (DA) is needed for a response to social isolation and recovery in males but not in females. Furthermore, only in males, DA levels are reduced after isolation and are not recovered after group housing. Finally, in socially enriched flies mutant for neuroligin3, DA levels are reduced in males, but not in females. We propose a model to explain how DA and neuroligin3 are involved in the behavioural response to social isolation and its recovery in a dynamic and sex-specific manner.
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Affiliation(s)
- Ryley T. Yost
- Department of Biology, Western University, London, Ontario, Canada
| | | | - Judy M. Kurbaj
- Department of Biology, Western University, London, Ontario, Canada
| | | | - Reuven Dukas
- Department of Psychology, Neuroscience and Behaviour, Animal Behaviour Group, McMaster University, Hamilton, Ontario, Canada
| | - Anne F. Simon
- Department of Biology, Western University, London, Ontario, Canada
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2
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Fiksinski AM, Hoftman GD, Vorstman JAS, Bearden CE. A genetics-first approach to understanding autism and schizophrenia spectrum disorders: the 22q11.2 deletion syndrome. Mol Psychiatry 2023; 28:341-353. [PMID: 36192458 PMCID: PMC9812786 DOI: 10.1038/s41380-022-01783-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 08/31/2022] [Accepted: 09/05/2022] [Indexed: 02/03/2023]
Abstract
Recently, increasing numbers of rare pathogenic genetic variants have been identified that are associated with variably elevated risks of a range of neurodevelopmental outcomes, notably including Autism Spectrum Disorders (ASD), Schizophrenia Spectrum Disorders (SSD), and Intellectual Disability (ID). This review is organized along three main questions: First, how can we unify the exclusively descriptive basis of our current psychiatric diagnostic classification system with the recognition of an identifiable, highly penetrant genetic risk factor in an increasing proportion of patients with ASD or SSD? Second, what can be learned from studies of individuals with ASD or SSD who share a common genetic basis? And third, what accounts for the observed variable penetrance and pleiotropy of neuropsychiatric phenotypes in individuals with the same pathogenic variant? In this review, we focus on findings of clinical and preclinical studies of the 22q11.2 deletion syndrome (22q11DS). This particular variant is not only one of the most common among the increasing list of known rare pathogenic variants, but also one that benefits from a relatively long research history. Consequently, 22q11DS is an appealing model as it allows us to: (1) elucidate specific genotype-phenotype associations, (2) prospectively study behaviorally defined classifications, such as ASD or SSD, in the context of a known, well-characterized genetic basis, and (3) elucidate mechanisms underpinning variable penetrance and pleiotropy, phenomena with far-reaching ramifications for research and clinical practice. We discuss how findings from animal and in vitro studies relate to observations in human studies and can help elucidate factors, including genetic, environmental, and stochastic, that impact the expression of neuropsychiatric phenotypes in 22q11DS, and how this may inform mechanisms underlying neurodevelopmental expression in the general population. We conclude with research priorities for the field, which may pave the way for novel therapeutics.
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Affiliation(s)
- Ania M Fiksinski
- Department of Psychology and Department of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Psychiatry and Neuropsychology, Division of Mental Health, MHeNS, Maastricht University, Maastricht, The Netherlands
| | - Gil D Hoftman
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Jacob A S Vorstman
- Program in Genetics and Genome Biology, Research Institute, and Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA.
- Department of Psychology, University of California, Los Angeles, CA, USA.
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3
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Buttermore E, Chamberlain S, Cody J, Costain G, Dang L, DeWoody A, DeWoody Y, Dies K, Eichler E, Girirajan S, Gramm M, Halladay A, Lal D, Lalli M, Levy T, Logsdon G, Lowenstein D, Mefford H, Mulle J, Muotri A, Murphy M, Perez Palma E, Pinter S, Pollak R, Purcell R, Samaco R, Shah B, Singh K, So J, Sundberg M, Veeraragavan S, Vogel-Farley V, Wynshaw-Boris A. Neurodevelopmental copy-number variants: A roadmap to improving outcomes by uniting patient advocates, researchers, and clinicians for collective impact. Am J Hum Genet 2022; 109:1353-1365. [PMID: 35931048 PMCID: PMC9388383 DOI: 10.1016/j.ajhg.2022.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Copy-number variants and structural variants (CNVs/SVs) drive many neurodevelopmental-related disorders. While many neurodevelopmental-related CNVs/SVs give rise to complex phenotypes, the overlap in phenotypic presentation between independent CNVs can be extensive and provides a motivation for shared approaches. This confluence at the level of clinical phenotype implies convergence in at least some aspects of the underlying genomic mechanisms. With this perspective, our Commission on Novel Technologies for Neurodevelopmental CNVs asserts that the time has arrived to approach neurodevelopmental-related CNVs/SVs as a class of disorders that can be identified, investigated, and treated on the basis of shared mechanisms and/or pathways (e.g., molecular, neurological, or developmental). To identify common etiologic mechanisms among uncommon neurodevelopmental-related disorders and to potentially identify common therapies, it is paramount for teams of scientists, clinicians, and patients to unite their efforts. We bring forward novel, collaborative, and integrative strategies to translational CNV/SV research that engages diverse stakeholders to help expedite therapeutic outcomes. We articulate a clear vision for piloted roadmap strategies to reduce patient/caregiver burden and redundancies, increase efficiency, avoid siloed data, and accelerate translational discovery across CNV/SV-based syndromes.
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4
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Grice SJ, Liu JL. Motor defects in a Drosophila model for spinal muscular atrophy result from SMN depletion during early neurogenesis. PLoS Genet 2022; 18:e1010325. [PMID: 35877682 PMCID: PMC9352204 DOI: 10.1371/journal.pgen.1010325] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/04/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Spinal muscular atrophy (SMA) is the most common autosomal recessive neurodegenerative disease, and is characterised by spinal motor neuron loss, impaired motor function and, often, premature death. Mutations and deletions in the widely expressed survival motor neuron 1 (SMN1) gene cause SMA; however, the mechanisms underlying the selectivity of motor neuron degeneration are not well understood. Although SMA is degenerative in nature, SMN function during embryonic and early postnatal development appears to be essential for motor neuron survival in animal models and humans. Notwithstanding, how developmental defects contribute to the subversion of postnatal and adult motor function remains elusive. Here, in a Drosophila SMA model, we show that neurodevelopmental defects precede gross locomotor dysfunction in larvae. Furthermore, to specifically address the relevance of SMN during neurogenesis and in neurogenic cell types, we show that SMN knockdown using neuroblast-specific and pan-neuronal drivers, but not differentiated neuron or glial cell drivers, impairs adult motor function. Using targeted knockdown, we further restricted SMN manipulation in neuroblasts to a defined time window. Our aim was to express specifically in the neuronal progenitor cell types that have not formed synapses, and thus a time that precedes neuromuscular junction formation and maturation. By restoring SMN levels in these distinct neuronal population, we partially rescue the larval locomotor defects of Smn mutants. Finally, combinatorial SMN knockdown in immature and mature neurons synergistically enhances the locomotor and survival phenotypes. Our in-vivo study is the first to directly rescue the motor defects of an SMA model by expressing Smn in an identifiable population of Drosophila neuroblasts and developing neurons, highlighting that neuronal sensitivity to SMN loss may arise before synapse establishment and nerve cell maturation. Spinal muscular atrophy (SMA) is the most common genetic cause of infant mortality and leads to the degeneration of the nerves that control muscle function. Loss-of-function mutations in the widely expressed survival motor neuron 1 (SMN1) gene cause SMA, but how low levels of SMN protein cause the neuronal dysfunction is not known. Although SMA is a disease of nerve degeneration, SMN function during nerve cell development may be important, particularly in severe forms of SMA. Nevertheless, how the defects during development and throughout early life contribute to the disease is not well understood. We have previously demonstrated that SMN protein becomes enriched in neuroblasts, which are the cells that divide to produce neurons. In the present study, motor defects observed in our fly model for SMA could be rescued by restoring SMN in neuroblasts alone. In addition, we show that knocking down SMN in healthy flies within the same cell type causes impaired motor function. The present study shows that the manipulation of SMN in a developmentally important cell type can cause motor defects, indicating that a period of abnormal neurodevelopment may contribute to SMA.
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Affiliation(s)
- Stuart J. Grice
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (SJG); , (J-LL)
| | - Ji-Long Liu
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- School of Life Science and Technology, Shanghai, Tech University, Shanghai, China
- * E-mail: (SJG); , (J-LL)
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5
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Muller K, Herrera K, Talyn B, Melchiorre E. Toxicological Effects of Roundup ® on Drosophila melanogaster Reproduction. TOXICS 2021; 9:161. [PMID: 34357904 PMCID: PMC8309847 DOI: 10.3390/toxics9070161] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022]
Abstract
Herbicide use has increased dramatically since 2001, particularly Roundup®. Effective in agricultural practice, Roundup® adversely affects non-target organisms, including reproductive and endocrine systems. We exposed fruit flies, Drosophila melanogaster, to either Roundup® Ready to Use, containing pelargonic acid and glyphosate, or Roundup® Super Concentrate, that includes glyphosate and POEA, at sublethal concentrations. Both Roundup® formulations reduced ovary volume with fewer mature oocytes, most adversely at the highest concentration tested. Flies exposed within 2 h of eclosion were affected more than at 4 h, suggesting a critical period of increased ovarian sensitivity. These results support multi-species evidence that glyphosate-based herbicides interfere with normal development of the reproductive systems of non-target organisms.
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Affiliation(s)
- Kelly Muller
- Department of Chemistry and Biochemistry, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA; (K.M.); (K.H.)
| | - Karina Herrera
- Department of Chemistry and Biochemistry, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA; (K.M.); (K.H.)
| | - Becky Talyn
- Department of Biology and College of Natural Sciences, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA
| | - Erik Melchiorre
- Department of Geology, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA;
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6
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Sefik E, Purcell RH, The Emory 3q29 Project AberizkKatrina2AverbachHallie1BlackEmily1BurrellT. Lindsey6CambalaShanthi1CarlockGrace1CasparyTamara1CubellsJoseph F.1CutlerDavid1DawsonPaul A.6EpsteinMichael T.1EspanaRoberto2GambelloMichael J.1GoinesKatrina2GuestRyan M.2JohnstonHenry R.1KlaimanCheryl2KohSookyong2LeslieElizabeth J.1LiLongchuan2MakBryan1MaloneTamika1MosleyTrenell1MurphyMelissa M.1PapettiAva1PollakRebecca M.1RussoRossana Sanchez1SaulnierCeline A.2ShultzSarah2SisodoyaNikisha1SloanSteven1WarrenStephen T.1WeinshenkerDavid1WenZhexing3WhiteStormi Pulver2ZwickMike1, Walker EF, Bassell GJ, Mulle JG. Convergent and distributed effects of the 3q29 deletion on the human neural transcriptome. Transl Psychiatry 2021; 11:357. [PMID: 34131099 PMCID: PMC8206125 DOI: 10.1038/s41398-021-01435-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 04/29/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
The 3q29 deletion (3q29Del) confers high risk for schizophrenia and other neurodevelopmental and psychiatric disorders. However, no single gene in this interval is definitively associated with disease, prompting the hypothesis that neuropsychiatric sequelae emerge upon loss of multiple functionally-connected genes. 3q29 genes are unevenly annotated and the impact of 3q29Del on the human neural transcriptome is unknown. To systematically formulate unbiased hypotheses about molecular mechanisms linking 3q29Del to neuropsychiatric illness, we conducted a systems-level network analysis of the non-pathological adult human cortical transcriptome and generated evidence-based predictions that relate 3q29 genes to novel functions and disease associations. The 21 protein-coding genes located in the interval segregated into seven clusters of highly co-expressed genes, demonstrating both convergent and distributed effects of 3q29Del across the interrogated transcriptomic landscape. Pathway analysis of these clusters indicated involvement in nervous-system functions, including synaptic signaling and organization, as well as core cellular functions, including transcriptional regulation, posttranslational modifications, chromatin remodeling, and mitochondrial metabolism. Top network-neighbors of 3q29 genes showed significant overlap with known schizophrenia, autism, and intellectual disability-risk genes, suggesting that 3q29Del biology is relevant to idiopathic disease. Leveraging "guilt by association", we propose nine 3q29 genes, including one hub gene, as prioritized drivers of neuropsychiatric risk. These results provide testable hypotheses for experimental analysis on causal drivers and mechanisms of the largest known genetic risk factor for schizophrenia and highlight the study of normal function in non-pathological postmortem tissue to further our understanding of psychiatric genetics, especially for rare syndromes like 3q29Del, where access to neural tissue from carriers is unavailable or limited.
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Affiliation(s)
- Esra Sefik
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Psychology, Emory University, Atlanta, GA USA
| | - Ryan H. Purcell
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | | | - Elaine F. Walker
- grid.189967.80000 0001 0941 6502Department of Psychology, Emory University, Atlanta, GA USA
| | - Gary J. Bassell
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Laboratory of Translational Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Jennifer G. Mulle
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA ,grid.189967.80000 0001 0941 6502Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA USA
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7
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Mak BC, Sanchez Russo R, Gambello MJ, Fleischer N, Black ED, Leslie E, Murphy MM, Mulle JG. Craniofacial features of 3q29 deletion syndrome: Application of next-generation phenotyping technology. Am J Med Genet A 2021; 185:2094-2101. [PMID: 33938623 PMCID: PMC8250870 DOI: 10.1002/ajmg.a.62227] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 12/21/2022]
Abstract
3q29 deletion syndrome (3q29del) is a recurrent deletion syndrome associated with neuropsychiatric disorders and congenital anomalies. Dysmorphic facial features have been described but not systematically characterized. This study aims to detail the 3q29del craniofacial phenotype and use a machine learning approach to categorize individuals with 3q29del through analysis of 2D photos. Detailed dysmorphology exam and 2D facial photos were ascertained from 31 individuals with 3q29del. Photos were used to train the next-generation phenotyping algorithm DeepGestalt (Face2Gene by FDNA, Inc, Boston, MA) to distinguish 3q29del cases from controls and all other recognized syndromes. Area under the curve of receiver operating characteristic curves (AUC-ROC) was used to determine the capacity of Face2Gene to identify 3q29del cases against controls. In this cohort, the most common observed craniofacial features were prominent forehead (48.4%), prominent nose tip (35.5%), and thin upper lip vermillion (25.8%). The FDNA technology showed an ability to distinguish cases from controls with an AUC-ROC value of 0.873 (p = 0.006) and led to the inclusion of 3q29del as one of the supported syndromes. This study found a recognizable facial pattern in 3q29del, as observed by trained clinical geneticists and next-generation phenotyping technology. These results expand the potential application of automated technology such as FDNA in identifying rare genetic syndromes, even when facial dysmorphology is subtle.
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Affiliation(s)
- Bryan C Mak
- Department of Human Genetics, Emory University School, of Medicine, Atlanta, Georgia, USA
| | - Rossana Sanchez Russo
- Department of Human Genetics, Emory University School, of Medicine, Atlanta, Georgia, USA
| | - Michael J Gambello
- Department of Human Genetics, Emory University School, of Medicine, Atlanta, Georgia, USA.,Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Emily D Black
- Department of Human Genetics, Emory University School, of Medicine, Atlanta, Georgia, USA
| | - Elizabeth Leslie
- Department of Human Genetics, Emory University School, of Medicine, Atlanta, Georgia, USA
| | - Melissa M Murphy
- Department of Human Genetics, Emory University School, of Medicine, Atlanta, Georgia, USA
| | -
- Department of Human Genetics, Emory University School, of Medicine, Atlanta, Georgia, USA
| | - Jennifer Gladys Mulle
- Department of Human Genetics, Emory University School, of Medicine, Atlanta, Georgia, USA.,Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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8
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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.
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9
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Rutkowski TP, Purcell RH, Pollak RM, Grewenow SM, Gafford GM, Malone T, Khan UA, Schroeder JP, Epstein MP, Bassell GJ, Warren ST, Weinshenker D, Caspary T, Mulle JG. Behavioral changes and growth deficits in a CRISPR engineered mouse model of the schizophrenia-associated 3q29 deletion. Mol Psychiatry 2021; 26:772-783. [PMID: 30976085 PMCID: PMC6788962 DOI: 10.1038/s41380-019-0413-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 02/13/2019] [Accepted: 03/18/2019] [Indexed: 12/27/2022]
Abstract
The 3q29 deletion confers increased risk for neuropsychiatric phenotypes including intellectual disability, autism spectrum disorder, generalized anxiety disorder, and a >40-fold increased risk for schizophrenia. To investigate consequences of the 3q29 deletion in an experimental system, we used CRISPR/Cas9 technology to introduce a heterozygous deletion into the syntenic interval on C57BL/6 mouse chromosome 16. mRNA abundance for 20 of the 21 genes in the interval was reduced by ~50%, while protein levels were reduced for only a subset of these, suggesting a compensatory mechanism. Mice harboring the deletion manifested behavioral impairments in multiple domains including social interaction, cognitive function, acoustic startle, and amphetamine sensitivity, with some sex-dependent manifestations. In addition, 3q29 deletion mice showed reduced body weight throughout development consistent with the phenotype of 3q29 deletion syndrome patients. Of the genes within the interval, DLG1 has been hypothesized as a contributor to the neuropsychiatric phenotypes. However, we show that Dlg1+/- mice did not exhibit the behavioral deficits seen in mice harboring the full 3q29 deletion. These data demonstrate the following: the 3q29 deletion mice are a valuable experimental system that can be used to interrogate the biology of 3q29 deletion syndrome; behavioral manifestations of the 3q29 deletion may have sex-dependent effects; and mouse-specific behavior phenotypes associated with the 3q29 deletion are not solely due to haploinsufficiency of Dlg1.
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Affiliation(s)
- Timothy P. Rutkowski
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Ryan H. Purcell
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Rebecca M. Pollak
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Stephanie M. Grewenow
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Georgette M. Gafford
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Tamika Malone
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Uswa A. Khan
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Jason P. Schroeder
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Michael P. Epstein
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Gary J. Bassell
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Stephen T. Warren
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - David Weinshenker
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Tamara Caspary
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322 USA
| | - Jennifer Gladys Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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10
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Urresti J, Zhang P, Moran-Losada P, Yu NK, Negraes PD, Trujillo CA, Antaki D, Amar M, Chau K, Pramod AB, Diedrich J, Tejwani L, Romero S, Sebat J, Yates III JR, Muotri AR, Iakoucheva LM. Cortical organoids model early brain development disrupted by 16p11.2 copy number variants in autism. Mol Psychiatry 2021; 26:7560-7580. [PMID: 34433918 PMCID: PMC8873019 DOI: 10.1038/s41380-021-01243-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 07/12/2021] [Accepted: 07/20/2021] [Indexed: 11/09/2022]
Abstract
Reciprocal deletion and duplication of the 16p11.2 region is the most common copy number variation (CNV) associated with autism spectrum disorders. We generated cortical organoids from skin fibroblasts of patients with 16p11.2 CNV to investigate impacted neurodevelopmental processes. We show that organoid size recapitulates macrocephaly and microcephaly phenotypes observed in the patients with 16p11.2 deletions and duplications. The CNV dosage affects neuronal maturation, proliferation, and synapse number, in addition to its effect on organoid size. We demonstrate that 16p11.2 CNV alters the ratio of neurons to neural progenitors in organoids during early neurogenesis, with a significant excess of neurons and depletion of neural progenitors observed in deletions. Transcriptomic and proteomic profiling revealed multiple pathways dysregulated by the 16p11.2 CNV, including neuron migration, actin cytoskeleton, ion channel activity, synaptic-related functions, and Wnt signaling. The level of the active form of small GTPase RhoA was increased in both, deletions and duplications. Inhibition of RhoA activity rescued migration deficits, but not neurite outgrowth. This study provides insights into potential neurobiological mechanisms behind the 16p11.2 CNV during neocortical development.
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Affiliation(s)
- Jorge Urresti
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Pan Zhang
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Patricia Moran-Losada
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Nam-Kyung Yu
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Priscilla D. Negraes
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Cleber A. Trujillo
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Danny Antaki
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA
| | - Megha Amar
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Kevin Chau
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Akula Bala Pramod
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
| | - Jolene Diedrich
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Leon Tejwani
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Sarah Romero
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA
| | - Jonathan Sebat
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242University of California San Diego, Beyster Center for Psychiatric Genomics, La Jolla, CA USA
| | - John R. Yates III
- grid.214007.00000000122199231Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA USA
| | - Alysson R. Muotri
- grid.266100.30000 0001 2107 4242Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242Department of Pediatrics/Rady Children’s Hospital San Diego, University of California, San Diego, La Jolla, CA USA ,grid.266100.30000 0001 2107 4242University of California San Diego, Kavli Institute for Brain and Mind, La Jolla, CA USA ,Center for Academic Research and Training in Anthropogeny (CARTA), La Jolla, CA USA
| | - Lilia M. Iakoucheva
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California San Diego, La Jolla, CA USA
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11
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Recent Advances in Drosophila Models of Charcot-Marie-Tooth Disease. Int J Mol Sci 2020; 21:ijms21197419. [PMID: 33049996 PMCID: PMC7582988 DOI: 10.3390/ijms21197419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 12/15/2022] Open
Abstract
Charcot-Marie-Tooth disease (CMT) is one of the most common inherited peripheral neuropathies. CMT patients typically show slowly progressive muscle weakness and sensory loss in a distal dominant pattern in childhood. The diagnosis of CMT is based on clinical symptoms, electrophysiological examinations, and genetic testing. Advances in genetic testing technology have revealed the genetic heterogeneity of CMT; more than 100 genes containing the disease causative mutations have been identified. Because a single genetic alteration in CMT leads to progressive neurodegeneration, studies of CMT patients and their respective models revealed the genotype-phenotype relationships of targeted genes. Conventionally, rodents and cell lines have often been used to study the pathogenesis of CMT. Recently, Drosophila has also attracted attention as a CMT model. In this review, we outline the clinical characteristics of CMT, describe the advantages and disadvantages of using Drosophila in CMT studies, and introduce recent advances in CMT research that successfully applied the use of Drosophila, in areas such as molecules associated with mitochondria, endosomes/lysosomes, transfer RNA, axonal transport, and glucose metabolism.
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12
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McNeill EM, Warinner C, Alkins S, Taylor A, Heggeness H, DeLuca TF, Fulga TA, Wall DP, Griffith LC, Van Vactor D. The conserved microRNA miR-34 regulates synaptogenesis via coordination of distinct mechanisms in presynaptic and postsynaptic cells. Nat Commun 2020; 11:1092. [PMID: 32107390 PMCID: PMC7046720 DOI: 10.1038/s41467-020-14761-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 01/31/2020] [Indexed: 01/30/2023] Open
Abstract
Micro(mi)RNA-based post-transcriptional regulatory mechanisms have been broadly implicated in the assembly and modulation of synaptic connections required to shape neural circuits, however, relatively few specific miRNAs have been identified that control synapse formation. Using a conditional transgenic toolkit for competitive inhibition of miRNA function in Drosophila, we performed an unbiased screen for novel regulators of synapse morphogenesis at the larval neuromuscular junction (NMJ). From a set of ten new validated regulators of NMJ growth, we discovered that miR-34 mutants display synaptic phenotypes and cell type-specific functions suggesting distinct downstream mechanisms in the presynaptic and postsynaptic compartments. A search for conserved downstream targets for miR-34 identified the junctional receptor CNTNAP4/Neurexin-IV (Nrx-IV) and the membrane cytoskeletal effector Adducin/Hu-li tai shao (Hts) as proteins whose synaptic expression is restricted by miR-34. Manipulation of miR-34, Nrx-IV or Hts-M function in motor neurons or muscle supports a model where presynaptic miR-34 inhibits Nrx-IV to influence active zone formation, whereas, postsynaptic miR-34 inhibits Hts to regulate the initiation of bouton formation from presynaptic terminals. Although micro(mi)RNA-based post-transcriptional regulatory mechanisms have been implicated in the assembly and modulation of synaptic connections, few miRNAs have been identified that control synapse formation. Here, authors performed an unbiased screen for novel regulators of synapse morphogenesis at the Drosophila larval neuromuscular junction and discovered that miR-34 inhibits Nrx-IV to influence active zone formation, whereas, postsynaptic miR-34 inhibits Hts to regulate the initiation of bouton formation from presynaptic terminals.
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Affiliation(s)
- Elizabeth M McNeill
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.,Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, USA
| | - Chloe Warinner
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephen Alkins
- Department of Biology and Volen National Center for Complex Systems, Brandeis University, Waltham, MA, 02454, USA
| | - Alicia Taylor
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.,Department of Food Science and Human Nutrition, Iowa State University, Ames, IA, USA
| | - Hansine Heggeness
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Todd F DeLuca
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA
| | - Tudor A Fulga
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.,Weatherall Institute, Oxford University, Oxford, UK
| | - Dennis P Wall
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Palo Alto, CA, 94305, USA
| | - Leslie C Griffith
- Department of Biology and Volen National Center for Complex Systems, Brandeis University, Waltham, MA, 02454, USA
| | - David Van Vactor
- Department of Cell Biology and Program in Neuroscience, Harvard Medical School, Boston, MA, 02115, USA.
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13
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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.
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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
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14
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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.
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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.
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15
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An autism-causing calcium channel variant functions with selective autophagy to alter axon targeting and behavior. PLoS Genet 2019; 15:e1008488. [PMID: 31805042 PMCID: PMC6894750 DOI: 10.1371/journal.pgen.1008488] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/21/2019] [Indexed: 11/22/2022] Open
Abstract
Common and rare variants of the CACNA1C voltage-gated calcium channel gene have been associated with autism and other neurodevelopmental disorders including schizophrenia, bipolar disorder and ADHD. However, little is known about how CACNA1C variants affect cellular processes to alter neurodevelopment. The Timothy syndrome mutation is a rare de novo gain-of-function variant in CACNA1C that causes autism with high penetrance, providing a powerful avenue into investigating the role of CACNA1C variants in neurodevelopmental disorders. Here, we use egl-19, the C. elegans homolog of CACNA1C, to investigate the role of voltage-gated calcium channels in autism. We show that an egl-19(gof) mutation that is equivalent to the Timothy syndrome mutation can alter axon targeting and affect behavior in C. elegans. We find that wildtype egl-19 negatively regulates axon termination. The egl-19(gof) mutation represses axon termination to cause axon targeting defects that lead to the misplacement of electrical synapses and alterations in habituation to light touch. Moreover, genetic interactions indicate that the egl-19(gof) mutation functions with genes that promote selective autophagy to cause defects in axon termination and behavior. These results reveal a novel genetic mechanism whereby a de novo mutation in CACNA1C can drive alterations in circuit formation and behavior. Autism is a disorder that affects neuronal development, leading to alterations in cognition and behavior. Imaging studies have revealed alterations in axonal connectivity as a key feature of autism. However, the underlying perturbations in cell biology that drive these alterations remain largely unknown. To address this issue, we have taken advantage of the Timothy syndrome mutation, a variant in a voltage-gated calcium channel that has the unusual property of causing autism with high penetrance. We identify a role for wild-type voltage-gated calcium channels in regulating axon targeting in C. elegans. Moreover, we find that two different versions of the Timothy syndrome mutation disrupt axon targeting. Our results suggest that the Timothy syndrome mutations disrupt axon targeting and behavior by interacting with genes that promote selective autophagy, the process through which cellular components are selected for degradation. These results reveal a mechanism through which variants in voltage-gated calcium channels can cause the disruptions in axonal connectivity that underlie autism.
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16
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Meijsen JJ, Rammos A, Campbell A, Hayward C, Porteous DJ, Deary IJ, Marioni RE, Nicodemus KK. Using tree-based methods for detection of gene-gene interactions in the presence of a polygenic signal: simulation study with application to educational attainment in the Generation Scotland Cohort Study. Bioinformatics 2019; 35:181-188. [PMID: 29931044 PMCID: PMC6330004 DOI: 10.1093/bioinformatics/bty462] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/14/2018] [Indexed: 11/13/2022] Open
Abstract
Motivation The genomic architecture of human complex diseases is thought to be attributable to single markers, polygenic components and epistatic components. No study has examined the ability of tree-based methods to detect epistasis in the presence of a polygenic signal. We sought to apply decision tree-based methods, C5.0 and logic regression, to detect epistasis under several simulated conditions, varying strength of interaction and linkage disequilibrium (LD) structure. We then applied the same methods to the phenotype of educational attainment in a large population cohort. Results LD pruning improved the power and reduced the type I error. C5.0 had a conservative type I error rate whereas logic regression had a type I error rate that exceeded 5%. Despite the more conservative type I error, C5.0 was observed to have higher power than logic regression across several conditions. In the presence of a polygenic signal, power was generally reduced. Applying both methods on educational attainment in a large population cohort yielded numerous interacting SNPs; notably a SNP in RCAN3 which is associated with reading and spelling and a SNP in NPAS3, a neurodevelopmental gene. Availability and implementation All methods used are implemented and freely available in R. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joeri J Meijsen
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Alexandros Rammos
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Department of Genetics, Smurfit Institute of Genetics and Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Kristin K Nicodemus
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.,Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
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17
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Ueoka I, Pham HTN, Matsumoto K, Yamaguchi M. Autism Spectrum Disorder-Related Syndromes: Modeling with Drosophila and Rodents. Int J Mol Sci 2019; 20:E4071. [PMID: 31438473 PMCID: PMC6747505 DOI: 10.3390/ijms20174071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/17/2019] [Accepted: 08/18/2019] [Indexed: 12/11/2022] Open
Abstract
Whole exome analyses have identified a number of genes associated with autism spectrum disorder (ASD) and ASD-related syndromes. These genes encode key regulators of synaptogenesis, synaptic plasticity, cytoskeleton dynamics, protein synthesis and degradation, chromatin remodeling, transcription, and lipid homeostasis. Furthermore, in silico studies suggest complex regulatory networks among these genes. Drosophila is a useful genetic model system for studies of ASD and ASD-related syndromes to clarify the in vivo roles of ASD-associated genes and the complex gene regulatory networks operating in the pathogenesis of ASD and ASD-related syndromes. In this review, we discuss what we have learned from studies with vertebrate models, mostly mouse models. We then highlight studies with Drosophila models. We also discuss future developments in the related field.
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Affiliation(s)
- Ibuki Ueoka
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 603-8585, Japan
| | - Hang Thi Nguyet Pham
- Department of Pharmacology and Biochemistry, National Institute of Medicinal Materials, Hanoi 110100, Vietnam
| | - Kinzo Matsumoto
- Division of Medicinal Pharmacology, Institute of Natural Medicine, University of Toyama, Toyama 930-0194, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 603-8585, Japan.
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18
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Talyn B, Lemon R, Badoella M, Melchiorre D, Villalobos M, Elias R, Muller K, Santos M, Melchiorre E. Roundup ®, but Not Roundup-Ready ® Corn, Increases Mortality of Drosophila melanogaster. TOXICS 2019; 7:E38. [PMID: 31370250 PMCID: PMC6789507 DOI: 10.3390/toxics7030038] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/29/2019] [Accepted: 07/29/2019] [Indexed: 02/06/2023]
Abstract
Genetically modified foods have become pervasive in diets of people living in the US. By far the most common genetically modified foods either tolerate herbicide application (HT) or produce endogenous insecticide (Bt). To determine whether these toxicological effects result from genetic modification per se, or from the increase in herbicide or insecticide residues present on the food, we exposed fruit flies, Drosophila melanogaster, to food containing HT corn that had been sprayed with the glyphosate-based herbicide Roundup®, HT corn that had not been sprayed with Roundup®, or Roundup® in a variety of known glyphosate concentrations and formulations. While neither lifespan nor reproductive behaviors were affected by HT corn, addition of Roundup® increased mortality with an LC50 of 7.1 g/L for males and 11.4 g/L for females after 2 days of exposure. Given the many genetic tools available, Drosophila are an excellent model system for future studies about genetic and biochemical mechanisms of glyphosate toxicity.
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Affiliation(s)
- Becky Talyn
- College of Natural Science, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA.
| | - Rachael Lemon
- Biology Department, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA
| | - Maryam Badoella
- Biology Department, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA
| | | | - Maryori Villalobos
- Biology Department, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA
| | - Raquel Elias
- Biology Department, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA
| | - Kelly Muller
- Chemistry and Biochemistry Department, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA
| | - Maggie Santos
- Biology Department, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA
| | - Erik Melchiorre
- Geology Department, California State University, 5500 University Parkway, San Bernardino, CA 92407, USA
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19
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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: 32] [Impact Index Per Article: 5.3] [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.
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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
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20
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Abstract
Variably expressive copy-number variants (CNVs) are characterized by extensive phenotypic heterogeneity of neuropsychiatric phenotypes. Approaches to identify single causative genes for these phenotypes within each CNV have not been successful. Here, we posit using multiple lines of evidence, including pathogenicity metrics, functional assays of model organisms, and gene expression data, that multiple genes within each CNV region are likely responsible for the observed phenotypes. We propose that candidate genes within each region likely interact with each other through shared pathways to modulate the individual gene phenotypes, emphasizing the genetic complexity of CNV-associated neuropsychiatric features.
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Affiliation(s)
- Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
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21
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Iyer J, Singh MD, Jensen M, Patel P, Pizzo L, Huber E, Koerselman H, Weiner AT, Lepanto P, Vadodaria K, Kubina A, Wang Q, Talbert A, Yennawar S, Badano J, Manak JR, Rolls MM, Krishnan A, Girirajan S. Pervasive genetic interactions modulate neurodevelopmental defects of the autism-associated 16p11.2 deletion in Drosophila melanogaster. Nat Commun 2018; 9:2548. [PMID: 29959322 PMCID: PMC6026208 DOI: 10.1038/s41467-018-04882-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/22/2018] [Indexed: 12/26/2022] Open
Abstract
As opposed to syndromic CNVs caused by single genes, extensive phenotypic heterogeneity in variably-expressive CNVs complicates disease gene discovery and functional evaluation. Here, we propose a complex interaction model for pathogenicity of the autism-associated 16p11.2 deletion, where CNV genes interact with each other in conserved pathways to modulate expression of the phenotype. Using multiple quantitative methods in Drosophila RNAi lines, we identify a range of neurodevelopmental phenotypes for knockdown of individual 16p11.2 homologs in different tissues. We test 565 pairwise knockdowns in the developing eye, and identify 24 interactions between pairs of 16p11.2 homologs and 46 interactions between 16p11.2 homologs and neurodevelopmental genes that suppress or enhance cell proliferation phenotypes compared to one-hit knockdowns. These interactions within cell proliferation pathways are also enriched in a human brain-specific network, providing translational relevance in humans. Our study indicates a role for pervasive genetic interactions within CNVs towards cellular and developmental phenotypes. The 16p11.2 deletion leads to a range of neurodevelopmental phenotypes, but to date, sequencing studies have not been able to pinpoint individual genes that are causative for the disease on their own. Here, using Drosophila homologs of 14 16p11.2 genes, the authors take a combinatorial approach to show that gene interactions contribute to a neurological phenotype.
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Affiliation(s)
- Janani Iyer
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Mayanglambam Dhruba Singh
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Matthew Jensen
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Payal Patel
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lucilla Pizzo
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Emily Huber
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Haley Koerselman
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA
| | - Alexis T Weiner
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Paola Lepanto
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Montevideo, CP11400, Uruguay
| | - Komal Vadodaria
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Alexis Kubina
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Qingyu Wang
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Abigail Talbert
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Sneha Yennawar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jose Badano
- Human Molecular Genetics Laboratory, Institut Pasteur de Montevideo, Montevideo, CP11400, Uruguay
| | - J Robert Manak
- Department of Biology, University of Iowa, Iowa City, IA, 52242, USA.,Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Melissa M Rolls
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Arjun Krishnan
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA.
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22
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Grice SJ, Sleigh JN, Zameel Cader M. Plexin-Semaphorin Signaling Modifies Neuromuscular Defects in a Drosophila Model of Peripheral Neuropathy. Front Mol Neurosci 2018. [PMID: 29520219 PMCID: PMC5827687 DOI: 10.3389/fnmol.2018.00055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Dominant mutations in GARS, encoding the ubiquitous enzyme glycyl-tRNA synthetase (GlyRS), cause peripheral nerve degeneration and Charcot-Marie-Tooth disease type 2D (CMT2D). This genetic disorder exemplifies a recurring paradigm in neurodegeneration, in which mutations in essential genes cause selective degeneration of the nervous system. Recent evidence suggests that the mechanism underlying CMT2D involves extracellular neomorphic binding of mutant GlyRS to neuronally-expressed proteins. Consistent with this, our previous studies indicate a non-cell autonomous mechanism, whereby mutant GlyRS is secreted and interacts with the neuromuscular junction (NMJ). In this Drosophila model for CMT2D, we have previously shown that mutant gars expression decreases viability and larval motor function, and causes a concurrent build-up of mutant GlyRS at the larval neuromuscular presynapse. Here, we report additional phenotypes that closely mimic the axonal branching defects of Drosophila plexin transmembrane receptor mutants, implying interference of plexin signaling in gars mutants. Individual dosage reduction of two Drosophila Plexins, plexin A (plexA) and B (plexB) enhances and represses the viability and larval motor defects caused by mutant GlyRS, respectively. However, we find plexB levels, but not plexA levels, modify mutant GlyRS association with the presynaptic membrane. Furthermore, increasing availability of the plexB ligand, Semaphorin-2a (Sema2a), alleviates the pathology and the build-up of mutant GlyRS, suggesting competition for plexB binding may be occurring between these two ligands. This toxic gain-of-function and subversion of neurodevelopmental processes indicate that signaling pathways governing axonal guidance could be integral to neuropathology and may underlie the non-cell autonomous CMT2D mechanism.
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Affiliation(s)
- Stuart J Grice
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - James N Sleigh
- Sobell Department of Motor Neuroscience and Movement Disorders, Institute of Neurology, University College London, London, United Kingdom
| | - M Zameel Cader
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom.,MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
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23
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Tian Y, Zhang ZC, Han J. Drosophila Studies on Autism Spectrum Disorders. Neurosci Bull 2017; 33:737-746. [PMID: 28795356 DOI: 10.1007/s12264-017-0166-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/23/2017] [Indexed: 02/07/2023] Open
Abstract
In the past decade, numerous genes associated with autism spectrum disorders (ASDs) have been identified. These genes encode key regulators of synaptogenesis, synaptic function, and synaptic plasticity. Drosophila is a prominent model system for ASD studies to define novel genes linked to ASDs and decipher their molecular roles in synaptogenesis, synaptic function, synaptic plasticity, and neural circuit assembly and consolidation. Here, we review Drosophila studies on ASD genes that regulate synaptogenesis, synaptic function, and synaptic plasticity through modulating chromatin remodeling, transcription, protein synthesis and degradation, cytoskeleton dynamics, and synaptic scaffolding.
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Affiliation(s)
- Yao Tian
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China
| | - Zi Chao Zhang
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China
| | - Junhai Han
- Institute of Life Sciences, The Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing, 210096, China.
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24
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Cardinal Epigenetic Role of non-coding Regulatory RNAs in Circadian Rhythm. Mol Neurobiol 2017; 55:3564-3576. [PMID: 28516429 DOI: 10.1007/s12035-017-0573-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/25/2017] [Indexed: 10/19/2022]
Abstract
Circadian rhythm which governs basic physiological activities like sleeping, feeding and energy consumption is regulated by light-controlled central clock genes in the pacemaker neuron. The timekeeping machinery with unique transcriptional and post-transcriptional feedback loops is controlled by different small regulatory RNAs in the brain. Roles of the multiple neuronal genes, especially post-transcriptional regulation, splicing, polyadenylation, mature mRNA editing, and stability of translation products, are controlled by epigenetic activities orchestrated via small RNAs. Collectively, these mechanisms regulate clock and light-controlled genes for effecting pacemaker activity and entrainment. Regulatory small RNAs of the circadian circuit, timekeeping mechanism, synchronization of regular entrainment, oscillation, and rhythmicity are regulated by diversified RNA molecules. Regulatory small RNAs operate critical roles in brain activities including the neuronal clock activity. In this report, we propose the emergence of the earlier unexpected small RNAs for a historic perspective of epigenetic regulation of the brain clock system.
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25
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Epistasis in Neuropsychiatric Disorders. Trends Genet 2017; 33:256-265. [PMID: 28268034 DOI: 10.1016/j.tig.2017.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/25/2017] [Accepted: 01/27/2017] [Indexed: 12/12/2022]
Abstract
The contribution of epistasis to human disease remains unclear. However, several studies have now identified epistatic interactions between common variants that increase the risk of a neuropsychiatric disorder, while there is growing evidence that genetic interactions contribute to the pathogenicity of rare, multigenic copy-number variants (CNVs) that have been observed in patients. This review discusses the current evidence for epistatic events and genetic interactions in neuropsychiatric disorders, how paradigm shifts in the phenotypic classification of patients would empower the search for epistatic effects, and how network and cellular models might be employed to further elucidate relevant epistatic interactions.
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26
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Kushima I, Aleksic B, Nakatochi M, Shimamura T, Shiino T, Yoshimi A, Kimura H, Takasaki Y, Wang C, Xing J, Ishizuka K, Oya-Ito T, Nakamura Y, Arioka Y, Maeda T, Yamamoto M, Yoshida M, Noma H, Hamada S, Morikawa M, Uno Y, Okada T, Iidaka T, Iritani S, Yamamoto T, Miyashita M, Kobori A, Arai M, Itokawa M, Cheng MC, Chuang YA, Chen CH, Suzuki M, Takahashi T, Hashimoto R, Yamamori H, Yasuda Y, Watanabe Y, Nunokawa A, Someya T, Ikeda M, Toyota T, Yoshikawa T, Numata S, Ohmori T, Kunimoto S, Mori D, Iwata N, Ozaki N. High-resolution copy number variation analysis of schizophrenia in Japan. Mol Psychiatry 2017; 22:430-440. [PMID: 27240532 DOI: 10.1038/mp.2016.88] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 12/30/2022]
Abstract
Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (<100 kb). Clinically significant CNVs were significantly more frequent in cases than in controls (odds ratio=3.04, P=9.3 × 10-9, 9.0% of cases). We confirmed a significant association of X-chromosome aneuploidies with SCZ and identified 11 de novo CNVs (e.g., MBD5 deletion) in cases. In patients with clinically significant CNVs, 41.7% had a history of congenital/developmental phenotypes, and the rate of treatment resistance was significantly higher (odds ratio=2.79, P=0.0036). We found more severe clinical manifestations in patients with two clinically significant CNVs. Gene set analysis replicated previous findings (e.g., synapse, calcium signaling) and identified novel biological pathways including oxidative stress response, genomic integrity, kinase and small GTPase signaling. Furthermore, involvement of multiple SCZ candidate genes and biological pathways in the pathogenesis of SCZ was suggested in established SCZ-associated CNV loci. Our study shows the high genetic heterogeneity of SCZ and its clinical features and raises the possibility that genomic instability is involved in its pathogenesis, which may be related to the increased burden of de novo CNVs and variable expressivity of CNVs.
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Affiliation(s)
- I Kushima
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.,Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - B Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Nakatochi
- Bioinformatics Section, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Shiino
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - A Yoshimi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Takasaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - C Wang
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - J Xing
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - K Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Oya-Ito
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Nakamura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Maeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yamamoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yoshida
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Noma
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Hamada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Iidaka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Iritani
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Miyashita
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - A Kobori
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Arai
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Itokawa
- Center for Medical Cooperation, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M-C Cheng
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - Y-A Chuang
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - C-H Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan.,Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - M Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - T Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - R Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita, Japan.,Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - H Yamamori
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Yasuda
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - A Nunokawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - T Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - M Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - T Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - T Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - S Numata
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - T Ohmori
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - S Kunimoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - D Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Brain and Mind Research Center, Nagoya University, Nagoya, Japan
| | - N Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - N Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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27
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Grice SJ, Sleigh JN, Motley WW, Liu JL, Burgess RW, Talbot K, Cader MZ. Dominant, toxic gain-of-function mutations in gars lead to non-cell autonomous neuropathology. Hum Mol Genet 2015; 24:4397-406. [PMID: 25972375 PMCID: PMC4492401 DOI: 10.1093/hmg/ddv176] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/06/2015] [Indexed: 12/15/2022] Open
Abstract
Charcot-Marie-Tooth (CMT) neuropathies are collectively the most common hereditary neurological condition and a major health burden for society. Dominant mutations in the gene GARS, encoding the ubiquitous enzyme, glycyl-tRNA synthetase (GlyRS), cause peripheral nerve degeneration and lead to CMT disease type 2D. This genetic disorder exemplifies a recurring motif in neurodegeneration, whereby mutations in essential, widely expressed genes have selective deleterious consequences for the nervous system. Here, using novel Drosophila models, we show a potential solution to this phenomenon. Ubiquitous expression of mutant GlyRS leads to motor deficits, progressive neuromuscular junction (NMJ) denervation and pre-synaptic build-up of mutant GlyRS. Intriguingly, neuronal toxicity is, at least in part, non-cell autonomous, as expression of mutant GlyRS in mesoderm or muscle alone results in similar pathology. This mutant GlyRS toxic gain-of-function, which is WHEP domain-dependent, coincides with abnormal NMJ assembly, leading to synaptic degeneration, and, ultimately, reduced viability. Our findings suggest that mutant GlyRS gains access to ectopic sub-compartments of the motor neuron, providing a possible explanation for the selective neuropathology caused by mutations in a widely expressed gene.
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Affiliation(s)
- Stuart J Grice
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | - James N Sleigh
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK, The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - William W Motley
- Neurogenetics Branch, National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA and
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3PT, UK
| | | | - Kevin Talbot
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - M Zameel Cader
- Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK, The Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK,
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