601
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Strong E, Butcher D, Singhania R, Mervis C, Morris C, De Carvalho D, Weksberg R, Osborne L. Symmetrical Dose-Dependent DNA-Methylation Profiles in Children with Deletion or Duplication of 7q11.23. Am J Hum Genet 2015; 97:216-27. [PMID: 26166478 DOI: 10.1016/j.ajhg.2015.05.019] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/27/2015] [Indexed: 12/11/2022] Open
Abstract
Epigenetic dysfunction has been implicated in a growing list of disorders that include cancer, neurodevelopmental disorders, and neurodegeneration. Williams syndrome (WS) and 7q11.23 duplication syndrome (Dup7) are rare neurodevelopmental disorders with broad phenotypic spectra caused by deletion and duplication, respectively, of a 1.5-Mb region that includes several genes with a role in epigenetic regulation. We have identified striking differences in DNA methylation across the genome between blood cells from children with WS or Dup7 and blood cells from typically developing (TD) children. Notably, regions that were differentially methylated in both WS and Dup7 displayed a significant and symmetrical gene-dose-dependent effect, such that WS typically showed increased and Dup7 showed decreased DNA methylation. Differentially methylated genes were significantly enriched with genes in pathways involved in neurodevelopment, autism spectrum disorder (ASD) candidate genes, and imprinted genes. Using alignment with ENCODE data, we also found the differentially methylated regions to be enriched with CCCTC-binding factor (CTCF) binding sites. These findings suggest that gene(s) within 7q11.23 alter DNA methylation at specific sites across the genome and result in dose-dependent DNA-methylation profiles in WS and Dup7. Given the extent of DNA-methylation changes and the potential impact on CTCF binding and chromatin regulation, epigenetic mechanisms most likely contribute to the complex neurological phenotypes of WS and Dup7. Our findings highlight the importance of DNA methylation in the pathogenesis of WS and Dup7 and provide molecular mechanisms that are potentially shared by WS, Dup7, and ASD.
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602
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Clinically relevant copy number variations detected in cerebral palsy. Nat Commun 2015; 6:7949. [PMID: 26236009 PMCID: PMC4532872 DOI: 10.1038/ncomms8949] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 06/30/2015] [Indexed: 12/29/2022] Open
Abstract
Cerebral palsy (CP) represents a group of non-progressive clinically heterogeneous disorders that are characterized by motor impairment and early age of onset, frequently accompanied by co-morbidities. The cause of CP has historically been attributed to environmental stressors resulting in brain damage. While genetic risk factors are also implicated, guidelines for diagnostic assessment of CP do not recommend for routine genetic testing. Given numerous reports of aetiologic copy number variations (CNVs) in other neurodevelopmental disorders, we used microarrays to genotype a population-based prospective cohort of children with CP and their parents. Here we identify de novo CNVs in 8/115 (7.0%) CP patients (∼1% rate in controls). In four children, large chromosomal abnormalities deemed likely pathogenic were found, and they were significantly more likely to have severe neuromotor impairments than those CP subjects without such alterations. Overall, the CNV data would have impacted our diagnosis or classification of CP in 11/115 (9.6%) families.
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603
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Krishnan N, Krishnan K, Connors CR, Choy MS, Page R, Peti W, Van Aelst L, Shea SD, Tonks NK. PTP1B inhibition suggests a therapeutic strategy for Rett syndrome. J Clin Invest 2015. [PMID: 26214522 DOI: 10.1172/jci80323] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The X-linked neurological disorder Rett syndrome (RTT) presents with autistic features and is caused primarily by mutations in a transcriptional regulator, methyl CpG-binding protein 2 (MECP2). Current treatment options for RTT are limited to alleviating some neurological symptoms; hence, more effective therapeutic strategies are needed. We identified the protein tyrosine phosphatase PTP1B as a therapeutic candidate for treatment of RTT. We demonstrated that the PTPN1 gene, which encodes PTP1B, was a target of MECP2 and that disruption of MECP2 function was associated with increased levels of PTP1B in RTT models. Pharmacological inhibition of PTP1B ameliorated the effects of MECP2 disruption in mouse models of RTT, including improved survival in young male (Mecp2-/y) mice and improved behavior in female heterozygous (Mecp2-/+) mice. We demonstrated that PTP1B was a negative regulator of tyrosine phosphorylation of the tyrosine kinase TRKB, the receptor for brain-derived neurotrophic factor (BDNF). Therefore, the elevated PTP1B that accompanies disruption of MECP2 function in RTT represents a barrier to BDNF signaling. Inhibition of PTP1B led to increased tyrosine phosphorylation of TRKB in the brain, which would augment BDNF signaling. This study presents PTP1B as a mechanism-based therapeutic target for RTT, validating a unique strategy for treating the disease by modifying signal transduction pathways with small-molecule drugs.
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604
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Griswold AJ, Dueker ND, Van Booven D, Rantus JA, Jaworski JM, Slifer SH, Schmidt MA, Hulme W, Konidari I, Whitehead PL, Cuccaro ML, Martin ER, Haines JL, Gilbert JR, Hussman JP, Pericak-Vance MA. Targeted massively parallel sequencing of autism spectrum disorder-associated genes in a case control cohort reveals rare loss-of-function risk variants. Mol Autism 2015; 6:43. [PMID: 26185613 PMCID: PMC4504419 DOI: 10.1186/s13229-015-0034-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 06/16/2015] [Indexed: 12/31/2022] Open
Abstract
Background Autism spectrum disorder (ASD) is highly heritable, yet genome-wide association studies (GWAS), copy number variation screens, and candidate gene association studies have found no single factor accounting for a large percentage of genetic risk. ASD trio exome sequencing studies have revealed genes with recurrent de novo loss-of-function variants as strong risk factors, but there are relatively few recurrently affected genes while as many as 1000 genes are predicted to play a role. As such, it is critical to identify the remaining rare and low-frequency variants contributing to ASD. Methods We have utilized an approach of prioritization of genes by GWAS and follow-up with massively parallel sequencing in a case-control cohort. Using a previously reported ASD noise reduction GWAS analyses, we prioritized 837 RefSeq genes for custom targeting and sequencing. We sequenced the coding regions of those genes in 2071 ASD cases and 904 controls of European white ancestry. We applied comprehensive annotation to identify single variants which could confer ASD risk and also gene-based association analysis to identify sets of rare variants associated with ASD. Results We identified a significant over-representation of rare loss-of-function variants in genes previously associated with ASD, including a de novo premature stop variant in the well-established ASD candidate gene RBFOX1. Furthermore, ASD cases were more likely to have two damaging missense variants in candidate genes than controls. Finally, gene-based rare variant association implicates genes functioning in excitatory neurotransmission and neurite outgrowth and guidance pathways including CACNAD2, KCNH7, and NRXN1. Conclusions We find suggestive evidence that rare variants in synaptic genes are associated with ASD and that loss-of-function mutations in ASD candidate genes are a major risk factor, and we implicate damaging mutations in glutamate signaling receptors and neuronal adhesion and guidance molecules. Furthermore, the role of de novo mutations in ASD remains to be fully investigated as we identified the first reported protein-truncating variant in RBFOX1 in ASD. Overall, this work, combined with others in the field, suggests a convergence of genes and molecular pathways underlying ASD etiology. Electronic supplementary material The online version of this article (doi:10.1186/s13229-015-0034-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anthony J Griswold
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Nicole D Dueker
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Joseph A Rantus
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - James M Jaworski
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Susan H Slifer
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Michael A Schmidt
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - William Hulme
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Ioanna Konidari
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ; Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ; Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106 USA
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ; Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
| | | | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA ; Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
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605
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Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, Schriml LM, Kibbe WA, Schofield PN, Beck T, Vasant D, Brookes AJ, Zankl A, Washington NL, Mungall CJ, Lewis SE, Haendel MA, Parkinson H, Robinson PN. The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Am J Hum Genet 2015; 97:111-24. [PMID: 26119816 PMCID: PMC4572507 DOI: 10.1016/j.ajhg.2015.05.020] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/22/2015] [Indexed: 12/24/2022] Open
Abstract
The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.
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Affiliation(s)
- Tudor Groza
- School of Information Technology and Electrical Engineering, University of Queensland, St. Lucia, QLD 4072, Australia; Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Sebastian Köhler
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Dawid Moldenhauer
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; University of Applied Sciences, Wiesenstrasse 14, 35390 Giessen, Germany
| | - Nicole Vasilevsky
- Library, Oregon Health & Science University, Portland, OR 97239, USA
| | - Gareth Baynam
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6840, Australia; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia; Office of Population Health Genomics, Public Health and Clinical Services Division, Department of Health, Perth, WA 6004, Australia; Genetic Services of Western Australia, King Edward Memorial Hospital, Perth, WA 6008, Australia; Telethon Kids Institute, Perth, WA 6008, Australia
| | - Tomasz Zemojtel
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznań, Poland
| | - Lynn Marie Schriml
- Department of Epidemiology and Public Health, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; Institute for Genome Sciences, School of Medicine, University of Maryland, Baltimore, MD 21201, USA
| | - Warren Alden Kibbe
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD 20850, USA
| | - Paul N Schofield
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK; The Jackson Laboratory, Bar Harbor, ME 04609, USA
| | - Tim Beck
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Drashtti Vasant
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
| | - Anthony J Brookes
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Andreas Zankl
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Academic Department of Medical Genetics, The Children's Hospital at Westmead, Sydney, NSW 2145, Australia; Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, NSW 2145, Australia
| | - Nicole L Washington
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Christopher J Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Suzanna E Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Melissa A Haendel
- Library, Oregon Health & Science University, Portland, OR 97239, USA
| | - Helen Parkinson
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK
| | - Peter N Robinson
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany.
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606
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Gamsiz ED, Sciarra LN, Maguire AM, Pescosolido MF, van Dyck LI, Morrow EM. Discovery of Rare Mutations in Autism: Elucidating Neurodevelopmental Mechanisms. Neurotherapeutics 2015; 12:553-71. [PMID: 26105128 PMCID: PMC4489950 DOI: 10.1007/s13311-015-0363-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Autism spectrum disorder (ASD) is a group of highly genetic neurodevelopmental disorders characterized by language, social, cognitive, and behavioral abnormalities. ASD is a complex disorder with a heterogeneous etiology. The genetic architecture of autism is such that a variety of different rare mutations have been discovered, including rare monogenic conditions that involve autistic symptoms. Also, de novo copy number variants and single nucleotide variants contribute to disease susceptibility. Finally, autosomal recessive loci are contributing to our understanding of inherited factors. We will review the progress that the field has made in the discovery of these rare genetic variants in autism. We argue that mutation discovery of this sort offers an important opportunity to identify neurodevelopmental mechanisms in disease. The hope is that these mechanisms will show some degree of convergence that may be amenable to treatment intervention.
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Affiliation(s)
- Ece D. Gamsiz
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Developmental Disorders Genetics Research Program, Emma Pendleton Bradley Hospital and Department of Psychiatry and Human Behavior, Brown University Medical School, Providence, RI USA
| | - Laura N. Sciarra
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Neuroscience Graduate Program (NSGP), Brown University, Providence, RI USA
| | - Abbie M. Maguire
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Molecular Biology, Cell Biology and Biochemistry (MCB) Graduate Training Program, Brown University, Providence, RI USA
| | - Matthew F. Pescosolido
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Neuroscience Graduate Program (NSGP), Brown University, Providence, RI USA
| | - Laura I. van Dyck
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
| | - Eric M. Morrow
- />Department of Molecular Biology, Cell Biology and Biochemistry (MCB), and Institute for Brain Science, Brown University, Providence, RI USA
- />Developmental Disorders Genetics Research Program, Emma Pendleton Bradley Hospital and Department of Psychiatry and Human Behavior, Brown University Medical School, Providence, RI USA
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607
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Li W, Mills AA. Architects of the genome: CHD dysfunction in cancer, developmental disorders and neurological syndromes. Epigenomics 2015; 6:381-95. [PMID: 25333848 DOI: 10.2217/epi.14.31] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Chromatin is vital to normal cells, and its deregulation contributes to a spectrum of human ailments. An emerging concept is that aberrant chromatin regulation culminates in gene expression programs that set the stage for the seemingly diverse pathologies of cancer, developmental disorders and neurological syndromes. However, the mechanisms responsible for such common etiology have been elusive. Recent evidence has implicated lesions affecting chromatin-remodeling proteins in cancer, developmental disorders and neurological syndromes, suggesting a common source for these different pathologies. Here, we focus on the chromodomain helicase DNA binding chromatin-remodeling family and the recent evidence for its deregulation in diverse pathological conditions, providing a new perspective on the underlying mechanisms and their implications for these prevalent human diseases.
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Affiliation(s)
- Wangzhi Li
- Cold Spring Harbor Laboratory Cold Spring Harbor, NY 11724, USA
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608
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Kerr EN, Bhan A, Héon E. Exploration of the cognitive, adaptive and behavioral functioning of patients affected with Bardet-Biedl syndrome. Clin Genet 2015; 89:426-433. [PMID: 25988237 DOI: 10.1111/cge.12614] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 05/13/2015] [Accepted: 05/14/2015] [Indexed: 01/12/2023]
Abstract
The aim of the study was to investigate the behavioral phenotype of patients affected with Bardet-Biedl syndrome (BBS). Twenty-four patients with molecularly confirmed diagnosis of BBS (6-38 years old) were evaluated using standardized neuropsychological tests. Results were compared with normative data. The mean intellectual functioning of participants fell 1.5 standard deviations below normal expectations; though, the majority of participants (75-80%) did not display an intellectual disability. The group's mean performance on most cognitive tasks and all scales of adaptive functioning was significantly weaker than norms. The majority (55-60%) of participants displayed broadly average verbal fluency and auditory rote learning, while 22-40% were severely impaired in the same areas. The majority of participants were severely impaired in perceptual reasoning (53%), attentional capacity (69%), and functional independence (74%). Symptoms associated with Autism were reported for 77% of participants. Behavioral issues were unrelated to intellectual ability but significantly correlated with adaptive functioning. This first neurocognitive evaluation of a molecularly confirmed cohort of BBS patients shows that the majority of patients experience significant difficulties with perceptual intellectual abilities, auditory attentional capacity, adaptive independence, and behavior. The frequency of autism-related symptoms far exceeds the incidence rate of diagnosed autism in general and warrants further investigations.
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Affiliation(s)
- E N Kerr
- Department of Psychology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Neurology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Paediatrics, The University of Toronto, Toronto, ON, Canada
| | - A Bhan
- Department of Ophthalmology and Vision Sciences, Program of Genetics and Genomic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - E Héon
- Department of Paediatrics, The University of Toronto, Toronto, ON, Canada.,Department of Ophthalmology and Vision Sciences, Program of Genetics and Genomic Medicine, The Hospital for Sick Children, Toronto, ON, Canada
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609
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Mottron L, Duret P, Mueller S, Moore RD, Forgeot d'Arc B, Jacquemont S, Xiong L. Sex differences in brain plasticity: a new hypothesis for sex ratio bias in autism. Mol Autism 2015; 6:33. [PMID: 26052415 PMCID: PMC4456778 DOI: 10.1186/s13229-015-0024-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 04/27/2015] [Indexed: 01/13/2023] Open
Abstract
Several observations support the hypothesis that differences in synaptic and regional cerebral plasticity between the sexes account for the high ratio of males to females in autism. First, males are more susceptible than females to perturbations in genes involved in synaptic plasticity. Second, sex-related differences in non-autistic brain structure and function are observed in highly variable regions, namely, the heteromodal associative cortices, and overlap with structural particularities and enhanced activity of perceptual associative regions in autistic individuals. Finally, functional cortical reallocations following brain lesions in non-autistic adults (for example, traumatic brain injury, multiple sclerosis) are sex-dependent. Interactions between genetic sex and hormones may therefore result in higher synaptic and consecutively regional plasticity in perceptual brain areas in males than in females. The onset of autism may largely involve mutations altering synaptic plasticity that create a plastic reaction affecting the most variable and sexually dimorphic brain regions. The sex ratio bias in autism may arise because males have a lower threshold than females for the development of this plastic reaction following a genetic or environmental event.
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Affiliation(s)
- Laurent Mottron
- Centre d'excellence en Troubles envahissants du dévelopement de l'Université de Montréal (CETEDUM), Montréal, Canada.,Hôpital Rivière-des-Prairies, Département de Psychiatrie, Montréal, Canada.,Centre de Recherche de l'Institut Universitaire en Santé Mentale de Montréal, Québec, Canada.,Department of Psychiatry, University of Montreal, Québec, Canada
| | - Pauline Duret
- Centre d'excellence en Troubles envahissants du dévelopement de l'Université de Montréal (CETEDUM), Montréal, Canada.,Hôpital Rivière-des-Prairies, Département de Psychiatrie, Montréal, Canada.,Centre de Recherche de l'Institut Universitaire en Santé Mentale de Montréal, Québec, Canada.,Department of Psychiatry, University of Montreal, Québec, Canada.,Département de Biologie, École Normale Supérieure de Lyon, Lyon, CEDEX 07 France
| | - Sophia Mueller
- Institute of Clinical Radiology, University Hospitals, Munich, Germany.,Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, MA 02129 USA.,Harvard University, Center for Brain Science, Cambridge, MA 02138 USA
| | - Robert D Moore
- Department of Psychiatry, University of Montreal, Québec, Canada.,Department of Health Sciences, University of Montreal, Montreal, Canada.,College of Applied Health Sciences, University of Illinois, Urbana-Champaign, USA
| | - Baudouin Forgeot d'Arc
- Centre d'excellence en Troubles envahissants du dévelopement de l'Université de Montréal (CETEDUM), Montréal, Canada.,Hôpital Rivière-des-Prairies, Département de Psychiatrie, Montréal, Canada.,Centre de Recherche de l'Institut Universitaire en Santé Mentale de Montréal, Québec, Canada.,Department of Psychiatry, University of Montreal, Québec, Canada
| | - Sebastien Jacquemont
- Department of Psychiatry, University of Montreal, Québec, Canada.,Centre de recherche, Centre Hospitalier Universitaire Sainte Justine, Montréal, Canada.,Service of Medical Genetics, University Hospital of Lausanne, University of Lausanne, Lausanne, 1011 Switzerland
| | - Lan Xiong
- Centre de Recherche de l'Institut Universitaire en Santé Mentale de Montréal, Québec, Canada.,Department of Psychiatry, University of Montreal, Québec, Canada
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610
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Munns CF, Fahiminiya S, Poudel N, Munteanu MC, Majewski J, Sillence DO, Metcalf JP, Biggin A, Glorieux F, Fassier F, Rauch F, Hinsdale ME. Homozygosity for frameshift mutations in XYLT2 result in a spondylo-ocular syndrome with bone fragility, cataracts, and hearing defects. Am J Hum Genet 2015; 96:971-8. [PMID: 26027496 PMCID: PMC4457947 DOI: 10.1016/j.ajhg.2015.04.017] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 04/24/2015] [Indexed: 01/05/2023] Open
Abstract
Heparan and chondroitin/dermatan sulfated proteoglycans have a wide range of roles in cellular and tissue homeostasis including growth factor function, morphogen gradient formation, and co-receptor activity. Proteoglycan assembly initiates with a xylose monosaccharide covalently attached by either xylosyltransferase I or II. Three individuals from two families were found that exhibited similar phenotypes. The index case subjects were two brothers, individuals 1 and 2, who presented with osteoporosis, cataracts, sensorineural hearing loss, and mild learning defects. Whole exome sequence analyses showed that both individuals had a homozygous c.692dup mutation (GenBank: NM_022167.3) in the xylosyltransferase II locus (XYLT2) (MIM: 608125), causing reduced XYLT2 mRNA and low circulating xylosyltransferase (XylT) activity. In an unrelated boy (individual 3) from the second family, we noted low serum XylT activity. Sanger sequencing of XYLT2 in this individual revealed a c.520del mutation in exon 2 that resulted in a frameshift and premature stop codon (p.Ala174Profs(∗)35). Fibroblasts from individuals 1 and 2 showed a range of defects including reduced XylT activity, GAG incorporation of (35)SO4, and heparan sulfate proteoglycan assembly. These studies demonstrate that human XylT2 deficiency results in vertebral compression fractures, sensorineural hearing loss, eye defects, and heart defects, a phenotype that is similar to the autosomal-recessive disorder spondylo-ocular syndrome of unknown cause. This phenotype is different from what has been reported in individuals with other linker enzyme deficiencies. These studies illustrate that the cells of the lens, retina, heart muscle, inner ear, and bone are dependent on XylT2 for proteoglycan assembly in humans.
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Affiliation(s)
- Craig F Munns
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Somayyeh Fahiminiya
- Department of Human Genetics, Faculty of Medicine, McGill University and Genome Quebec Innovation Center, Montréal, QC H3A 1B1, Canada
| | - Nabin Poudel
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | | | - Jacek Majewski
- Department of Human Genetics, Faculty of Medicine, McGill University and Genome Quebec Innovation Center, Montréal, QC H3A 1B1, Canada
| | - David O Sillence
- Discipline of Genetic Medicine, The Children's Hospital at Westmead Clinical School, Sydney Medicine, Westmead, NSW 2145, Australia
| | - Jordan P Metcalf
- Department of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA
| | - Andrew Biggin
- Institute of Endocrinology and Diabetes, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | | | | | - Frank Rauch
- Shriners Hospital for Children, Montréal, QC H3G 1A6, Canada
| | - Myron E Hinsdale
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA; Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA.
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611
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Eriksson MA, Liedén A, Westerlund J, Bremer A, Wincent J, Sahlin E, Gillberg C, Fernell E, Anderlid BM. Rare copy number variants are common in young children with autism spectrum disorder. Acta Paediatr 2015; 104:610-8. [PMID: 25661985 DOI: 10.1111/apa.12969] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/21/2014] [Accepted: 02/03/2015] [Indexed: 11/27/2022]
Abstract
AIM Several studies have suggested that rare copy number variants (CNVs) are an important genetic contributor to autism spectrum disorders. The aims of the study were to use chromosomal microarray to investigate the presence of rare copy number variants in a population-based cohort of well-characterised young children with autism spectrum disorders and to relate the genetic results to neurodevelopmental profiles and medical conditions. METHODS We performed chromosomal microarray on samples from 162 children who had been referred to the Stockholm Autism Centre for Young Children in Sweden after being diagnosed with autism spectrum disorder between 20 and 54 months of age. RESULTS Pathogenic aberrations were detected in 8.6% of the children and variants of uncertain significance were present in another 8.6%. CNVs were more frequent in children with congenital malformations or dysmorphic features as well as in the subgroup with intellectual disability. CONCLUSION Our results support the use of chromosomal microarray methods for the first tier genetic analysis of autism spectrum disorder. However, it is likely in the near future that chromosomal microarray methods will probably be replaced by whole-exome and whole-genome sequencing technologies in clinical genetic testing.
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Affiliation(s)
- Mats Anders Eriksson
- Department of Women's and Children's Health; Karolinska Institutet; Stockholm Sweden
- Department of Neuropediatrics; Astrid Lindgren's Children's Hospital; Karolinska University Hospital; Stockholm Sweden
- Gillberg Neuropsychiatry Centre; Sahlgrenska Academy; Gothenburg University; Gothenburg Sweden
| | - Agne Liedén
- Department of Molecular Medicine and Surgery and Centre for Molecular Medicine; Karolinska Institutet; Stockholm Sweden
- Department of Clinical Genetics; Karolinska University Hospital; Stockholm Sweden
| | | | - Anna Bremer
- Division of Clinical Genetics; University Hospital; Linköping Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery and Centre for Molecular Medicine; Karolinska Institutet; Stockholm Sweden
| | - Ellika Sahlin
- Department of Molecular Medicine and Surgery and Centre for Molecular Medicine; Karolinska Institutet; Stockholm Sweden
- Department of Clinical Genetics; Karolinska University Hospital; Stockholm Sweden
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre; Sahlgrenska Academy; Gothenburg University; Gothenburg Sweden
| | - Elisabeth Fernell
- Gillberg Neuropsychiatry Centre; Sahlgrenska Academy; Gothenburg University; Gothenburg Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery and Centre for Molecular Medicine; Karolinska Institutet; Stockholm Sweden
- Department of Clinical Genetics; Karolinska University Hospital; Stockholm Sweden
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612
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Diagnosis and management of autism spectrum disorder in the era of genomics: rare disorders can pave the way for targeted treatments. Pediatr Clin North Am 2015; 62:607-18. [PMID: 26022165 PMCID: PMC4449456 DOI: 10.1016/j.pcl.2015.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Although the diagnosis of autism spectrum disorder (ASD) is based on behavioral signs and symptoms, the evaluation of a child with ASD has become increasingly focused on the identification of the genetic etiology of the disorder. In this review, we begin with a clinical overview of ASD, highlighting the heterogeneity of the disorder. We then discuss the genetics of ASD and present updated guidelines on genetic testing. We then consider the insights gained from the identification of both single gene disorders and rare variants, with regard to clinical phenomenology and potential treatment targets.
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613
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Lee BH, Smith T, Paciorkowski AR. Autism spectrum disorder and epilepsy: Disorders with a shared biology. Epilepsy Behav 2015; 47:191-201. [PMID: 25900226 PMCID: PMC4475437 DOI: 10.1016/j.yebeh.2015.03.017] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/06/2015] [Accepted: 03/13/2015] [Indexed: 12/17/2022]
Abstract
There is an increasing recognition of clinical overlap in patients presenting with epilepsy and autism spectrum disorder (ASD), and a great deal of new information regarding the genetic causes of both disorders is available. Several biological pathways appear to be involved in both disease processes, including gene transcription regulation, cellular growth, synaptic channel function, and maintenance of synaptic structure. We review several genetic disorders where ASD and epilepsy frequently co-occur, and we discuss the screening tools available for practicing neurologists and epileptologists to help determine which patients should be referred for formal ASD diagnostic evaluation. Finally, we make recommendations regarding the workflow of genetic diagnostic testing available for children with both ASD and epilepsy. This article is part of a Special Issue entitled "Autism and Epilepsy".
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Affiliation(s)
- Bo Hoon Lee
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Tristram Smith
- Division of Neurodevelopmental and Behavioral Pediatrics, Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Alex R Paciorkowski
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA; Department of Neurology, University of Rochester Medical Center, Rochester, NY, USA; Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, USA; Center for Neural Development and Disease, University of Rochester Medical Center, Rochester, NY, USA.
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614
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Liu Y, Zhang Y, Zhao D, Dong R, Yang X, Tammimies K, Uddin M, Scherer SW, Gai Z. Rare de novo deletion of metabotropic glutamate receptor 7 (GRM7) gene in a patient with autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet 2015; 168B:258-64. [PMID: 25921429 DOI: 10.1002/ajmg.b.32306] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 02/22/2015] [Indexed: 12/28/2022]
Abstract
GRM7, the gene encoding metabotropic glutamate receptor 7 (mGluR7), have been implicated in multiple neuropsychiatric disorders and shown to mediate excitatory synaptic neurotransmitter signaling and plasticity in the mammalian brain. Here we report a 303 kb de novo deletion at band 3p26.1, disrupting five coding exons of GRM7 in a proband with autism spectrum disorder, and hyperactivity. Our exon transcriptome-mutation contingency index method shows that three of the exons within the breakpoint boundaries are under purifying selection and highly expressed in prenatal brain regions. Based on our results and a thorough review of the literature, we propose that haploinsufficiency of the GRM7 product (mGluR7) contributes to autism spectrum disorders and hyperactivity phenotype as seen in the patient described here.
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Affiliation(s)
- Yi Liu
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Yanqing Zhang
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Dongmei Zhao
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Rui Dong
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Kristiina Tammimies
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.,The Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND), Pediatric Neuropsychiatry Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Mohammed Uddin
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.,McLaughlin Centre and Department of Molecular Genetics, University ofToronto, Toronto, Canada
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China.,Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
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615
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Saritas-Yildirim B, Childers CP, Elsik CG, Silva EM. Identification of REST targets in the Xenopus tropicalis genome. BMC Genomics 2015; 16:380. [PMID: 25971704 PMCID: PMC4430910 DOI: 10.1186/s12864-015-1591-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 04/28/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND A major role of REST (repressor element-1 silencing transcription factor) is to inhibit the expression of neuronal genes in neural stem cells and non-neuronal cells by binding to a 21 bp consensus sequence and recruiting epigenetic and regulatory cofactors to gene regulatory regions. In neural stem cells, REST silences differentiation-promoting genes to prevent their premature expression and is central to the regulation of neurogenesis and the balance of neural stem cells and neurons. RESULTS To understand the role of REST in vertebrate neurogenesis, we performed a genome-wide screen for REST targets in Xenopus tropicalis. We identified 742 neuron-restrictive silencer elements (NRSE) associated with 1396 genes that are enriched in neuronal function. Comparative analyses revealed that characteristics of NRSE motifs in frog are similar to those in mammals in terms of the distance to target genes, frequency of motifs and the repertoire of putative target genes. In addition, we identified four F-box ubiquitin ligases as putative REST targets and determined that they are expressed in neuronal tissues during Xenopus development. CONCLUSION We identified a conserved core of putative target genes in human, mouse and frog that may be fundamental to REST function in vertebrates. We demonstrate that NRSE sites are associated with both protein-coding genes and lncRNAs in the human genome. Furthermore, we demonstrate that REST binding sites are abundant in low gene-occupancy regions of the human genome but this is not due to an increased association with non-coding RNAs. Our findings identify novel targets of REST and broaden the known mechanism of REST-mediated silencing in neurogenesis.
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Affiliation(s)
- Banu Saritas-Yildirim
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA.
| | - Christopher P Childers
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA. .,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Christine G Elsik
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA. .,Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA. .,Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Elena M Silva
- Department of Biology, Georgetown University, 411 Regents Hall, Washington, DC, 20057, USA.
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616
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Gockley J, Willsey AJ, Dong S, Dougherty JD, Constantino JN, Sanders SJ. The female protective effect in autism spectrum disorder is not mediated by a single genetic locus. Mol Autism 2015; 6:25. [PMID: 25973162 PMCID: PMC4429476 DOI: 10.1186/s13229-015-0014-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/25/2015] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND A 4:1 male to female sex bias has consistently been observed in autism spectrum disorder (ASD). Epidemiological and genetic studies suggest a female protective effect (FPE) may account for part of this bias; however, the mechanism of such protection is unknown. Quantitative assessment of ASD symptoms using the Social Responsiveness Scale (SRS) shows a bimodal distribution unique to females in multiplex families. This leads to the hypothesis that a single, common genetic locus on chromosome X might mediate the FPE and produce the ASD sex bias. Such a locus would represent a major therapeutic target and is likely to have been missed by conventional genome-wide association study (GWAS) analysis. METHODS To explore this possibility, we performed an association study in affected versus unaffected females, considering three tiers of single nucleotide polymorphisms (SNPs) as follows: 1) regions of chromosome X that escape X-inactivation, 2) all of chromosome X, and 3) genome-wide. RESULTS No evidence of a SNP meeting the criteria for a single FPE locus was observed, despite the analysis being well powered to detect this effect. CONCLUSIONS The results do not support the hypothesis that the FPE is mediated by a single genetic locus; however, this does not exclude the possibility of multiple genetic loci playing a role in the FPE.
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Affiliation(s)
- Jake Gockley
- />Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA
| | - A Jeremy Willsey
- />Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA
- />Department of Psychiatry, University of California, San Francisco, 401 Parnassus Avenue, San Francisco, CA 94143 USA
| | - Shan Dong
- />Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA
- />Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing, 100871 People’s Republic of China
| | - Joseph D Dougherty
- />Department of Psychiatry, Washington University, 660 South Euclid Avenue, St Louis, MO 63110 USA
- />Department of Genetics, Washington University, 4566 Scott Ave, St Louis, MO 63110 USA
| | - John N Constantino
- />Department of Psychiatry, Washington University, 660 South Euclid Avenue, St Louis, MO 63110 USA
| | - Stephan J Sanders
- />Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA
- />Department of Psychiatry, University of California, San Francisco, 401 Parnassus Avenue, San Francisco, CA 94143 USA
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617
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Excess of rare, inherited truncating mutations in autism. Nat Genet 2015; 47:582-8. [PMID: 25961944 PMCID: PMC4449286 DOI: 10.1038/ng.3303] [Citation(s) in RCA: 404] [Impact Index Per Article: 44.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 04/20/2015] [Indexed: 12/15/2022]
Abstract
To assess the relative impact of inherited and de novo variants on autism risk, we generated a comprehensive set of exonic single nucleotide variants (SNVs) and copy number variants (CNVs) from 2,377 autism families. We find that private, inherited truncating SNVs in conserved genes are enriched in probands (odds ratio=1.14, p=0.0002) compared to unaffected siblings, an effect with significant maternal transmission bias to sons. We also observe a bias for inherited CNVs, specifically for small (<100 kbp), maternally inherited events (p=0.01) that are enriched in CHD8 target genes (p=7.4×10−3). Using a logistic regression model, we show that private truncating SNVs and rare, inherited CNVs are statistically independent autism risk factors, with odds ratios of 1.11 (p=0.0002) and 1.23 (p=0.01), respectively. This analysis identifies a second class of candidate genes (e.g., RIMS1, CUL7, and LZTR1) where transmitted mutations may create a sensitized background but are unlikely to be completely penetrant.
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618
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Parr JR, De Jonge MV, Wallace S, Pickles A, Rutter ML, Le Couteur AS, van Engeland H, Wittemeyer K, McConachie H, Roge B, Mantoulan C, Pedersen L, Isager T, Poustka F, Bolte S, Bolton P, Weisblatt E, Green J, Papanikolaou K, Baird G, Bailey AJ. New Interview and Observation Measures of the Broader Autism Phenotype: Description of Strategy and Reliability Findings for the Interview Measures. Autism Res 2015; 8:522-33. [PMID: 25959701 PMCID: PMC4690162 DOI: 10.1002/aur.1466] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 01/26/2015] [Accepted: 01/31/2015] [Indexed: 12/26/2022]
Abstract
Clinical genetic studies confirm the broader autism phenotype (BAP) in some relatives of individuals with autism, but there are few standardized assessment measures. We developed three BAP measures (informant interview, self-report interview, and impression of interviewee observational scale) and describe the development strategy and findings from the interviews. International Molecular Genetic Study of Autism Consortium data were collected from families containing at least two individuals with autism. Comparison of the informant and self-report interviews was restricted to samples in which the interviews were undertaken by different researchers from that site (251 UK informants, 119 from the Netherlands). Researchers produced vignettes that were rated blind by others. Retest reliability was assessed in 45 participants. Agreement between live scoring and vignette ratings was very high. Retest stability for the interviews was high. Factor analysis indicated a first factor comprising social-communication items and rigidity (but not other repetitive domain items), and a second factor comprised mainly of reading and spelling impairments. Whole scale Cronbach's alphas were high for both interviews. The correlation between interviews for factor 1 was moderate (adult items 0.50; childhood items 0.43); Kappa values for between-interview agreement on individual items were mainly low. The correlations between individual items and total score were moderate. The inclusion of several factor 2 items lowered the overall Cronbach's alpha for the total set. Both interview measures showed good reliability and substantial stability over time, but the findings were better for factor 1 than factor 2. We recommend factor 1 scores be used for characterising the BAP.
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Affiliation(s)
- Jeremy R Parr
- From University of Oxford Department of Psychiatry, UK.,Institutes of Neuroscience, and Health and Society, Newcastle University, UK
| | - Maretha V De Jonge
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Simon Wallace
- From University of Oxford Department of Psychiatry, UK
| | - Andrew Pickles
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - Michael L Rutter
- MRC Centre for Social, Genetic and Developmental Psychiatry, King's College London, UK
| | - Ann S Le Couteur
- Institutes of Neuroscience, and Health and Society, Newcastle University, UK
| | - Herman van Engeland
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Helen McConachie
- Institutes of Neuroscience, and Health and Society, Newcastle University, UK
| | - Bernadette Roge
- Centre d'Etudes et de Recherches en Psychopathologie, Toulouse, France
| | - Carine Mantoulan
- Centre d'Etudes et de Recherches en Psychopathologie, Toulouse, France
| | | | | | - Fritz Poustka
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, Germany
| | - Sven Bolte
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, J.W. Goethe University Frankfurt, Germany.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Patrick Bolton
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, UK
| | - Emma Weisblatt
- Cambridge University and Department of General and Adolescent Paediatrics, Institute of Child Health, University College London, London, UK
| | - Jonathan Green
- Academic Department of Child Psychiatry, University of Manchester, Manchester, UK
| | | | - Gillian Baird
- Guy's and St Thomas' NHS Trust & King's College London, UK
| | - Anthony J Bailey
- From University of Oxford Department of Psychiatry, UK.,Department of Psychiatry, University of British Columbia, Vancouver, Canada
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619
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Lal D, Ruppert AK, Trucks H, Schulz H, de Kovel CG, Kasteleijn-Nolst Trenité D, Sonsma ACM, Koeleman BP, Lindhout D, Weber YG, Lerche H, Kapser C, Schankin CJ, Kunz WS, Surges R, Elger CE, Gaus V, Schmitz B, Helbig I, Muhle H, Stephani U, Klein KM, Rosenow F, Neubauer BA, Reinthaler EM, Zimprich F, Feucht M, Møller RS, Hjalgrim H, De Jonghe P, Suls A, Lieb W, Franke A, Strauch K, Gieger C, Schurmann C, Schminke U, Nürnberg P, Sander T. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies. PLoS Genet 2015; 11:e1005226. [PMID: 25950944 PMCID: PMC4423931 DOI: 10.1371/journal.pgen.1005226] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/16/2015] [Indexed: 01/06/2023] Open
Abstract
Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
- EPICURE Consortium
| | - Ann-Kathrin Ruppert
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Holger Trucks
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Herbert Schulz
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Carolien G. de Kovel
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Anja C. M. Sonsma
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P. Koeleman
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Lindhout
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- SEIN Epilepsy Institute in the Netherlands, Hoofddorp, The Netherlands
| | - Yvonne G. Weber
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Holger Lerche
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Kapser
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Christoph J. Schankin
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Wolfram S. Kunz
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Rainer Surges
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Christian E. Elger
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Verena Gaus
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
| | - Bettina Schmitz
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
- Department of Neurology, Vivantes Humboldt-Klinikum, Berlin, Germany
| | - Ingo Helbig
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Hiltrud Muhle
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Ulrich Stephani
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Karl M. Klein
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Felix Rosenow
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Eva M. Reinthaler
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Fritz Zimprich
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Martha Feucht
- EPICURE Consortium
- Department of Pediatrics and Neonatology, Medical University of Vienna, Vienna, Austria
| | - Rikke S. Møller
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Helle Hjalgrim
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Peter De Jonghe
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, and Chair of Genetic Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University, Greifswald, Germany
| | - Ulf Schminke
- Department of Neurology, University Medicine Greifswald, Ernst Moritz Arndt University, Greifswald, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- EPICURE Consortium
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Thomas Sander
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
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620
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Holmes GL, Tian C, Hernan AE, Flynn S, Camp D, Barry J. Alterations in sociability and functional brain connectivity caused by early-life seizures are prevented by bumetanide. Neurobiol Dis 2015; 77:204-19. [PMID: 25766676 PMCID: PMC4682568 DOI: 10.1016/j.nbd.2015.02.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 12/29/2014] [Accepted: 02/13/2015] [Indexed: 01/02/2023] Open
Abstract
There is a well-described association between infantile epilepsy and pervasive cognitive and behavioral deficits, including a high incidence of autism spectrum disorders. Despite the robustness of the relationship between early-life seizures and the development of autism, the pathophysiological mechanism by which this occurs has not been explored. As a result of increasing evidence that autism is a disorder of brain connectivity we hypothesized that early-life seizures would interrupt normal brain connectivity during brain maturation and result in an autistic phenotype. Normal rat pups underwent recurrent flurothyl-induced seizures from postnatal (P)days 5-14 and then tested, along with controls, for developmental alterations of development brain oscillatory activity from P18-P25. Specifically we wished to understand how normal changes in rhythmicity in and between brain regions change as a function of age and if this rhythmicity is altered or interrupted by early life seizures. In rat pups with early-life seizures, field recordings from dorsal and ventral hippocampus and prefrontal cortex demonstrated marked increase in coherence as well as a decrease in voltage correlation at all bandwidths compared to controls while there were minimal differences in total power and relative power spectral densities. Rats with early-life seizures had resulting impairment in the sociability and social novelty tests but demonstrated no evidence of increased activity or generalized anxiety as measured in the open field. In addition, rats with early-life seizures had lower seizure thresholds than controls, indicating long-standing alterations in the excitatory/inhibition balance. Bumetanide, a pharmacological agent that blocks the activity of NKCC1 and induces a significant shift of ECl toward more hyperpolarized values, administration at the time of the seizures precluded the subsequent abnormalities in coherence and voltage correlation and resulted in normal sociability and seizure threshold. Taken together these findings indicate that early-life seizures alter the development of oscillations and result in autistic-like behaviors. The altered communication between these brain regions could reflect the physiological underpinnings underlying social cognitive deficits seen in autism spectrum disorders.
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Affiliation(s)
- Gregory L Holmes
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT05405, USA.
| | - Chengju Tian
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT05405, USA
| | - Amanda E Hernan
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT05405, USA
| | - Sean Flynn
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT05405, USA
| | - Devon Camp
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT05405, USA
| | - Jeremy Barry
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT05405, USA
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621
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Kozol RA, Cukier HN, Zou B, Mayo V, De Rubeis S, Cai G, Griswold AJ, Whitehead PL, Haines JL, Gilbert JR, Cuccaro ML, Martin ER, Baker JD, Buxbaum JD, Pericak-Vance MA, Dallman JE. Two knockdown models of the autism genes SYNGAP1 and SHANK3 in zebrafish produce similar behavioral phenotypes associated with embryonic disruptions of brain morphogenesis. Hum Mol Genet 2015; 24:4006-23. [PMID: 25882707 DOI: 10.1093/hmg/ddv138] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 04/13/2015] [Indexed: 01/09/2023] Open
Abstract
Despite significant progress in the genetics of autism spectrum disorder (ASD), how genetic mutations translate to the behavioral changes characteristic of ASD remains largely unknown. ASD affects 1-2% of children and adults, and is characterized by deficits in verbal and non-verbal communication, and social interactions, as well as the presence of repetitive behaviors and/or stereotyped interests. ASD is clinically and etiologically heterogeneous, with a strong genetic component. Here, we present functional data from syngap1 and shank3 zebrafish loss-of-function models of ASD. SYNGAP1, a synaptic Ras GTPase activating protein, and SHANK3, a synaptic scaffolding protein, were chosen because of mounting evidence that haploinsufficiency in these genes is highly penetrant for ASD and intellectual disability (ID). Orthologs of both SYNGAP1 and SHANK3 are duplicated in the zebrafish genome and we find that all four transcripts (syngap1a, syngap1b, shank3a and shank3b) are expressed at the earliest stages of nervous system development with pronounced expression in the larval brain. Consistent with early expression of these genes, knockdown of syngap1b or shank3a cause common embryonic phenotypes including delayed mid- and hindbrain development, disruptions in motor behaviors that manifest as unproductive swim attempts, and spontaneous, seizure-like behaviors. Our findings indicate that both syngap1b and shank3a play novel roles in morphogenesis resulting in common brain and behavioral phenotypes.
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Affiliation(s)
- Robert A Kozol
- Department of Biology, University of Miami, Coral Gables, FL, USA,
| | - Holly N Cukier
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bing Zou
- Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Vera Mayo
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA and
| | - Guiqing Cai
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA and
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Patrice L Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Institute for Computational Biology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael L Cuccaro
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - James D Baker
- Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA and
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Julia E Dallman
- Department of Biology, University of Miami, Coral Gables, FL, USA,
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622
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The 16p11.2 deletion mouse model of autism exhibits altered cortical progenitor proliferation and brain cytoarchitecture linked to the ERK MAPK pathway. J Neurosci 2015; 35:3190-200. [PMID: 25698753 DOI: 10.1523/jneurosci.4864-13.2015] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Autism spectrum disorders are complex, highly heritable neurodevelopmental disorders affecting ∼1 in 100 children. Copy number variations of human chromosomal region 16p11.2 are genetically linked to 1% of autism-related disorders. This interval contains the MAPK3 gene, which encodes the MAP kinase, ERK1. Mutations in upstream elements regulating the ERK pathway are genetically linked to autism and other disorders of cognition including the neuro-cardio-facial cutaneous syndromes and copy number variations. We report that a murine model of human 16p11.2 deletion exhibits a reduction in brain size and perturbations in cortical cytoarchitecture. We observed enhanced progenitor proliferation and premature cell cycle exit, which are a consequence of altered levels of downstream ERK effectors cyclin D1 and p27(Kip1) during mid-neurogenesis. The increased progenitor proliferation and cell cycle withdrawal resulted in premature depletion of progenitor pools, altering the number and frequency of neurons ultimately populating cortical lamina. Specifically, we found a reduced number of upper layer pyramidal neurons and an increase in layer VI corticothalamic projection neurons, reflecting the altered cortical progenitor proliferation dynamics in these mice. Importantly, we observed a paradoxical increase in ERK signaling in mid-neurogenesis in the 16p11.2del mice, which is coincident with the development of aberrant cortical cytoarchitecture. The 16p11.2del mice exhibit anxiety-like behaviors and impaired memory. Our findings provide evidence of ERK dysregulation, developmental abnormalities in neurogenesis, and behavioral impairment associated with the 16p11.2 chromosomal deletion.
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623
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Quintela I, Fernandez-Prieto M, Gomez-Guerrero L, Resches M, Eiris J, Barros F, Carracedo A. A 6q14.1-q15 microdeletion in a male patient with severe autistic disorder, lack of oral language, and dysmorphic features with concomitant presence of a maternally inherited Xp22.31 copy number gain. Clin Case Rep 2015; 3:415-23. [PMID: 26185640 PMCID: PMC4498854 DOI: 10.1002/ccr3.255] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 02/22/2015] [Indexed: 12/14/2022] Open
Abstract
We report on a male patient with severe autistic disorder, lack of oral language, and dysmorphic features who carries a rare interstitial microdeletion of 4.96 Mb at chromosome 6q14.1-q15. The patient also harbors a maternally inherited copy number gain of 1.69 Mb at chromosome Xp22.31, whose pathogenicity is under debate.
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Affiliation(s)
- Ines Quintela
- Grupo de Medicina Xenomica, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformaticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - Montse Fernandez-Prieto
- Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS Santiago de Compostela, Spain
| | - Lorena Gomez-Guerrero
- Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS Santiago de Compostela, Spain
| | - Mariela Resches
- Departamento de Psicologia Evolutiva y de la Educacion, Universidade de Santiago de Compostela Santiago de Compostela, Spain
| | - Jesus Eiris
- Unidad de Neurologia Pediatrica, Departamento de Pediatria, Hospital Clinico Universitario de Santiago de Compostela Santiago de Compostela, Spain
| | - Francisco Barros
- Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS Santiago de Compostela, Spain
| | - Angel Carracedo
- Grupo de Medicina Xenomica, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformaticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Universidade de Santiago de Compostela Santiago de Compostela, Spain ; Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica - SERGAS Santiago de Compostela, Spain ; Center of Excellence in Genomic Medicine Research, King Abdulaziz University Jeddah, Saudi Arabia
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624
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Haplotype phasing and inheritance of copy number variants in nuclear families. PLoS One 2015; 10:e0122713. [PMID: 25853576 PMCID: PMC4390228 DOI: 10.1371/journal.pone.0122713] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 02/12/2015] [Indexed: 11/19/2022] Open
Abstract
DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.
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625
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Liu Y, Zhao D, Dong R, Yang X, Zhang Y, Tammimies K, Uddin M, Scherer SW, Gai Z. De novo exon 1 deletion ofAUTS2gene in a patient with autism spectrum disorder and developmental delay: A case report and a brief literature review. Am J Med Genet A 2015; 167:1381-5. [PMID: 25851617 DOI: 10.1002/ajmg.a.37050] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 02/20/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Yi Liu
- Pediatric Research Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Dongmei Zhao
- Pediatric Health Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Rui Dong
- Pediatric Research Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Xiaomeng Yang
- Pediatric Research Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Yanqing Zhang
- Pediatric Health Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Kristiina Tammimies
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Canada
| | - Mohammed Uddin
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Canada
- McLaughlin Centre and Department of Molecular Genetics; University of Toronto; Toronto Canada
| | - Zhongtao Gai
- Pediatric Research Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
- Pediatric Health Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
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626
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Sullivan PF, Posthuma D. Biological pathways and networks implicated in psychiatric disorders. Curr Opin Behav Sci 2015. [DOI: 10.1016/j.cobeha.2014.09.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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627
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Devitt NM, Gallagher L, Reilly RB. Autism Spectrum Disorder (ASD) and Fragile X Syndrome (FXS): Two Overlapping Disorders Reviewed through Electroencephalography-What Can be Interpreted from the Available Information? Brain Sci 2015; 5:92-117. [PMID: 25826237 PMCID: PMC4493458 DOI: 10.3390/brainsci5020092] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/11/2015] [Accepted: 03/17/2015] [Indexed: 02/07/2023] Open
Abstract
Autism Spectrum Disorder (ASD) and Fragile X syndrome (FXS) are neurodevelopmental disorders with different but potentially related neurobiological underpinnings, which exhibit significant overlap in their behavioural symptoms. FXS is a neurogenetic disorder of known cause whereas ASD is a complex genetic disorder, with both rare and common genetic risk factors and likely genetic and environmental interaction effects. A comparison of the phenotypic presentation of the two disorders may highlight those symptoms that are more likely to be under direct genetic control, for example in FXS as opposed to shared symptoms that are likely to be under the control of multiple mechanisms. This review is focused on the application and analysis of electroencephalography data (EEG) in ASD and FXS. Specifically, Event Related Potentials (ERP) and resting state studies (rEEG) studies investigating ASD and FXS cohorts are compared. This review explores the electrophysiological similarities and differences between the two disorders in addition to the potentially associated neurobiological mechanisms at play. A series of pertinent research questions which are suggested in the literature are also posed within the review.
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Affiliation(s)
- Niamh Mc Devitt
- School of Medicine, Trinity College, the University of Dublin, Dublin, Ireland.
- Trinity Centre for Bioengineering, Trinity College Dublin, the University of Dublin, Dublin, Ireland.
| | - Louise Gallagher
- School of Medicine, Trinity College, the University of Dublin, Dublin, Ireland.
- Trinity College Institute for Neuroscience, Trinity College Dublin, the University of Dublin, Dublin, Ireland.
- Department of Psychiatry, Trinity College Dublin, the University of Dublin, Dublin, Ireland.
- Institute of Molecular Medicine, Trinity Centre for Health Sciences, St James' Hospital, Dublin, Ireland.
- Linn Dara Child and Adolescent Mental Health Services, Cherry Orchard Hospital Dublin 10, Dublin, Ireland.
| | - Richard B Reilly
- School of Medicine, Trinity College, the University of Dublin, Dublin, Ireland.
- Trinity Centre for Bioengineering, Trinity College Dublin, the University of Dublin, Dublin, Ireland.
- Trinity College Institute for Neuroscience, Trinity College Dublin, the University of Dublin, Dublin, Ireland.
- School of Engineering, Trinity College Dublin, the University of Dublin, Dublin, Ireland.
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628
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Tabet AC, Verloes A, Pilorge M, Delaby E, Delorme R, Nygren G, Devillard F, Gérard M, Passemard S, Héron D, Siffroi JP, Jacquette A, Delahaye A, Perrin L, Dupont C, Aboura A, Bitoun P, Coleman M, Leboyer M, Gillberg C, Benzacken B, Betancur C. Complex nature of apparently balanced chromosomal rearrangements in patients with autism spectrum disorder. Mol Autism 2015; 6:19. [PMID: 25844147 PMCID: PMC4384291 DOI: 10.1186/s13229-015-0015-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 03/06/2015] [Indexed: 12/21/2022] Open
Abstract
Background Apparently balanced chromosomal rearrangements can be associated with an abnormal phenotype, including intellectual disability and autism spectrum disorder (ASD). Genome-wide microarrays reveal cryptic genomic imbalances, related or not to the breakpoints, in 25% to 50% of patients with an abnormal phenotype carrying a microscopically balanced chromosomal rearrangement. Here we performed microarray analysis of 18 patients with ASD carrying balanced chromosomal abnormalities to identify submicroscopic imbalances implicated in abnormal neurodevelopment. Methods Eighteen patients with ASD carrying apparently balanced chromosomal abnormalities were screened using single nucleotide polymorphism (SNP) arrays. Nine rearrangements were de novo, seven inherited, and two of unknown inheritance. Genomic imbalances were confirmed by fluorescence in situ hybridization and quantitative PCR. Results We detected clinically significant de novo copy number variants in four patients (22%), including three with de novo rearrangements and one with an inherited abnormality. The sizes ranged from 3.3 to 4.9 Mb; three were related to the breakpoint regions and one occurred elsewhere. We report a patient with a duplication of the Wolf-Hirschhorn syndrome critical region, contributing to the delineation of this rare genomic disorder. The patient has a chromosome 4p inverted duplication deletion, with a 0.5 Mb deletion of terminal 4p and a 4.2 Mb duplication of 4p16.2p16.3. The other cases included an apparently balanced de novo translocation t(5;18)(q12;p11.2) with a 4.2 Mb deletion at the 18p breakpoint, a subject with de novo pericentric inversion inv(11)(p14q23.2) in whom the array revealed a de novo 4.9 Mb deletion in 7q21.3q22.1, and a patient with a maternal inv(2)(q14.2q37.3) with a de novo 3.3 Mb terminal 2q deletion and a 4.2 Mb duplication at the proximal breakpoint. In addition, we identified a rare de novo deletion of unknown significance on a chromosome unrelated to the initial rearrangement, disrupting a single gene, RFX3. Conclusions These findings underscore the utility of SNP arrays for investigating apparently balanced chromosomal abnormalities in subjects with ASD or related neurodevelopmental disorders in both clinical and research settings.
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Affiliation(s)
- Anne-Claude Tabet
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Alain Verloes
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Marion Pilorge
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Elsa Delaby
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
| | - Richard Delorme
- Department of Child and Adolescent Psychiatry, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Fondation Fondamental, 40 rue de Mesly, 94000 Créteil, France
| | - Gudrun Nygren
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Kungsgatan 12, 41119 Göteborg, Sweden
| | - Françoise Devillard
- Département de Génétique et Procréation, CHU de Grenoble, Hôpital Couple-Enfant, avenue du Maquis du Grésivaudan, 38043 Grenoble, France
| | - Marion Gérard
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Sandrine Passemard
- INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Neurology Unit, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Delphine Héron
- Medical Genetics Unit, AP-HP, Pitié-Salpêtrière University Hospital, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Jean-Pierre Siffroi
- Service de Génétique et d'Embryologie Médicales, AP-HP, Trousseau Hospital, 26 avenue du Docteur Arnold Netter, 75012 Paris, France
| | - Aurelia Jacquette
- Medical Genetics Unit, AP-HP, Pitié-Salpêtrière University Hospital, 47 boulevard de l'Hôpital, 75013 Paris, France
| | - Andrée Delahaye
- INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Cytogenetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France ; Paris 13 University, Sorbonne Paris Cité, UFR SMBH, 74 rue Marcel Cachin, 93000 Bobigny, France
| | - Laurence Perrin
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Céline Dupont
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Azzedine Aboura
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France
| | - Pierre Bitoun
- Medical Genetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France
| | - Mary Coleman
- Foundation for Autism Research, 3081 Quail Hollow, Sarasota, FL 34235 USA
| | - Marion Leboyer
- Fondation Fondamental, 40 rue de Mesly, 94000 Créteil, France ; Department of Psychiatry, AP-HP, Henri Mondor-Albert Chenevier Hospital, 40 rue de Mesly, 94000 Créteil, France ; INSERM U955, Institut Mondor de Recherche Biomédicale, Psychiatric Genetics, 8 rue du Général Sarrail, 94000 Créteil, France ; Faculty of Medicine, University Paris-Est Créteil, 8 rue du Général Sarrail, 94000 Créteil, France
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Kungsgatan 12, 41119 Göteborg, Sweden
| | - Brigitte Benzacken
- Department of Genetics, AP-HP, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; INSERM, UMR 1141, Robert Debré University Hospital, 48 boulevard Sérurier, 75019 Paris, France ; Cytogenetics Unit, AP-HP, Jean Verdier Hospital, allée du 14 Juillet, 93140 Bondy, France ; Paris 13 University, Sorbonne Paris Cité, UFR SMBH, 74 rue Marcel Cachin, 93000 Bobigny, France
| | - Catalina Betancur
- INSERM, UMR 1130, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; CNRS, UMR 8246, Neuroscience Paris Seine, 9 quai Saint Bernard, 75005 Paris, France ; Sorbonne Universités, UPMC Univ Paris 6, Institut de Biologie Paris-Seine, 9 quai Saint Bernard, 75005 Paris, France
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629
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Multifactorial Origin of Neurodevelopmental Disorders: Approaches to Understanding Complex Etiologies. TOXICS 2015; 3:89-129. [PMID: 29056653 PMCID: PMC5634696 DOI: 10.3390/toxics3010089] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 03/06/2015] [Accepted: 03/18/2015] [Indexed: 12/12/2022]
Abstract
A significant body of evidence supports the multifactorial etiology of neurodevelopmental disorders (NDDs) affecting children. The present review focuses on early exposure to environmental chemicals as a risk factor for neurodevelopment, and presents the major lines of evidence derived from epidemiological studies, underlying key uncertainties and research needs in this field. We introduce the exposome concept that, encompassing the totality of human environmental exposures to multiple risk factors, aims at explaining individual vulnerability and resilience to early chemical exposure. In this framework, we synthetically review the role of variable gene backgrounds, the involvement of epigenetic mechanisms as well as the function played by potential effect modifiers such as socioeconomic status. We describe laboratory rodent studies where the neurodevelopmental effects of environmental chemicals are assessed in the presence of either a “vulnerable” gene background or adverse pregnancy conditions (i.e., maternal stress). Finally, we discuss the need for more descriptive and “lifelike” experimental models of NDDs, to identify candidate biomarkers and pinpoint susceptible groups or life stages to be translated to large prospective studies within the exposome framework.
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630
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Irimia M, Weatheritt RJ, Ellis JD, Parikshak NN, Gonatopoulos-Pournatzis T, Babor M, Quesnel-Vallières M, Tapial J, Raj B, O'Hanlon D, Barrios-Rodiles M, Sternberg MJE, Cordes SP, Roth FP, Wrana JL, Geschwind DH, Blencowe BJ. A highly conserved program of neuronal microexons is misregulated in autistic brains. Cell 2015; 159:1511-23. [PMID: 25525873 DOI: 10.1016/j.cell.2014.11.035] [Citation(s) in RCA: 422] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/20/2014] [Accepted: 11/18/2014] [Indexed: 12/16/2022]
Abstract
Alternative splicing (AS) generates vast transcriptomic and proteomic complexity. However, which of the myriad of detected AS events provide important biological functions is not well understood. Here, we define the largest program of functionally coordinated, neural-regulated AS described to date in mammals. Relative to all other types of AS within this program, 3-15 nucleotide "microexons" display the most striking evolutionary conservation and switch-like regulation. These microexons modulate the function of interaction domains of proteins involved in neurogenesis. Most neural microexons are regulated by the neuronal-specific splicing factor nSR100/SRRM4, through its binding to adjacent intronic enhancer motifs. Neural microexons are frequently misregulated in the brains of individuals with autism spectrum disorder, and this misregulation is associated with reduced levels of nSR100. The results thus reveal a highly conserved program of dynamic microexon regulation associated with the remodeling of protein-interaction networks during neurogenesis, the misregulation of which is linked to autism.
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Affiliation(s)
- Manuel Irimia
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona 08003, Spain.
| | - Robert J Weatheritt
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jonathan D Ellis
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Neelroop N Parikshak
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | | | - Mariana Babor
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | | | - Javier Tapial
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona 08003, Spain
| | - Bushra Raj
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Dave O'Hanlon
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Miriam Barrios-Rodiles
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sabine P Cordes
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Frederick P Roth
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Department of Computer Science, University of Toronto, 10 King's College Road, Toronto, ON M5S 3G4, Canada; Canadian Institute For Advanced Research, 180 Dundas Street West, Toronto, ON M5G 1Z8, Canada
| | - Jeffrey L Wrana
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Daniel H Geschwind
- Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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631
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Wang HG, Jeffries JJ, Wang TF. Genetic and Developmental Perspective of Language Abnormality in Autism and Schizophrenia. Neuroscientist 2015; 22:119-31. [DOI: 10.1177/1073858415572078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Language and communication through it are two of the defining features of normally developed human beings. However, both these functions are often impaired in autism and schizophrenia. In the former disorder, the problem usually emerges in early childhood (~2 years old) and typically includes a lack of communication. In the latter condition, the language problems usually occur in adolescence and adulthood and presents as disorganized speech. What are the fundamental mechanisms underlying these two disorders? Is there a shared genetic basis? Are the traditional beliefs about them true? Are there any common strategies for their prevention and management? To answer these questions, we searched PubMed by using autism, schizophrenia, gene, and language abnormality as keywords, and we reconsidered the basic concepts about these two diseases or syndromes. We found many functional genes, for example, FOXP2, COMT, GABRB3, and DISC1, are actually implicated in both of them. After observing the symptoms, genetic correlates, and temporal progression of these two disorders as well as their relationships more carefully, we now infer that the occurrence of these two diseases is likely developmentally regulated via interaction between the genome and the environment. Furthermore, we propose a unified view of autism and schizophrenia: a single age-dependently occurred disease that is newly named as Systemic Integral Disorder: if occurring in children before age 2, it is called autism; if in adolescence or a later age, it is called schizophrenia.
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Affiliation(s)
- Haoran George Wang
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Joseph Joel Jeffries
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Tianren Frank Wang
- Department of Molecular Genetics, Mount Sinai Hospital, Toronto, Ontario, Canada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
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632
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Bacchelli E, Battaglia A, Cameli C, Lomartire S, Tancredi R, Thomson S, Sutcliffe JS, Maestrini E. Analysis of CHRNA7 rare variants in autism spectrum disorder susceptibility. Am J Med Genet A 2015; 167A:715-23. [PMID: 25655306 DOI: 10.1002/ajmg.a.36847] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/30/2014] [Indexed: 11/11/2022]
Abstract
Chromosome 15q13.3 recurrent microdeletions are causally associated with a wide range of phenotypes, including autism spectrum disorder (ASD), seizures, intellectual disability, and other psychiatric conditions. Whether the reciprocal microduplication is pathogenic is less certain. CHRNA7, encoding for the alpha7 subunit of the neuronal nicotinic acetylcholine receptor, is considered the likely culprit gene in mediating neurological phenotypes in 15q13.3 deletion cases. To assess if CHRNA7 rare variants confer risk to ASD, we performed copy number variant analysis and Sanger sequencing of the CHRNA7 coding sequence in a sample of 135 ASD cases. Sequence variation in this gene remains largely unexplored, given the existence of a fusion gene, CHRFAM7A, which includes a nearly identical partial duplication of CHRNA7. Hence, attempts to sequence coding exons must distinguish between CHRNA7 and CHRFAM7A, making next-generation sequencing approaches unreliable for this purpose. A CHRNA7 microduplication was detected in a patient with autism and moderate cognitive impairment; while no rare damaging variants were identified in the coding region, we detected rare variants in the promoter region, previously described to functionally reduce transcription. This study represents the first sequence variant analysis of CHRNA7 in a sample of idiopathic autism.
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Affiliation(s)
- Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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633
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Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the human genome. Nat Rev Genet 2015; 16:172-83. [DOI: 10.1038/nrg3871] [Citation(s) in RCA: 565] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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634
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Prados J, Stenz L, Courtet P, Prada P, Nicastro R, Adouan W, Guillaume S, Olié E, Aubry JM, Dayer A, Perroud N. Borderline personality disorder and childhood maltreatment: a genome-wide methylation analysis. GENES BRAIN AND BEHAVIOR 2015; 14:177-88. [PMID: 25612291 DOI: 10.1111/gbb.12197] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/17/2014] [Accepted: 12/17/2014] [Indexed: 12/30/2022]
Abstract
Early life adversity plays a critical role in the emergence of borderline personality disorder (BPD) and this could occur through epigenetic programming. In this perspective, we aimed to determine whether childhood maltreatment could durably modify epigenetic processes by the means of a whole-genome methylation scan of BPD subjects. Using the Illumina Infinium® HumanMethylation450 BeadChip, global methylation status of DNA extracted from peripheral blood leucocytes was correlated to the severity of childhood maltreatment in 96 BPD subjects suffering from a high level of child adversity and 93 subjects suffering from major depressive disorder (MDD) and reporting a low rate of child maltreatment. Several CpGs within or near the following genes (IL17RA, miR124-3, KCNQ2, EFNB1, OCA2, MFAP2, RPH3AL, WDR60, CST9L, EP400, A2ML1, NT5DC2, FAM163A and SPSB2) were found to be differently methylated, either in BPD compared with MDD or in relation to the severity of childhood maltreatment. A highly relevant biological result was observed for cg04927004 close to miR124-3 that was significantly associated with BPD and severity of childhood maltreatment. miR124-3 codes for a microRNA (miRNA) targeting several genes previously found to be associated with BPD such as NR3C1. Our results highlight the potentially important role played by miRNAs in the etiology of neuropsychiatric disorders such as BPD and the usefulness of using methylome-wide association studies to uncover such candidate genes. Moreover, they offer new understanding of the impact of maltreatments on biological processes leading to diseases and may ultimately result in the identification of relevant biomarkers.
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Affiliation(s)
- J Prados
- Department of Psychiatry, University of Geneva, Switzerland
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635
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D'Angelo CS, Moller Dos Santos MF, Alonso LG, Koiffmann CP. Two New Cases of 1p21.3 Deletions and an Unbalanced Translocation t(8;12) among Individuals with Syndromic Obesity. Mol Syndromol 2015; 6:63-70. [PMID: 26279650 DOI: 10.1159/000371600] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2014] [Indexed: 01/09/2023] Open
Abstract
Obesity is a highly heritable but genetically heterogeneous disorder. Various well-known microdeletion syndromes (e.g. 1p36, 2q37, 6q16, 9q34, 17p11.2) can cause this phenotype along with intellectual disability (ID) and other findings. Chromosomal microarrays have identified 'new' microdeletion/duplication syndromes often associated with obesity. We report on 2 unrelated patients with an overlapping region of deletion at 1p21.3p21.2, and a third patient with a de novo recurrent unbalanced translocation der(8)t(8;12)(p23.1;p13.31), detected by 180K array CGH in a prospective cohort of syndromic obesity patients. Deletion of 1p21.3 is a rare condition, and there have been only 11 cases of the same recurrent translocation between chromosomes 8 and 12 [t(8;12)] reported to date. The former has been associated with ID, autistic spectrum disorder (ASD) and mild dysmorphic features, and in 4 patients who were obese or had a tendency to obesity, a minimal overlapping region of 2 genes, DPYD and MIR137, was detected; t(8;12) has recently been recognized to cause a childhood obesity syndrome due to duplication of the GNB3 gene. Thus, our findings add to the existing literature on the clinical description of these new syndromes, providing additional support that these loci are associated with syndromic obesity. We suggest that heterozygous loss of MIR137 may contribute to obesity as well as ID and ASD.
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Affiliation(s)
- Carla S D'Angelo
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Mauren F Moller Dos Santos
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Luis G Alonso
- Genetics Division, Department of Morphology and Genetics, Federal University of São Paulo, São Paulo, Brazil
| | - Celia P Koiffmann
- Department of Genetics and Evolutionary Biology, Human Genome and Stem Cell Center, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
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636
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Whole-genome sequencing of quartet families with autism spectrum disorder. Nat Med 2015; 21:185-91. [PMID: 25621899 DOI: 10.1038/nm.3792] [Citation(s) in RCA: 355] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/22/2014] [Indexed: 12/19/2022]
Abstract
Autism spectrum disorder (ASD) is genetically heterogeneous, with evidence for hundreds of susceptibility loci. Previous microarray and exome-sequencing studies have examined portions of the genome in simplex families (parents and one ASD-affected child) having presumed sporadic forms of the disorder. We used whole-genome sequencing (WGS) of 85 quartet families (parents and two ASD-affected siblings), consisting of 170 individuals with ASD, to generate a comprehensive data resource encompassing all classes of genetic variation (including noncoding variants) and accompanying phenotypes, in apparently familial forms of ASD. By examining de novo and rare inherited single-nucleotide and structural variations in genes previously reported to be associated with ASD or other neurodevelopmental disorders, we found that some (69.4%) of the affected siblings carried different ASD-relevant mutations. These siblings with discordant mutations tended to demonstrate more clinical variability than those who shared a risk variant. Our study emphasizes that substantial genetic heterogeneity exists in ASD, necessitating the use of WGS to delineate all genic and non-genic susceptibility variants in research and in clinical diagnostics.
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637
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Insights into the genetic foundations of human communication. Neuropsychol Rev 2015; 25:3-26. [PMID: 25597031 DOI: 10.1007/s11065-014-9277-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 12/22/2014] [Indexed: 12/19/2022]
Abstract
The human capacity to acquire sophisticated language is unmatched in the animal kingdom. Despite the discontinuity in communicative abilities between humans and other primates, language is built on ancient genetic foundations, which are being illuminated by comparative genomics. The genetic architecture of the language faculty is also being uncovered by research into neurodevelopmental disorders that disrupt the normally effortless process of language acquisition. In this article, we discuss the strategies that researchers are using to reveal genetic factors contributing to communicative abilities, and review progress in identifying the relevant genes and genetic variants. The first gene directly implicated in a speech and language disorder was FOXP2. Using this gene as a case study, we illustrate how evidence from genetics, molecular cell biology, animal models and human neuroimaging has converged to build a picture of the role of FOXP2 in neurodevelopment, providing a framework for future endeavors to bridge the gaps between genes, brains and behavior.
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638
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Engchuan W, Dhindsa K, Lionel AC, Scherer SW, Chan JH, Merico D. Performance of case-control rare copy number variation annotation in classification of autism. BMC Med Genomics 2015; 8 Suppl 1:S7. [PMID: 25783485 PMCID: PMC4315323 DOI: 10.1186/1755-8794-8-s1-s7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A substantial proportion of Autism Spectrum Disorder (ASD) risk resides in de novo germline and rare inherited genetic variation. In particular, rare copy number variation (CNV) contributes to ASD risk in up to 10% of ASD subjects. Despite the striking degree of genetic heterogeneity, case-control studies have detected specific burden of rare disruptive CNV for neuronal and neurodevelopmental pathways. Here, we used machine learning methods to classify ASD subjects and controls, based on rare CNV data and comprehensive gene annotations. We investigated performance of different methods and estimated the percentage of ASD subjects that could be reliably classified based on presumed etiologic CNV they carry. RESULTS We analyzed 1,892 Caucasian ASD subjects and 2,342 matched controls. Rare CNVs (frequency 1% or less) were detected using Illumina 1M and 1M-Duo BeadChips. Conditional Inference Forest (CF) typically performed as well as or better than other classification methods. We found a maximum AUC (area under the ROC curve) of 0.533 when considering all ASD subjects with rare genic CNVs, corresponding to 7.9% correctly classified ASD subjects and less than 3% incorrectly classified controls; performance was significantly higher when considering only subjects harboring de novo or pathogenic CNVs. We also found rare losses to be more predictive than gains and that curated neurally-relevant annotations (brain expression, synaptic components and neurodevelopmental phenotypes) outperform Gene Ontology and pathway-based annotations. CONCLUSIONS CF is an optimal classification approach for case-control rare CNV data and it can be used to prioritize subjects with variants potentially contributing to ASD risk not yet recognized. The neurally-relevant annotations used in this study could be successfully applied to rare CNV case-control data-sets for other neuropsychiatric disorders.
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639
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Chen R, Wei Q, Zhan X, Zhong X, Sutcliffe JS, Cox NJ, Cook EH, Li C, Chen W, Li B. A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis. ACTA ACUST UNITED AC 2015; 31:1452-9. [PMID: 25568282 DOI: 10.1093/bioinformatics/btu860] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 12/23/2014] [Indexed: 12/30/2022]
Abstract
MOTIVATION A major focus of current sequencing studies for human genetics is to identify rare variants associated with complex diseases. Aside from reduced power of detecting associated rare variants, controlling for population stratification is particularly challenging for rare variants. Transmission/disequilibrium tests (TDT) based on family designs are robust to population stratification and admixture, and therefore provide an effective approach to rare variant association studies to eliminate spurious associations. To increase power of rare variant association analysis, gene-based collapsing methods become standard approaches for analyzing rare variants. Existing methods that extend this strategy to rare variants in families usually combine TDT statistics at individual variants and therefore lack the flexibility of incorporating other genetic models. RESULTS In this study, we describe a haplotype-based framework for group-wise TDT (gTDT) that is flexible to encompass a variety of genetic models such as additive, dominant and compound heterozygous (CH) (i.e. recessive) models as well as other complex interactions. Unlike existing methods, gTDT constructs haplotypes by transmission when possible and inherently takes into account the linkage disequilibrium among variants. Through extensive simulations we showed that type I error was correctly controlled for rare variants under all models investigated, and this remained true in the presence of population stratification. Under a variety of genetic models, gTDT showed increased power compared with the single marker TDT. Application of gTDT to an autism exome sequencing data of 118 trios identified potentially interesting candidate genes with CH rare variants. AVAILABILITY AND IMPLEMENTATION We implemented gTDT in C++ and the source code and the detailed usage are available on the authors' website (https://medschool.vanderbilt.edu/cgg). CONTACT bingshan.li@vanderbilt.edu or wei.chen@chp.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rui Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Qiang Wei
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xiaowei Zhan
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xue Zhong
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - James S Sutcliffe
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nancy J Cox
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Edwin H Cook
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chun Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University, TN, 37221, USA, Quantitative Biomedical Research Center, University of Texas Southwestern Medical Center, Dallas, TX, USA, Center for Quantitative Sciences, Vanderbilt University, TN, 37221, USA, Department of Medicine, University of Chicago, Chicago, IL, USA, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA, Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
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640
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Lai MC, Lombardo MV, Auyeung B, Chakrabarti B, Baron-Cohen S. Sex/gender differences and autism: setting the scene for future research. J Am Acad Child Adolesc Psychiatry 2015; 54:11-24. [PMID: 25524786 PMCID: PMC4284309 DOI: 10.1016/j.jaac.2014.10.003] [Citation(s) in RCA: 556] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/10/2014] [Accepted: 10/13/2014] [Indexed: 12/22/2022]
Abstract
OBJECTIVE The relationship between sex/gender differences and autism has attracted a variety of research ranging from clinical and neurobiological to etiological, stimulated by the male bias in autism prevalence. Findings are complex and do not always relate to each other in a straightforward manner. Distinct but interlinked questions on the relationship between sex/gender differences and autism remain underaddressed. To better understand the implications from existing research and to help design future studies, we propose a 4-level conceptual framework to clarify the embedded themes. METHOD We searched PubMed for publications before September 2014 using search terms "'sex OR gender OR females' AND autism." A total of 1,906 articles were screened for relevance, along with publications identified via additional literature reviews, resulting in 329 articles that were reviewed. RESULTS Level 1, "Nosological and diagnostic challenges," concerns the question, "How should autism be defined and diagnosed in males and females?" Level 2, "Sex/gender-independent and sex/gender-dependent characteristics," addresses the question, "What are the similarities and differences between males and females with autism?" Level 3, "General models of etiology: liability and threshold," asks the question, "How is the liability for developing autism linked to sex/gender?" Level 4, "Specific etiological-developmental mechanisms," focuses on the question, "What etiological-developmental mechanisms of autism are implicated by sex/gender and/or sexual/gender differentiation?" CONCLUSIONS Using this conceptual framework, findings can be more clearly summarized, and the implications of the links between findings from different levels can become clearer. Based on this 4-level framework, we suggest future research directions, methodology, and specific topics in sex/gender differences and autism.
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Affiliation(s)
- Meng-Chuan Lai
- National Taiwan University Hospital and College of Medicine, Taipei, Taiwan and the Autism Research Centre, University of Cambridge, Cambridge, UK.
| | - Michael V Lombardo
- University of Cyprus, Nicosia, Cyprus and the Autism Research Centre, University of Cambridge
| | - Bonnie Auyeung
- University of Edinburgh and the Autism Research Centre, University of Cambridge
| | - Bhismadev Chakrabarti
- Centre for Integrative Neuroscience and Neurodynamics, School of Psychology and Clinical Language Sciences, University of Reading, Reading, UK and the Autism Research Centre, University of Cambridge
| | - Simon Baron-Cohen
- Cambridge Lifespan Asperger Syndrome Service (CLASS) Clinic, Cambridgeshire and Peterborough National Health Service Foundation Trust, Cambridge, and the Autism Research Centre, University of Cambridge
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641
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642
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Ferretti CJ, Hollander E. The Role of Inflammation in Autism Spectrum Disorder. CURRENT TOPICS IN NEUROTOXICITY 2015. [DOI: 10.1007/978-3-319-13602-8_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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643
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Ankrd11 is a chromatin regulator involved in autism that is essential for neural development. Dev Cell 2014; 32:31-42. [PMID: 25556659 DOI: 10.1016/j.devcel.2014.11.031] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/08/2014] [Accepted: 11/20/2014] [Indexed: 02/05/2023]
Abstract
Ankrd11 is a potential chromatin regulator implicated in neural development and autism spectrum disorder (ASD) with no known function in the brain. Here, we show that knockdown of Ankrd11 in developing murine or human cortical neural precursors caused decreased proliferation, reduced neurogenesis, and aberrant neuronal positioning. Similar cellular phenotypes and aberrant ASD-like behaviors were observed in Yoda mice carrying a point mutation in the Ankrd11 HDAC-binding domain. Consistent with a role for Ankrd11 in histone acetylation, Ankrd11 was associated with chromatin and colocalized with HDAC3, and expression and histone acetylation of Ankrd11 target genes were altered in Yoda neural precursors. Moreover, the Ankrd11 knockdown-mediated decrease in precursor proliferation was rescued by inhibiting histone acetyltransferase activity or expressing HDAC3. Thus, Ankrd11 is a crucial chromatin regulator that controls histone acetylation and gene expression during neural development, thereby providing a likely explanation for its association with cognitive dysfunction and ASD.
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644
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Li J, Shi M, Ma Z, Zhao S, Euskirchen G, Ziskin J, Urban A, Hallmayer J, Snyder M. Integrated systems analysis reveals a molecular network underlying autism spectrum disorders. Mol Syst Biol 2014; 10:774. [PMID: 25549968 PMCID: PMC4300495 DOI: 10.15252/msb.20145487] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Autism is a complex disease whose etiology remains elusive. We integrated previously and newly generated data and developed a systems framework involving the interactome, gene expression and genome sequencing to identify a protein interaction module with members strongly enriched for autism candidate genes. Sequencing of 25 patients confirmed the involvement of this module in autism, which was subsequently validated using an independent cohort of over 500 patients. Expression of this module was dichotomized with a ubiquitously expressed subcomponent and another subcomponent preferentially expressed in the corpus callosum, which was significantly affected by our identified mutations in the network center. RNA-sequencing of the corpus callosum from patients with autism exhibited extensive gene mis-expression in this module, and our immunochemical analysis showed that the human corpus callosum is predominantly populated by oligodendrocyte cells. Analysis of functional genomic data further revealed a significant involvement of this module in the development of oligodendrocyte cells in mouse brain. Our analysis delineates a natural network involved in autism, helps uncover novel candidate genes for this disease and improves our understanding of its molecular pathology.
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Affiliation(s)
- Jingjing Li
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
| | - Minyi Shi
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
| | - Zhihai Ma
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
| | - Shuchun Zhao
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ghia Euskirchen
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
| | - Jennifer Ziskin
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alexander Urban
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Joachim Hallmayer
- Department of Psychiatry & Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael Snyder
- Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA
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645
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Sanz R, Ferraro GB, Fournier AE. IgLON cell adhesion molecules are shed from the cell surface of cortical neurons to promote neuronal growth. J Biol Chem 2014; 290:4330-42. [PMID: 25538237 DOI: 10.1074/jbc.m114.628438] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Matrix metalloproteinases and a disintegrin and metalloproteinases are members of the zinc endopeptidases, which cleave components of the extracellular matrix as well as cell surface proteins resulting in degradation or release of biologically active fragments. Surface ectodomain shedding affects numerous biological processes, including survival, axon outgrowth, axon guidance, and synaptogenesis. In this study, we evaluated the role of metalloproteinases in regulating cortical neurite growth. We found that treatment of mature cortical neurons with pan-metalloproteinase inhibitors or with tissue inhibitors of metalloproteinase-3 reduced neurite outgrowth. Through mass spectrometry, we characterized the metalloproteinase-sensitive cell surface proteome of mature cortical neurons. Members of the IgLON family of glycosylphosphatidylinositol-anchored neural cell adhesion molecules were identified and validated as proteins that were shed from the surface of mature cortical neurons in a metalloproteinase-dependent manner. Introduction of two members of the IgLON family, neurotrimin and NEGR1, in early embryonic neurons was sufficient to confer sensitivity to metalloproteinase inhibitors in neurite outgrowth assays. Outgrowth experiments on immobilized IgLON proteins revealed a role for all IgLON family members in promoting neurite extension from cortical neurons. Together, our findings support a role for metalloproteinase-dependent shedding of IgLON family members in regulating neurite outgrowth from mature cortical neurons.
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Affiliation(s)
- Ricardo Sanz
- From the Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Gino B Ferraro
- From the Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
| | - Alyson E Fournier
- From the Department of Neurology and Neurosurgery, Montréal Neurological Institute, McGill University, Montréal, Québec H3A 2B4, Canada
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646
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Demily C, Rossi M, Chesnoy-Servanin G, Martin B, Poisson A, Sanlaville D, Edery P. Complex phenotype with social communication disorder caused by mosaic supernumerary ring chromosome 19p. BMC MEDICAL GENETICS 2014; 15:132. [PMID: 25496186 PMCID: PMC4411819 DOI: 10.1186/s12881-014-0132-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 12/02/2014] [Indexed: 12/21/2022]
Abstract
BACKGROUND Deletions or duplications of chromosome 19 are rare and there is no previous report in the literature of a ring chromosome derived from proximal 19p. Copy Number Variants (CNVs) responsible for complex phenotypes with Social Communication Disorder (SCD), may contribute to improve knowledge about the distinction between intellectual deficiency and autism spectrum disorders. CASE PRESENTATION We report the clinical and cytogenetic characterization of a patient (male, 33 years-old, first child of healthy Portuguese non-consanguineous parents) presenting with a complex phenotype including SCD without intellectual deficiency and carrying a mosaic supernumerary ring chromosome 19p. Microarray-Based Comparative Genomic Hybridization and Fluorescence in situ Hybridization were performed. Genetic analysis showed a large mosaic interstitial duplication 19p13.12p12 of the short arm of chromosome 19, spanning 8.35 Mb. Our data suggested a putative association between psychosocial dysfunction and mosaic pure trisomy 19p13.2p12. CONCLUSION This clinical report demonstrated the need to analyze more discreet trait-based subsets of complex phenotypes to improve the ability to detect genetic effects. To address this question and the broader issue of deciphering the yet unknown genetic contributors to complex phenotype with SCD, we suggest performing systematic psychological and psychiatric assessments in patients with chromosomal abnormalities.
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Affiliation(s)
- Caroline Demily
- Centre de dépistage et de prises en charge des troubles psychiatriques d'origine génétique, Pôle Ouest, Centre Hospitalier le Vinatier, 95 bld Pinel, 69677, Bron cedex, France. .,Centre de Neuroscience Cognitive, UMR 5229 (CNRS et Université Lyon 1), Lyon, France.
| | - Massimiliano Rossi
- Hospices Civils de Lyon, service de génétique et centre de référence des anomalies du développement, GHE, Lyon, France. .,Centre de Recherche en Neurosciences de Lyon, Inserm U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France.
| | - Gabrielle Chesnoy-Servanin
- Centre de dépistage et de prises en charge des troubles psychiatriques d'origine génétique, Pôle Ouest, Centre Hospitalier le Vinatier, 95 bld Pinel, 69677, Bron cedex, France. .,Centre de Neuroscience Cognitive, UMR 5229 (CNRS et Université Lyon 1), Lyon, France.
| | - Brice Martin
- Centre de Neuroscience Cognitive, UMR 5229 (CNRS et Université Lyon 1), Lyon, France. .,Service Universitaire de Réhabilitation, Centre Hospitalier le Vinatier, Bron, France.
| | - Alice Poisson
- Centre de dépistage et de prises en charge des troubles psychiatriques d'origine génétique, Pôle Ouest, Centre Hospitalier le Vinatier, 95 bld Pinel, 69677, Bron cedex, France. .,Centre de Neuroscience Cognitive, UMR 5229 (CNRS et Université Lyon 1), Lyon, France.
| | - Damien Sanlaville
- Centre de Recherche en Neurosciences de Lyon, Inserm U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France. .,Hospices Civils de Lyon, service de génétique, centre de référence des anomalies du développement, laboratoire de cytogénétique, GHE, Lyon, France.
| | - Patrick Edery
- Hospices Civils de Lyon, service de génétique et centre de référence des anomalies du développement, GHE, Lyon, France. .,Centre de Recherche en Neurosciences de Lyon, Inserm U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France.
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647
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Gupta S, Ellis SE, Ashar FN, Moes A, Bader JS, Zhan J, West AB, Arking DE. Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism. Nat Commun 2014; 5:5748. [PMID: 25494366 PMCID: PMC4270294 DOI: 10.1038/ncomms6748] [Citation(s) in RCA: 348] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Accepted: 11/03/2014] [Indexed: 12/27/2022] Open
Abstract
Recent studies of genomic variation associated with autism have suggested the existence of extreme heterogeneity. Large-scale transcriptomics should complement these results to identify core molecular pathways underlying autism. Here we report results from a large-scale RNA sequencing effort, utilizing region-matched autism and control brains to identify neuronal and microglial genes robustly dysregulated in autism cortical brain. Remarkably, we note that a gene expression module corresponding to M2-activation states in microglia is negatively correlated with a differentially expressed neuronal module, implicating dysregulated microglial responses in concert with altered neuronal activity-dependent genes in autism brains. These observations provide pathways and candidate genes that highlight the interplay between innate immunity and neuronal activity in the aetiology of autism. Autism spectrum disorder (ASD) is a common, highly heritable neurodevelopmental condition characterized by marked genetic heterogeneity. In this study, the authors use RNA sequencing analyses to characterize differences in the transcriptome between autistic and typically developing brains.
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Affiliation(s)
- Simone Gupta
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Shannon E Ellis
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Foram N Ashar
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Anna Moes
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Joel S Bader
- 1] Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA [2] Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jianan Zhan
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Andrew B West
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Dan E Arking
- Department of Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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648
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Duan J, Shi J, Fiorentino A, Leites C, Chen X, Moy W, Chen J, Alexandrov BS, Usheva A, He D, Freda J, O'Brien NL, McQuillin A, Sanders AR, Gershon ES, DeLisi LE, Bishop AR, Gurling HMD, Pato MT, Levinson DF, Kendler KS, Pato CN, Gejman PV. A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder. Am J Hum Genet 2014; 95:744-53. [PMID: 25434007 PMCID: PMC4259974 DOI: 10.1016/j.ajhg.2014.11.001] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/03/2014] [Indexed: 12/17/2022] Open
Abstract
Schizophrenia (SZ) genome-wide association studies (GWASs) have identified common risk variants in >100 susceptibility loci; however, the contribution of rare variants at these loci remains largely unexplored. One of the strongly associated loci spans MIR137 (miR137) and MIR2682 (miR2682), two microRNA genes important for neuronal function. We sequenced ∼6.9 kb MIR137/MIR2682 and upstream regulatory sequences in 2,610 SZ cases and 2,611 controls of European ancestry. We identified 133 rare variants with minor allele frequency (MAF) <0.5%. The rare variant burden in promoters and enhancers, but not insulators, was associated with SZ (p = 0.021 for MAF < 0.5%, p = 0.003 for MAF < 0.1%). A rare enhancer SNP, 1:g.98515539A>T, presented exclusively in 11 SZ cases (nominal p = 4.8 × 10(-4)). We further identified its risk allele T in 2 of 2,434 additional SZ cases, 11 of 4,339 bipolar (BP) cases, and 3 of 3,572 SZ/BP study controls and 1,688 population controls; yielding combined p values of 0.0007, 0.0013, and 0.0001 for SZ, BP, and SZ/BP, respectively. The risk allele T of 1:g.98515539A>T reduced enhancer activity of its flanking sequence by >50% in human neuroblastoma cells, predicting lower expression of MIR137/MIR2682. Both empirical and computational analyses showed weaker transcription factor (YY1) binding by the risk allele. Chromatin conformation capture (3C) assay further indicated that 1:g.98515539A>T influenced MIR137/MIR2682, but not the nearby DPYD or LOC729987. Our results suggest that rare noncoding risk variants are associated with SZ and BP at MIR137/MIR2682 locus, with risk alleles decreasing MIR137/MIR2682 expression.
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Affiliation(s)
- Jubao Duan
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA.
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alessia Fiorentino
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London WC1E 6JJ, UK
| | - Catherine Leites
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Xiangning Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Winton Moy
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Jingchun Chen
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Boian S Alexandrov
- Harvard Medical School, Boston, MA 02115, USA; Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Anny Usheva
- Harvard Medical School, Boston, MA 02115, USA
| | - Deli He
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Jessica Freda
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA
| | - Niamh L O'Brien
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London WC1E 6JJ, UK
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London WC1E 6JJ, UK
| | - Alan R Sanders
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
| | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
| | - Lynn E DeLisi
- VA Boston Healthcare System, Harvard Medical School, Brockton, MA 02301, USA
| | - Alan R Bishop
- Los Alamos National Laboratory, Los Alamos, NM 87544, USA
| | - Hugh M D Gurling
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London WC1E 6JJ, UK
| | - Michele T Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine at USC, Los Angeles, CA 90033, USA
| | - Douglas F Levinson
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Carlos N Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine at USC, Los Angeles, CA 90033, USA
| | - Pablo V Gejman
- Center for Psychiatric Genetics, Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA; Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL 60637, USA
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649
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Abstract
PURPOSE OF REVIEW Recent studies clearly demonstrate that copy number variations (CNVs) are widespread in our genome and play an important role in human genetic variation, accounting for both human population diversity and human genetic disease. This review will discuss the most current knowledge regarding our understanding of the biology of CNVs in relation to human genetic disease. RECENT FINDINGS CNVs associated with human genetic disease can be either recurrent, with a common size and breakpoint clustering, or nonrecurrent, with different sizes and variable breakpoints. Two types of recurrent CNVs have been distinguished, including the syndromic forms in which the phenotypic features are relatively consistent, and those in which the same recurrent CNV can be associated with a diverse set of diagnoses. Recently, the 'Two-hit model' was used to explain the phenotypic variability associated with the latter group of recurrent CNVs. Nonrecurrent CNVs, on the contrary, occur at a relatively lower frequency at the individual locus level but collectively they are as common as recurrent CNVs. Finally, the study of CNV burden in different diseases demonstrated a clear trend of an increasing CNV burden in diseases with more severe phenotypes. SUMMARY In spite of the advances in the study of the CNV landscape associated with human genetic disease, there still remain many unexplored questions especially regarding the role of CNVs in the pathogenesis of complex human genetic diseases.
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650
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Using extended pedigrees to identify novel autism spectrum disorder (ASD) candidate genes. Hum Genet 2014; 134:191-201. [DOI: 10.1007/s00439-014-1513-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/20/2014] [Indexed: 01/01/2023]
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