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Colijn MA, Smith CS, Thomas MA. Maternal 15q11.2-q13.1 duplication syndrome-associated psychosis and mania: a new case and review of the literature. Psychiatr Genet 2024; 34:1-7. [PMID: 38019137 DOI: 10.1097/ypg.0000000000000354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Maternal 15q11.2-q13.1 duplication syndrome is associated with a variety of developmental and neuropsychiatric abnormalities. Although schizophrenia-like presentations have been reported, details pertaining to the nature of the corresponding psychotic symptoms and their response to treatment have only been described in a few cases, and no reviews summarizing the literature currently exist. As such, we describe a new case of 15q11.2-q13.1 duplication syndrome-associated schizoaffective disorder and also performed a systematic review of the literature. Our patient's presentation is somewhat unique as she experienced visual hallucinations in the absence of auditory hallucinations. This is also the first report to describe full symptomatic remission in response to relatively low-dose atypical antipsychotic therapy.
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Affiliation(s)
- Mark Ainsley Colijn
- Department of Psychiatry, Hotchkiss Brain Institute, Mathison Centre for Mental Health Research and Education, University of Calgary
| | - Christopher S Smith
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary
| | - Mary Ann Thomas
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
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2
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Kim IB, Lee T, Lee J, Kim J, Lee S, Koh IG, Kim JH, An JY, Lee H, Kim WK, Ju YS, Cho Y, Yu SJ, Kim SA, Oh M, Han DW, Kim E, Choi JK, Yoo HJ, Lee JH. Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder. Mol Psychiatry 2022; 27:4680-4694. [PMID: 35840799 DOI: 10.1038/s41380-022-01697-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/27/2022] [Accepted: 07/01/2022] [Indexed: 12/14/2022]
Abstract
Three-dimensional chromatin interactions regulate gene expressions. The significance of de novo mutations (DNMs) in chromatin interactions remains poorly understood for autism spectrum disorder (ASD). We generated 813 whole-genome sequences from 242 Korean simplex families to detect DNMs, and identified target genes which were putatively affected by non-coding DNMs in chromatin interactions. Non-coding DNMs in chromatin interactions were significantly involved in transcriptional dysregulations related to ASD risk. Correspondingly, target genes showed spatiotemporal expressions relevant to ASD in developing brains and enrichment in biological pathways implicated in ASD, such as histone modification. Regarding clinical features of ASD, non-coding DNMs in chromatin interactions particularly contributed to low intelligence quotient levels in ASD probands. We further validated our findings using two replication cohorts, Simons Simplex Collection (SSC) and MSSNG, and showed the consistent enrichment of non-coding DNM-disrupted chromatin interactions in ASD probands. Generating human induced pluripotent stem cells in two ASD families, we were able to demonstrate that non-coding DNMs in chromatin interactions alter the expression of target genes at the stage of early neural development. Taken together, our findings indicate that non-coding DNMs in ASD probands lead to early neurodevelopmental disruption implicated in ASD risk via chromatin interactions.
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Affiliation(s)
- Il Bin Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, Hanyang University Guri Hospital, Guri, 11923, Republic of Korea
| | - Taeyeop Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.,Department of Psychiatry, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, Republic of Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Jonghun Kim
- Department of Genetics, Yale Stem Cell Center, Yale Child Study Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Suho Lee
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea
| | - In Gyeong Koh
- Industry-University Cooperation Foundation, Hanyang University, Seoul, 04763, Republic of Korea
| | - Jae Hyun Kim
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea.,BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.,School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea
| | - Hyunseong Lee
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, 05030, Republic of Korea
| | - Woo Kyeong Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Yongseong Cho
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Seok Jong Yu
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Soon Ae Kim
- Department of Pharmacology, Eulji University, Daejeon, 13135, Republic of Korea
| | - Miae Oh
- Department of Psychiatry, Kyung Hee University Hospital, Seoul, 02447, Republic of Korea
| | - Dong Wook Han
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China.,Organoid sciences, Ltd., Bundang-gu, Seongnam, 13488, Republic of Korea
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, 34141, Republic of Korea. .,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Jung Kyoon Choi
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| | - Hee Jeong Yoo
- Department of Psychiatry, Seoul National University Bundang Hospital, Seongnam, 13620, Republic of Korea. .,Department of Psychiatry, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea.
| | - Jeong Ho Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,Sovargen Co. Ltd., Daejeon, 34051, Republic of Korea.
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3
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Phenotypic Diversity of 15q11.2 BP1-BP2 Deletion in Three Korean Families with Development Delay and/or Intellectual Disability: A Case Series and Literature Review. Diagnostics (Basel) 2021; 11:diagnostics11040722. [PMID: 33921555 PMCID: PMC8072617 DOI: 10.3390/diagnostics11040722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 11/30/2022] Open
Abstract
The 15q11.2 breakpoint (BP) 1–BP2 deletion syndrome is emerging as the most frequent pathogenic copy number variation in humans related to neurodevelopmental diseases, with changes in cognition, behavior, and brain morphology. Previous publications have reported that patients with 15q11.2 BP1–BP2 deletion showed intellectual disability (ID), speech impairment, developmental delay (DD), and/or behavioral problems. We describe three new cases, aged 3 or 6 years old and belonging to three unrelated Korean families, with a 350-kb 15q11.2 BP1–BP2 deletion of four highly conserved genes, namely, the TUBGCP5, CYFIP1, NIPA2, and NIPA1 genes. All of our cases presented with global DD and/or ID, and the severity ranged from mild to severe, but common facial dysmorphism and congenital malformations in previous reports were not characteristic. The 15q11.2 BP1–BP2 deletion was inherited from an unaffected parent in all cases. Our three cases, together with previous findings from the literature review, confirm some of the features earlier reported to be associated with 15q11.2 BP1–BP2 deletion and help to further delineate the phenotype associated with 15q11.2 deletion. Identification of more cases with 15q11.2 BP1–BP2 deletion will allow us to obtain a better understanding of the clinical phenotypes. Further explanation of the functions of the genes within the 15q11.2 BP1–BP2 region is required to resolve the pathogenic effects on neurodevelopment.
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Tao H, Zhou X, Chen J, Zhou H, Huang L, Cai Y, Fu J, Liu Z, Chen Y, Sun C, Zhao B, Zhong W, Li K. Genetic Effects of the Schizophrenia-Related Gene DTNBP1 in Temporal Lobe Epilepsy. Front Genet 2021; 12:553974. [PMID: 33679873 PMCID: PMC7933566 DOI: 10.3389/fgene.2021.553974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 01/15/2021] [Indexed: 11/13/2022] Open
Abstract
Recent studies have reported patients who concurrently exhibit conditions of epilepsy and schizophrenia, indicating certain shared pathologies between them. This study aimed to investigate the genetic effects of the schizophrenia-related gene DTNBP1 in temporal lobe epilepsy (TLE). A total of 496 TLE patients and 528 healthy individuals were successfully genotyped for six DTNBP1 polymorphisms (rs760665, rs1011313, rs2619528, rs2619522, rs909706, and rs2619538), including 335 TLE patients and 325 healthy controls in cohort 1, and 161 TLE patients and 203 healthy controls in cohort 2. The frequency of the TT genotype at rs909706 T > C was lower in TLE patients than in normal controls in the initial cohort (cohort 1), which was confirmed in an independent cohort (cohort 2). However, the intronic T allele failed to be in linkage disequilibrium (LD) with any functional variations nearby; thus, together with the CCAC and TCAT haplotypes (rs1011313-rs2619528-rs2619522-rs909706) observed in the study, this allele acts only as a protective factor against susceptibility to TLE. Meanwhile, a novo mutant allele rs2619538 T > A was exclusively observed in TLE patients, and a dual-luciferase assay revealed that the mutant allele was increased by approximately 22% in the DTNBP2 promoter compared with the wild-type allele. Together with the trend of increasing DTNBP1 expression in epilepsy patients and animal models in this study, these are the first findings to demonstrate the genetic association of DTNBP1 with TLE. Homozygous mutation of rs2619538 T > A likely promotes DTNBP1 expression and facilitates subsequent processes in epilepsy pathologies. Thus, the role of DTNBP1 in TLE deserves further exploration in the future.
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Affiliation(s)
- Hua Tao
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Guangdong Key Laboratory of Age-related Cardiac and Cerebral Diseases, Guangdong Medical University, Zhanjiang, China
| | - Xu Zhou
- Guangdong Key Laboratory of Age-related Cardiac and Cerebral Diseases, Guangdong Medical University, Zhanjiang, China
| | - Jun Chen
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Haihong Zhou
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Lidan Huang
- Guangdong Key Laboratory of Age-related Cardiac and Cerebral Diseases, Guangdong Medical University, Zhanjiang, China
| | - Yujie Cai
- Guangdong Key Laboratory of Age-related Cardiac and Cerebral Diseases, Guangdong Medical University, Zhanjiang, China
| | - Jiawu Fu
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Zhou Liu
- Guangdong Key Laboratory of Age-related Cardiac and Cerebral Diseases, Guangdong Medical University, Zhanjiang, China
| | - Yanyan Chen
- Guangdong Key Laboratory of Age-related Cardiac and Cerebral Diseases, Guangdong Medical University, Zhanjiang, China
| | - Chaowen Sun
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Bin Zhao
- Guangdong Key Laboratory of Age-related Cardiac and Cerebral Diseases, Guangdong Medical University, Zhanjiang, China
| | - Wangtao Zhong
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Keshen Li
- Institute of Neurology, Guangdong Medical University, Zhanjiang, China.,Neurology and Neurosurgery Division, Stroke Center, The First Affiliated Hospital, Clinical Medicine Research Institute, Jinan University, Guangzhou, China
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5
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Vanzo RJ, Prasad A, Staunch L, Hensel CH, Serrano MA, Wassman ER, Kaplun A, Grandin T, Boles RG. The Temple Grandin Genome: Comprehensive Analysis in a Scientist with High-Functioning Autism. J Pers Med 2020; 11:21. [PMID: 33383702 PMCID: PMC7824360 DOI: 10.3390/jpm11010021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/31/2022] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous condition with a complex genetic etiology. The objective of this study is to identify the complex genetic factors that underlie the ASD phenotype and other clinical features of Professor Temple Grandin, an animal scientist and woman with high-functioning ASD. Identifying the underlying genetic cause for ASD can impact medical management, personalize services and treatment, and uncover other medical risks that are associated with the genetic diagnosis. Prof. Grandin underwent chromosomal microarray analysis, whole exome sequencing, and whole genome sequencing, as well as a comprehensive clinical and family history intake. The raw data were analyzed in order to identify possible genotype-phenotype correlations. Genetic testing identified variants in three genes (SHANK2, ALX1, and RELN) that are candidate risk factors for ASD. We identified variants in MEFV and WNT10A, reported to be disease-associated in previous studies, which are likely to contribute to some of her additional clinical features. Moreover, candidate variants in genes encoding metabolic enzymes and transporters were identified, some of which suggest potential therapies. This case report describes the genomic findings in Prof. Grandin and it serves as an example to discuss state-of-the-art clinical diagnostics for individuals with ASD, as well as the medical, logistical, and economic hurdles that are involved in clinical genetic testing for an individual on the autism spectrum.
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Affiliation(s)
- Rena J. Vanzo
- Lineagen, Inc., Salt Lake City, UT 84109, USA; (A.P.); (L.S.); (C.H.H.); (M.A.S.); (E.R.W.)
| | - Aparna Prasad
- Lineagen, Inc., Salt Lake City, UT 84109, USA; (A.P.); (L.S.); (C.H.H.); (M.A.S.); (E.R.W.)
| | - Lauren Staunch
- Lineagen, Inc., Salt Lake City, UT 84109, USA; (A.P.); (L.S.); (C.H.H.); (M.A.S.); (E.R.W.)
| | - Charles H. Hensel
- Lineagen, Inc., Salt Lake City, UT 84109, USA; (A.P.); (L.S.); (C.H.H.); (M.A.S.); (E.R.W.)
| | - Moises A. Serrano
- Lineagen, Inc., Salt Lake City, UT 84109, USA; (A.P.); (L.S.); (C.H.H.); (M.A.S.); (E.R.W.)
| | - E. Robert Wassman
- Lineagen, Inc., Salt Lake City, UT 84109, USA; (A.P.); (L.S.); (C.H.H.); (M.A.S.); (E.R.W.)
| | | | - Temple Grandin
- Department of Animal Science, Colorado State University, Fort Collins, CO 80523, USA;
| | - Richard G. Boles
- The Center for Neurological and Neurodevelopmental Health, Voorhees, NJ 08043, USA;
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6
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Luza S, Opazo CM, Bousman CA, Pantelis C, Bush AI, Everall IP. The ubiquitin proteasome system and schizophrenia. Lancet Psychiatry 2020; 7:528-537. [PMID: 32061320 DOI: 10.1016/s2215-0366(19)30520-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/22/2019] [Accepted: 12/03/2019] [Indexed: 12/12/2022]
Abstract
The ubiquitin-proteasome system is a master regulator of neural development and the maintenance of brain structure and function. It influences neurogenesis, synaptogenesis, and neurotransmission by determining the localisation, interaction, and turnover of scaffolding, presynaptic, and postsynaptic proteins. Moreover, ubiquitin-proteasome system signalling transduces epigenetic changes in neurons independently of protein degradation and, as such, dysfunction of components and substrates of this system has been linked to a broad range of brain conditions. Although links between ubiquitin-proteasome system dysfunction and neurodegenerative disorders have been known for some time, only recently have similar links emerged for neurodevelopmental disorders, such as schizophrenia. Here, we review the components of the ubiquitin-proteasome system that are reported to be dysregulated in schizophrenia, and discuss specific molecular changes to these components that might, in part, explain the complex causes of this mental disorder.
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Affiliation(s)
- Sandra Luza
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia; Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia
| | - Carlos M Opazo
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia; Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia
| | - Chad A Bousman
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia; The Cooperative Research Centre for Mental Health, Carlton South, VIC, Australia; Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Departments of Medical Genetics, Psychiatry, and Physiology & Pharmacology, University of Calgary, Calgary, AB, Canada; University of Calgary, Calgary, AB, Canada
| | - Christos Pantelis
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia; Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia; Centre for Neural Engineering, Department of Electrical and Electronic Engineering, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia; The Cooperative Research Centre for Mental Health, Carlton South, VIC, Australia; Alberta Children's Hospital Research Institute, Calgary, AB, Canada; NorthWestern Mental Health, Melbourne, VIC, Australia
| | - Ashley I Bush
- Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia.
| | - Ian P Everall
- Melbourne Neuropsychiatry Centre, Department of Psychiatry, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia; Melbourne Dementia Research Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia; Centre for Neural Engineering, Department of Electrical and Electronic Engineering, The University of Melbourne & Melbourne Health, Parkville, VIC, Australia; The Cooperative Research Centre for Mental Health, Carlton South, VIC, Australia; Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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7
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Castronovo P, Baccarin M, Ricciardello A, Picinelli C, Tomaiuolo P, Cucinotta F, Frittoli M, Lintas C, Sacco R, Persico AM. Phenotypic spectrum of NRXN1 mono- and bi-allelic deficiency: A systematic review. Clin Genet 2019; 97:125-137. [PMID: 30873608 DOI: 10.1111/cge.13537] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/01/2019] [Accepted: 03/10/2019] [Indexed: 01/13/2023]
Abstract
Neurexins are presynaptic cell adhesion molecules critically involved in synaptogenesis and vesicular neurotransmitter release. They are encoded by three genes (NRXN1-3), each yielding a longer alpha (α) and a shorter beta (β) transcript. Deletions spanning the promoter and the initial exons of the NRXN1 gene, located in chromosome 2p16.3, are associated with a variety of neurodevelopmental, psychiatric, neurological and neuropsychological phenotypes. We have performed a systematic review to define (a) the clinical phenotypes most associated with mono-allelic exonic NRXN1 deletions, and (b) the phenotypic features of NRXN1 bi-allelic deficiency due to compound heterozygous deletions/mutations. Clinically, three major conclusions can be drawn: (a) incomplete penetrance and pleiotropy do not allow reliable predictions of clinical outcome following prenatal detection of mono-allelic exonic NRXN1 deletions. Newborn carriers should undergo periodic neuro-behavioral observations for the timely detection of warning signs and the prescription of early behavioral intervention; (b) the presence of additional independent genetic risk factors should always be sought, as they may influence prognosis; (c) children with exonic NRXN1 deletions displaying early-onset, severe psychomotor delay in the context of a Pitt-Hopkins-like syndrome 2 phenotype, should undergo DNA sequencing of the spared NRXN1 allele in search for mutations or very small insertions/deletions.
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Affiliation(s)
- Paola Castronovo
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Marco Baccarin
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Arianna Ricciardello
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Chiara Picinelli
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Pasquale Tomaiuolo
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Francesca Cucinotta
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
| | - Myriam Frittoli
- Laboratory for Pervasive Developmental Disorders, Mafalda Luce Center, Milan, Italy
| | - Carla Lintas
- Service for Neurodevelopmental Disorders & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Roberto Sacco
- Service for Neurodevelopmental Disorders & Laboratory of Molecular Psychiatry and Neurogenetics, University "Campus Bio-Medico", Rome, Italy
| | - Antonio M Persico
- Interdepartmental Program "Autism 0-90", "Gaetano Martino" University Hospital, University of Messina, Messina, Italy
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8
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Kunisawa K, Shimizu T, Kushima I, Aleksic B, Mori D, Osanai Y, Kobayashi K, Taylor AM, Bhat MA, Hayashi A, Baba H, Ozaki N, Ikenaka K. Dysregulation of schizophrenia-related aquaporin 3 through disruption of paranode influences neuronal viability. J Neurochem 2018; 147:395-408. [PMID: 30025158 PMCID: PMC6205917 DOI: 10.1111/jnc.14553] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 06/28/2018] [Accepted: 07/16/2018] [Indexed: 12/23/2022]
Abstract
Myelinated axons segregate the axonal membrane into four defined regions: the node of Ranvier, paranode, juxtaparanode, and internode. The paranodal junction consists of specific component proteins, such as neurofascin155 (NF155) on the glial side, and Caspr and Contactin on the axonal side. Although paranodal junctions are thought to play crucial roles in rapid saltatory conduction and nodal assembly, the role of their interaction with neurons is not fully understood. In a previous study, conditional NF155 knockout in oligodendrocytes led to disorganization of the paranodal junctions. To examine if disruption of paranodal junctions affects neuronal gene expression, we prepared total RNA from the retina of NF155 conditional knockout, and performed expression analysis. We found that the expression level of 433 genes changed in response to paranodal junction ablation. Interestingly, expression of aquaporin 3 (AQP3) was significantly reduced in NF155 conditional knockout mice, but not in cerebroside sulfotransferase knockout (CST-KO) mice, whose paranodes are not originally formed during development. Copy number variations have an important role in the etiology of schizophrenia (SCZ). We observed rare duplications of AQP3 in SCZ patients, suggesting a correlation between abnormal AQP3 expression and SCZ. To determine if AQP3 over-expression in NF155 conditional knockout mice influences neuronal function, we performed adeno-associated virus (AAV)-mediated over-expression of AQP3 in the motor cortex of mice and found a significant increase in caspase 3-dependent neuronal apoptosis in AQP3-transduced cells. This study may provide new insights into therapeutic approaches for SCZ by regulating AQP3 expression, which is associated with paranodal disruption.
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Affiliation(s)
- Kazuo Kunisawa
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki 444-8787, Japan
- SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8787, Japan
| | - Takeshi Shimizu
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki 444-8787, Japan
- SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8787, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Brain and Mind Research Center, Nagoya University, Nagoya 466-8550, Japan
| | - Yasuyuki Osanai
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki 444-8787, Japan
- SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8787, Japan
| | - Kenta Kobayashi
- Section of Viral Vector Development, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
- SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8787, Japan
| | - Anna M. Taylor
- Department of Cellular and Integrative Physiology, School of Medicine, University of Texas Health Science Center, San Antonio 78229-3900, USA
| | - Manzoor A. Bhat
- Department of Cellular and Integrative Physiology, School of Medicine, University of Texas Health Science Center, San Antonio 78229-3900, USA
| | - Akiko Hayashi
- Department of Molecular Neurobiology, Tokyo University of Pharmacy and Life Sciences, Hachioji 192-0392, Japan
| | - Hiroko Baba
- Department of Molecular Neurobiology, Tokyo University of Pharmacy and Life Sciences, Hachioji 192-0392, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kazuhiro Ikenaka
- Division of Neurobiology and Bioinformatics, National Institute for Physiological Sciences, Okazaki 444-8787, Japan
- SOKENDAI (The Graduate University for Advanced Studies), Okazaki 444-8787, Japan
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9
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Wu J, Yu P, Jin X, Xu X, Li J, Li Z, Wang M, Wang T, Wu X, Jiang Y, Cai W, Mei J, Min Q, Xu Q, Zhou B, Guo H, Wang P, Zhou W, Hu Z, Li Y, Cai T, Wang Y, Xia K, Jiang YH, Sun ZS. Genomic landscapes of Chinese sporadic autism spectrum disorders revealed by whole-genome sequencing. J Genet Genomics 2018; 45:527-538. [PMID: 30392784 DOI: 10.1016/j.jgg.2018.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/25/2018] [Accepted: 09/09/2018] [Indexed: 12/12/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with considerable clinical and genetic heterogeneity. In this study, we identified all classes of genomic variants from whole-genome sequencing (WGS) dataset of 32 Chinese trios with ASD, including de novo mutations, inherited variants, copy number variants (CNVs) and genomic structural variants. A higher mutation rate (Poisson test, P < 2.2 × 10-16) in exonic (1.37 × 10-8) and 3'-UTR regions (1.42 × 10-8) was revealed in comparison with that of whole genome (1.05 × 10-8). Using an integrated model, we identified 87 potentially risk genes (P < 0.01) from 4832 genes harboring various rare deleterious variants, including CHD8 and NRXN2, implying that the disorders may be in favor to multiple-hit. In particular, frequent rare inherited mutations of several microcephaly-associated genes (ASPM, WDR62, and ZNF335) were found in ASD. In chromosomal structure analyses, we found four de novo CNVs and one de novo chromosomal rearrangement event, including a de novo duplication of UBE3A-containing region at 15q11.2-q13.1, which causes Angelman syndrome and microcephaly, and a disrupted TNR due to de novo chromosomal translocation t(1; 5)(q25.1; q33.2). Taken together, our results suggest that abnormalities of centrosomal function and chromatin remodeling of the microcephaly-associated genes may be implicated in pathogenesis of ASD. Adoption of WGS as a new yet efficient technique to illustrate the full genetic spectrum in complex disorders, such as ASD, could provide novel insights into pathogenesis, diagnosis and treatment.
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Affiliation(s)
- Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Ping Yu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiu Xu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Jinchen Li
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | | | - Tao Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xueli Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Wanshi Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qingjie Min
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Qiong Xu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Bingrui Zhou
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Hui Guo
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | - Ping Wang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wenhao Zhou
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Zhengmao Hu
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | | | - Tao Cai
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Yi Wang
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China.
| | - Yong-Hui Jiang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Zhong Sheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
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10
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Grochowski CM, Gu S, Yuan B, Tcw J, Brennand KJ, Sebat J, Malhotra D, McCarthy S, Rudolph U, Lindstrand A, Chong Z, Levy DL, Lupski JR, Carvalho CMB. Marker chromosome genomic structure and temporal origin implicate a chromoanasynthesis event in a family with pleiotropic psychiatric phenotypes. Hum Mutat 2018; 39:939-946. [PMID: 29696747 PMCID: PMC5995661 DOI: 10.1002/humu.23537] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/11/2018] [Accepted: 04/16/2018] [Indexed: 12/13/2022]
Abstract
Small supernumerary marker chromosomes (sSMC) are chromosomal fragments difficult to characterize genomically. Here, we detail a proband with schizoaffective disorder and a mother with bipolar disorder with psychotic features who present with a marker chromosome that segregates with disease. We explored the architecture of this marker and investigated its temporal origin. Array comparative genomic hybridization (aCGH) analysis revealed three duplications and three triplications that spanned the short arm of chromosome 9, suggestive of a chromoanasynthesis-like event. Segregation of marker genotypes, phased using sSMC mosaicism in the mother, provided evidence that it was generated during a germline-level event in the proband's maternal grandmother. Whole-genome sequencing (WGS) was performed to resolve the structure and junctions of the chromosomal fragments, revealing further complexities. While structural variations have been previously associated with neuropsychiatric disorders and marker chromosomes, here we detail the precise architecture, human life-cycle genesis, and propose a DNA replicative/repair mechanism underlying formation.
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Affiliation(s)
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Julia Tcw
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kristen J Brennand
- Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jonathan Sebat
- Beyster Center for Psychiatric Genomics, Department of Psychiatry, University of California at San Diego, San Diego, California
| | | | - Shane McCarthy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Uwe Rudolph
- Laboratory of Genetic Neuropharmacology, McLean Hospital, Belmont, Massachusetts
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Zechen Chong
- Department of Genetics and the Informatics Institute, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Deborah L Levy
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
- Psychology Research Laboratory, McLean Hospital, Belmont, Massachusetts
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas
- Texas Children's Hospital, Houston, Texas
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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11
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Koeleman BP. What do genetic studies tell us about the heritable basis of common epilepsy? Polygenic or complex epilepsy? Neurosci Lett 2018; 667:10-16. [DOI: 10.1016/j.neulet.2017.03.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 12/23/2022]
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12
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Afshari P, Yao WD, Middleton FA. Reduced Slc1a1 expression is associated with neuroinflammation and impaired sensorimotor gating and cognitive performance in mice: Implications for schizophrenia. PLoS One 2017; 12:e0183854. [PMID: 28886095 PMCID: PMC5590851 DOI: 10.1371/journal.pone.0183854] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 08/11/2017] [Indexed: 12/11/2022] Open
Abstract
We previously reported a 84-Kb hemi-deletion copy number variant at the SLC1A1 gene locus that reduces its expression and appeared causally linked to schizophrenia. In this report, we characterize the in vivo and in vitro consequences of reduced expression of Slc1a1 in mice. Heterozygous (HET) Slc1a1+/- mice, which more closely model the hemi-deletion we found in human subjects, were examined in a series of behavioral, anatomical and biochemical assays. Knockout (KO) mice were also included in the behavioral studies for comparative purposes. Both HET and KO mice exhibited evidence of increased anxiety-like behavior, impaired working memory, decreased exploratory activity and impaired sensorimotor gating, but no changes in overall locomotor activity. The magnitude of changes was approximately equivalent in the HET and KO mice suggesting a dominant effect of the haploinsufficiency. Behavioral changes in the HET mice were accompanied by reduced thickness of the dorsomedial prefrontal cortex. Whole transcriptome RNA-Seq analysis detected expression changes of genes and pathways involved in cytokine signaling and synaptic functions in both brain and blood. Moreover, the brains of Slc1a1+/- mice displayed elevated levels of oxidized glutathione, a trend for increased oxidative DNA damage, and significantly increased levels of cytokines. This latter finding was further supported by SLC1A1 knockdown and overexpression studies in differentiated human neuroblastoma cells, which led to decreased or increased cytokine expression, respectively. Taken together, our results suggest that partial loss of the Slc1a1 gene in mice causes haploinsufficiency associated with behavioral, histological and biochemical changes that reflect an altered redox state and may promote the expression of behavioral features and inflammatory states consistent with those observed in schizophrenia.
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Affiliation(s)
- Parisa Afshari
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY United States of America
| | - Wei-Dong Yao
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY United States of America.,Department of Psychiatry & Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, United States of America
| | - Frank A Middleton
- Department of Neuroscience & Physiology, SUNY Upstate Medical University, Syracuse, NY United States of America.,Department of Psychiatry & Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, United States of America.,Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, United States of America
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13
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Reggiani C, Coppens S, Sekhara T, Dimov I, Pichon B, Lufin N, Addor MC, Belligni EF, Digilio MC, Faletra F, Ferrero GB, Gerard M, Isidor B, Joss S, Niel-Bütschi F, Perrone MD, Petit F, Renieri A, Romana S, Topa A, Vermeesch JR, Lenaerts T, Casimir G, Abramowicz M, Bontempi G, Vilain C, Deconinck N, Smits G. Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability. Genome Med 2017; 9:67. [PMID: 28724449 PMCID: PMC5518101 DOI: 10.1186/s13073-017-0452-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 06/20/2017] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. METHODS Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play. RESULTS Integrating genomics, transcriptomics, and epigenomics data, we describe two novel DLG2 promoters and coding first exons expressed in human fetal brain. Their murine conservation and protein-level evidence allowed us to produce new DLG2 gene models for human and mouse. These new genic elements are deleted in 90% of 29 patients (public and in-house) showing partial deletion of the DLG2 gene. The patients' clinical characteristics expand the neurodevelopmental phenotypic spectrum linked to DLG2 gene disruption to cognitive and behavioral categories. CONCLUSIONS While protein-coding genes are regarded as well known, our work shows that integration of multiple omics datasets can unveil novel coding elements. From a clinical perspective, our work demonstrates that two new DLG2 promoters and exons are crucial for the neurodevelopmental phenotypes associated with this gene. In addition, our work brings evidence for the lack of cross-annotation in human versus mouse reference genomes and nucleotide versus protein databases.
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Affiliation(s)
- Claudio Reggiani
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, 1050 Belgium
| | - Sandra Coppens
- Department of Neurology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
- Neuropediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
| | - Tayeb Sekhara
- Neuropediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
- Present address: Neuropediatrics, Clinique Saint-Anne Saint-Rémy - CHIREC, Brussels, 1070 Belgium
| | - Ivan Dimov
- Faculté de Médecine, Université Libre de Bruxelles, Brussels, 1070 Belgium
| | - Bruno Pichon
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
| | - Nicolas Lufin
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
| | - Marie-Claude Addor
- Service de Médecine Génétique, Centre Hospitalier Universitaire Vaudois CHUV, Lausanne, 1011 Switzerland
| | - Elga Fabia Belligni
- Department of Public Health and Pediatrics, University of Torino, Turin, 10126 Italy
| | | | - Flavio Faletra
- S.C. Medical Genetics, Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, Trieste, 34137 Italy
| | | | - Marion Gerard
- Laboratory of Medical Genetics, CHU de Caen - Hôpital Clémenceau, Caen, 14033 Caen Cedex, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, 44093 Nantes Cedex 1, France
| | - Shelagh Joss
- West of Scotland Clinical Genetics Service, South Glasgow University Hospitals, Glasgow, G51 4TF UK
| | - Florence Niel-Bütschi
- Service de Médecine Génétique, Centre Hospitalier Universitaire Vaudois CHUV, Lausanne, 1011 Switzerland
| | - Maria Dolores Perrone
- S.C. Medical Genetics, Institute for Maternal and Child Health - IRCCS “Burlo Garofolo”, Trieste, 34137 Italy
- Present address: Assisted Fertilization Department, Casa di Cura Città di Udine, Udine, 33100 Italy
| | - Florence Petit
- Service de Génétique, CHRU de Lille - Hôpital Jeanne de Flandre, Lille, 59000 France
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, 53100 Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, 53100 Italy
| | - Serge Romana
- Service d’Histologie Embryologie Cytogénétique, Hôpital Necker Enfants Malades, Paris, 75015 France
- Université Paris Descartes - Institut IMAGINE, Paris, 75015 France
| | - Alexandra Topa
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, 413 45 Sweden
| | | | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, 1050 Belgium
- AI lab, Vrije Universiteit Brussel, Brussels, 1050 Belgium
| | - Georges Casimir
- Pediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
| | - Marc Abramowicz
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
| | - Gianluca Bontempi
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- Machine Learning Group, Université Libre de Bruxelles, Brussels, 1050 Belgium
| | - Catheline Vilain
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
- Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
| | - Nicolas Deconinck
- Neuropediatrics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels ULB-VUB, Brussels, 1050 Belgium
- ULB Center of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles, Brussels, 1070 Belgium
- Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, 1020 Belgium
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14
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Matsumoto M, Walton NM, Yamada H, Kondo Y, Marek GJ, Tajinda K. The impact of genetics on future drug discovery in schizophrenia. Expert Opin Drug Discov 2017; 12:673-686. [PMID: 28521526 DOI: 10.1080/17460441.2017.1324419] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Failures of investigational new drugs (INDs) for schizophrenia have left huge unmet medical needs for patients. Given the recent lackluster results, it is imperative that new drug discovery approaches (and resultant drug candidates) target pathophysiological alterations that are shared in specific, stratified patient populations that are selected based on pre-identified biological signatures. One path to implementing this paradigm is achievable by leveraging recent advances in genetic information and technologies. Genome-wide exome sequencing and meta-analysis of single nucleotide polymorphism (SNP)-based association studies have already revealed rare deleterious variants and SNPs in patient populations. Areas covered: Herein, the authors review the impact that genetics have on the future of schizophrenia drug discovery. The high polygenicity of schizophrenia strongly indicates that this disease is biologically heterogeneous so the identification of unique subgroups (by patient stratification) is becoming increasingly necessary for future investigational new drugs. Expert opinion: The authors propose a pathophysiology-based stratification of genetically-defined subgroups that share deficits in particular biological pathways. Existing tools, including lower-cost genomic sequencing and advanced gene-editing technology render this strategy ever more feasible. Genetically complex psychiatric disorders such as schizophrenia may also benefit from synergistic research with simpler monogenic disorders that share perturbations in similar biological pathways.
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Affiliation(s)
- Mitsuyuki Matsumoto
- a Unit 2, Candidate Discovery Science Labs., Drug Discovery Research , Astellas Pharma Inc. , Tsukuba , Ibaraki , Japan
| | - Noah M Walton
- b La Jolla Laboratory , Astellas Research Institute of America LLC , San Diego , CA , USA
| | - Hiroshi Yamada
- b La Jolla Laboratory , Astellas Research Institute of America LLC , San Diego , CA , USA
| | - Yuji Kondo
- a Unit 2, Candidate Discovery Science Labs., Drug Discovery Research , Astellas Pharma Inc. , Tsukuba , Ibaraki , Japan
| | - Gerard J Marek
- c Development Medical Sciences, Astellas Pharma Global Development , Northbrook , IL , USA
| | - Katsunori Tajinda
- b La Jolla Laboratory , Astellas Research Institute of America LLC , San Diego , CA , USA
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15
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Chen T, Giri M, Xia Z, Subedi YN, Li Y. Genetic and epigenetic mechanisms of epilepsy: a review. Neuropsychiatr Dis Treat 2017; 13:1841-1859. [PMID: 28761347 PMCID: PMC5516882 DOI: 10.2147/ndt.s142032] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Epilepsy is a common episodic neurological disorder or condition characterized by recurrent epileptic seizures, and genetics seems to play a key role in its etiology. Early linkage studies have localized multiple loci that may harbor susceptibility genes to epilepsy, and mutational analyses have detected a number of mutations involved in both ion channel and nonion channel genes in patients with idiopathic epilepsy. Genome-wide studies of epilepsy have found copy number variants at 2q24.2-q24.3, 7q11.22, 15q11.2-q13.3, and 16p13.11-p13.2, some of which disrupt multiple genes, such as NRXN1, AUTS2, NLGN1, CNTNAP2, GRIN2A, PRRT2, NIPA2, and BMP5, implicated for neurodevelopmental disorders, including intellectual disability and autism. Unfortunately, only a few common genetic variants have been associated with epilepsy. Recent exome-sequencing studies have found some genetic mutations, most of which are located in nonion channel genes such as the LGI1, PRRT2, EFHC1, PRICKLE, RBFOX1, and DEPDC5 and in probands with rare forms of familial epilepsy, and some of these genes are involved with the neurodevelopment. Since epigenetics plays a role in neuronal function from embryogenesis and early brain development to tissue-specific gene expression, epigenetic regulation may contribute to the genetic mechanism of neurodevelopment through which a gene and the environment interacting with each other affect the development of epilepsy. This review focused on the analytic tools used to identify epilepsy and then provided a summary of recent linkage and association findings, indicating the existence of novel genes on several chromosomes for further understanding of the biology of epilepsy.
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Affiliation(s)
- Tian Chen
- Department of Health Management Center, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
| | - Mohan Giri
- National Center for Rheumatic Diseases, Ratopul, Gaushala, Kathmandu, Nepal
| | - Zhenyi Xia
- Department of Thoracic Surgery, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
| | - Yadu Nanda Subedi
- National Center for Rheumatic Diseases, Ratopul, Gaushala, Kathmandu, Nepal
| | - Yan Li
- Department of Health Management Center, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
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16
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Rutkowski TP, Schroeder JP, Gafford GM, Warren ST, Weinshenker D, Caspary T, Mulle JG. Unraveling the genetic architecture of copy number variants associated with schizophrenia and other neuropsychiatric disorders. J Neurosci Res 2016; 95:1144-1160. [PMID: 27859486 DOI: 10.1002/jnr.23970] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/20/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022]
Abstract
Recent studies show that the complex genetic architecture of schizophrenia (SZ) is driven in part by polygenic components, or the cumulative effect of variants of small effect in many genes, as well as rare single-locus variants with large effect sizes. Here we discuss genetic aberrations known as copy number variants (CNVs), which fall in the latter category and are associated with a high risk for SZ and other neuropsychiatric disorders. We briefly review recurrent CNVs associated with SZ, and then highlight one CNV in particular, a recurrent 1.6-Mb deletion on chromosome 3q29, which is estimated to confer a 40-fold increased risk for SZ. Additionally, we describe the use of genetic mouse models, behavioral tools, and patient-derived induced pluripotent stem cells as a means to study CNVs in the hope of gaining mechanistic insight into their respective disorders. Taken together, the genomic data connecting CNVs with a multitude of human neuropsychiatric disease, our current technical ability to model such chromosomal anomalies in mouse, and the existence of precise behavioral measures of endophenotypes argue that the time is ripe for systematic dissection of the genetic mechanisms underlying such disease. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Timothy P Rutkowski
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jason P Schroeder
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Georgette M Gafford
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - David Weinshenker
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Tamara Caspary
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.,Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
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17
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A Novel Relationship for Schizophrenia, Bipolar, and Major Depressive Disorder. Part 8: a Hint from Chromosome 8 High Density Association Screen. Mol Neurobiol 2016; 54:5868-5882. [DOI: 10.1007/s12035-016-0102-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
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18
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Noor A, Dupuis L, Mittal K, Lionel AC, Marshall CR, Scherer SW, Stockley T, Vincent JB, Mendoza-Londono R, Stavropoulos DJ. 15q11.2 Duplication Encompassing Only the UBE3A Gene Is Associated with Developmental Delay and Neuropsychiatric Phenotypes. Hum Mutat 2016; 36:689-93. [PMID: 25884337 DOI: 10.1002/humu.22800] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 03/31/2015] [Indexed: 01/08/2023]
Abstract
Duplications of chromosome region 15q11-q13 with the maternal imprint are associated with a wide spectrum of neuropsychiatric disorders, including autism spectrum disorders, developmental delay, learning difficulties, schizophrenia, and seizures. These observations suggest there is a dosage-sensitive imprinted gene or genes within this region that explains the increased risk for neuropsychiatric phenotypes. We present a female patient with developmental delay in whom we identified a maternally inherited 129-Kb duplication in chromosome region 15q11.2 encompassing only the UBE3A gene. Expression analysis in cultured fibroblasts confirmed overexpression of UBE3A in the proband, compared with age- and sex-matched controls. We further tested segregation of this duplication in four generations and found it segregated with neuropsychiatric phenotypes. Our study shows for the first time clinical features associated with overexpression of UBE3A in humans and underscores the significance of this gene in the phenotype of individuals with 15q11-q13 duplication.
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Affiliation(s)
- Abdul Noor
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Pathology and Laboratory Medicine, Mount Sinai Hospital Joseph and Wolf Lebovic Health Complex, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Lucie Dupuis
- The Hospital for Sick Children, Department of Pediatrics, Division of Clinical and Metabolic Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Kirti Mittal
- Molecular Neuropsychiatry & Development Lab, The Campbell Family Brain Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Anath C Lionel
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tracy Stockley
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - John B Vincent
- Molecular Neuropsychiatry & Development Lab, The Campbell Family Brain Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Roberto Mendoza-Londono
- The Hospital for Sick Children, Department of Pediatrics, Division of Clinical and Metabolic Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
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19
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Ziats MN, Goin-Kochel RP, Berry LN, Ali M, Ge J, Guffey D, Rosenfeld JA, Bader P, Gambello MJ, Wolf V, Penney LS, Miller R, Lebel RR, Kane J, Bachman K, Troxell R, Clark G, Minard CG, Stankiewicz P, Beaudet A, Schaaf CP. The complex behavioral phenotype of 15q13.3 microdeletion syndrome. Genet Med 2016; 18:1111-1118. [PMID: 26963284 DOI: 10.1038/gim.2016.9] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/09/2016] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Chromosome 15q13.3 represents a hotspot for genomic rearrangements due to repetitive sequences mediating nonallelic homologous recombination. Deletions of 15q13.3 have been identified in the context of multiple neurological and psychiatric disorders, but a prospective clinical and behavioral assessment of affected individuals has not yet been reported. METHODS Eighteen subjects with 15q13.3 microdeletion underwent a series of behavioral assessments, along with clinical history and physical examination, to comprehensively define their behavioral phenotypes. RESULTS Cognitive deficits are the most prevalent feature in 15q13.3 deletion syndrome, with an average nonverbal IQ of 60 among the patients studied. Autism spectrum disorder was highly penetrant, with 31% of patients meeting clinical criteria and exceeding cutoff scores on both ADOS-2 and ADI-R. Affected individuals exhibited a complex pattern of behavioral abnormalities, most notably hyperactivity, attention problems, withdrawal, and externalizing symptoms, as well as impairments in functional communication, leadership, adaptive skills, and activities of daily living. CONCLUSIONS The 15q13.3 deletion syndrome encompasses a heterogeneous behavioral phenotype that poses a major challenge to parents, caregivers, and treating providers. Further work to more clearly delineate genotype-phenotype relationships in 15q13.3 deletions will be important for anticipatory guidance and development of targeted therapies.Genet Med 18 11, 1111-1118.
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Affiliation(s)
- Mark N Ziats
- Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas, USA
| | - Robin P Goin-Kochel
- Autism Center, Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Leandra N Berry
- Autism Center, Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - May Ali
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Jun Ge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Danielle Guffey
- Dan L. Duncan Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Jill A Rosenfeld
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Michael J Gambello
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Varina Wolf
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Lynette S Penney
- Department of Pediatrics, IWK Health Centre, Halifax, Nova Scotia, Canada
| | - Ryan Miller
- Section of Medical Genetics, Department of Pediatrics, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Robert Roger Lebel
- Section of Medical Genetics, Department of Pediatrics, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Jeffrey Kane
- 'Specially for Children Medical Group, Austin, Texas, USA
| | - Kristine Bachman
- Department of Pediatrics, Geisinger Medical Center, Danville, Pennsylvania, USA
| | | | - Gary Clark
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Charles G Minard
- Dan L. Duncan Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Pawel Stankiewicz
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Arthur Beaudet
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Christian P Schaaf
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
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20
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New discoveries in schizophrenia genetics reveal neurobiological pathways: A review of recent findings. Eur J Med Genet 2015; 58:704-14. [PMID: 26493318 DOI: 10.1016/j.ejmg.2015.10.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 10/14/2015] [Accepted: 10/15/2015] [Indexed: 02/08/2023]
Abstract
Schizophrenia research has undergone a recent transformation. By leveraging large sample sizes, genome-wide association studies of common genetic variants have approximately tripled the number of candidate genetic loci. Rare variant studies have identified copy number variants that are schizophrenia risk loci. Among these, the 3q29 microdeletion is now known to be the single largest schizophrenia risk factor. Next-generation sequencing studies are increasingly used for rare variant association testing, and have already facilitated identification of large effect alleles. Collectively, recent findings implicate voltage-gated calcium channel and cytoskeletal pathways in the pathogenesis of schizophrenia. Taken together, these results suggest the possibility of imminent breakthroughs in the molecular understanding of schizophrenia.
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21
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Afshari P, Myles-Worsley M, Cohen OS, Tiobech J, Faraone SV, Byerley W, Middleton FA. Characterization of a Novel Mutation in SLC1A1 Associated with Schizophrenia. MOLECULAR NEUROPSYCHIATRY 2015; 1:125-44. [PMID: 26380821 DOI: 10.1159/000433599] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 05/20/2015] [Indexed: 01/25/2023]
Abstract
We have recently described a hemi-deletion on chromosome 9p24.2 at the SLC1A1 gene locus and its co-segregation with schizophrenia in an extended Palauan pedigree. This finding represents a point of convergence for several pathophysiological models of schizophrenia. The present report sought to characterize the biological consequences of this hemi-deletion. Dual luciferase assays demonstrated that the partially deleted allele (lacking exon 1 and the native promoter) can drive expression of a 5'-truncated SLC1A1 using sequence upstream of exon 2 as a surrogate promoter. However, confocal microscopy and electrophysiological recordings demonstrate that the 5'-truncated SLC1A1 lacks normal membrane localization and glutamate transport ability. To identify downstream consequences of the hemi-deletion, we first used a themed qRT-PCR array to compare expression of 84 GABA and glutamate genes in RNA from peripheral blood leukocytes in deletion carriers (n = 11) versus noncarriers (n = 8) as well as deletion carriers with psychosis (n = 5) versus those without (n = 3). Then, targeted RNA-Seq (TREx) was used to quantify expression of 375 genes associated with neuropsychiatric disorders in HEK293 cells subjected to either knockdown of SLC1A1 or overexpression of full-length or 5'-truncated SLC1A1. Expression changes of several genes strongly implicated in schizophrenia pathophysiology were detected (e.g. SLC1A2, SLC1A3, SLC1A6, SLC7A11, GRIN2A, GRIA1 and DLX1).
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Affiliation(s)
- Parisa Afshari
- Departments of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, N.Y., USA
| | - Marina Myles-Worsley
- Departments of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, N.Y., USA
| | - Ori S Cohen
- Departments of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, N.Y., USA
| | | | - Stephen V Faraone
- Departments of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, N.Y., USA; Departments of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, N.Y., USA
| | - William Byerley
- Department of Psychiatry, University of California at San Francisco, San Francisco, Calif., USA
| | - Frank A Middleton
- Departments of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, N.Y., USA; Departments of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, N.Y., USA; Departments of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, N.Y., USA
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22
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Gillentine MA, Schaaf CP. The human clinical phenotypes of altered CHRNA7 copy number. Biochem Pharmacol 2015; 97:352-362. [PMID: 26095975 DOI: 10.1016/j.bcp.2015.06.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 06/10/2015] [Indexed: 01/03/2023]
Abstract
Copy number variants (CNVs) have been implicated in multiple neuropsychiatric conditions, including autism spectrum disorder (ASD), schizophrenia, and intellectual disability (ID). Chromosome 15q13 is a hotspot for such CNVs due to the presence of low copy repeat (LCR) elements, which facilitate non-allelic homologous recombination (NAHR). Several of these CNVs have been overrepresented in individuals with neuropsychiatric disorders; yet variable expressivity and incomplete penetrance are commonly seen. Dosage sensitivity of the CHRNA7 gene, which encodes for the α7 nicotinic acetylcholine receptor in the human brain, has been proposed to have a major contribution to the observed cognitive and behavioral phenotypes, as it represents the smallest region of overlap to all the 15q13.3 deletions and duplications. Individuals with zero to four copies of CHRNA7 have been reported in the literature, and represent a range of clinical severity, with deletions causing generally more severe and more highly penetrant phenotypes. Potential mechanisms to account for the variable expressivity within each group of 15q13.3 CNVs will be discussed.
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Affiliation(s)
- Madelyn A Gillentine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, United States.
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23
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Takahashi S, Suzuki T, Nakamura-Tomizuka S, Osaki K, Sotome Y, Sagawa T, Uchiyama M. Case history and genome-wide scans for copy number variants in a family with patient having 15q11.1-q11.2 duplication and 22q11.2 deletion, and schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2015; 168B:229-35. [PMID: 25776014 DOI: 10.1002/ajmg.b.32307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 02/24/2015] [Indexed: 11/07/2022]
Abstract
Many studies have indicated that chromosomes 15q11 and 22q11 may be associated with the genetic etiologies of schizophrenia. We have followed an adult schizophrenia case with 15q11.1-q11.2 duplication and 22q11.2 deletion. Here we report his clinical history, and copy number variants (CNVs) identified by microarray and real-time PCR in the patient and his parents. This is the first report describing a detailed phenotype of an adult schizophrenic case with both 15q11 and 22q11 CNVs as revealed by novel and trustworthy technologies. Subjects were a 33-year-old male patient with 15q11 and 22q11 CNVs, and his normal parents. He fulfilled the DSM-IV criteria for schizophrenia at age 18 years. He was also diagnosed with 22q11.2 deletion syndrome by fluorescence in situ hybridization (FISH) at age 18 years. To search for CNVs in more detail, whole-genome array-CGH analyses including ∼ 420,000 probes were carried out in the patient and his parents. For validations of the CNVs detected by array-CGH, real-time PCR analyses of these CNVs were performed. The patient had two disease-specific CNVs, 15q11.1-q11.2 duplication (∼ 2.7 Mb) and 22q11.21 deletion (∼ 2.9 Mb). These two regions are important for the development of schizophrenia, and this patient had shown symptoms of schizophrenia. Thus, the two areas may contain causal genes for schizophrenia.
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Affiliation(s)
- Sakae Takahashi
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
| | - Takahiro Suzuki
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
| | - Sakura Nakamura-Tomizuka
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
| | - Koichi Osaki
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
| | - Yuta Sotome
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
| | - Tomoaki Sagawa
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
| | - Makoto Uchiyama
- Division of Psychiatry, Department of Psychiatry, Nihon University, School of Medicine, Tokyo, Japan
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24
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Haerian BS, Sha'ari HM, Tan HJ, Fong CY, Wong SW, Ong LC, Raymond AA, Tan CT, Mohamed Z. RORA gene rs12912233 and rs880626 polymorphisms and their interaction with SCN1A rs3812718 in the risk of epilepsy: A case–control study in Malaysia. Genomics 2015; 105:229-36. [DOI: 10.1016/j.ygeno.2015.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/24/2015] [Accepted: 02/02/2015] [Indexed: 11/26/2022]
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25
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Clinical and molecular delineation of duplication 9p24.3q21.11 in a patient with psychotic behavior. Gene 2015; 560:124-7. [PMID: 25667990 DOI: 10.1016/j.gene.2015.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 02/01/2015] [Accepted: 02/06/2015] [Indexed: 12/11/2022]
Abstract
This article describes a 19-year-old female with mild facial dysmorphism, asociality, decreased school performance, and psychotic behavior in whom the karyotype showed an extra-chromosomal marker characterized as 9p24.3-9q21.11 duplication by array-CGH. The 69Mbp duplicated segment in this patient includes the critical 9p duplication syndrome region, the GLDC and C90RF72 genes associated with psychotic behavior and other conduct disorders, and a potential locus for autism.
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26
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Beal JC. Case report: Neuronal migration disorder associated with chromosome 15q13.3 duplication in a boy with autism and seizures. J Child Neurol 2014; 29:NP186-8. [PMID: 24282185 DOI: 10.1177/0883073813510356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Neuronal migration disorders are a group of disorders that cause structural brain abnormalities and varying degrees of neurocognitive impairment, resulting from abnormal neuronal migration during brain development. There are several mutations that have been associated with these disorders. Here the case of a 4-year-old autistic boy is presented, who was found to have evidence of a neuronal migration disorder on magnetic resonance imaging (MRI) during a workup for seizures. Genetic testing did not reveal any of the gene mutations known to be associated with neuronal migration disorders but did reveal a microduplication at chromosome 15q13.3, a locus that has been previously associated with autism, cognitive impairment, and seizures. Although the concurrent presence of the genetic and structural abnormalities does not necessarily imply causality, the simultaneous independent occurrence of both conditions is certainly unusual. It is possible that there may be an association between this duplication syndrome and aberrant neuronal migration.
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Affiliation(s)
- Jules C Beal
- Saul R. Korey Department of Neurology and Epilepsy Management Center, Albert Einstein college of Medicine and Montefiore Medical Center, Bronx, NY, USA
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27
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Davis BA, Isles AR. Modelling the genetic contribution to mental illness: a timely end for the psychiatric rodent? Eur J Neurosci 2014; 39:1933-42. [DOI: 10.1111/ejn.12607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 03/11/2014] [Accepted: 04/01/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Brittany A. Davis
- MRC Centre for Neuropsychiatric Genetics and Genomics; Neuroscience and Mental Health Research Institute; Cardiff University; Hadyn Ellis Building Maindy Road Cardiff CF24 4HQ UK
| | - Anthony R. Isles
- MRC Centre for Neuropsychiatric Genetics and Genomics; Neuroscience and Mental Health Research Institute; Cardiff University; Hadyn Ellis Building Maindy Road Cardiff CF24 4HQ UK
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28
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Tan ES, Yong MH, Lim EC, Li ZH, Brett MS, Tan EC. Chromosome 15q11-q13 copy number gain detected by array-CGH in two cases with a maternal methylation pattern. Mol Cytogenet 2014; 7:32. [PMID: 24959201 PMCID: PMC4067100 DOI: 10.1186/1755-8166-7-32] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/11/2014] [Indexed: 11/25/2022] Open
Abstract
Background The 15q11-q13 region contains many low copy repeats and is well known for its genomic instability. Several syndromes are associated with genomic imbalance or copy-number-neutral uniparental disomy. We report on two patients: Patient 1 is a boy with developmental delay and autism; and Patient 2 is a girl with developmental delay, hypotonia and dysmorphism. We performed analyses to delineate their dosage in the 15q region, determine whether the patients’ dosage correlates with phenotypic severity, and whether genes in the amplified regions are significantly associated with identified functional networks. Results For the proximal region of 15q, molecular cytogenetic analysis with Agilent oligonucleotide array showed a copy number of 3 for Patient 1 and a copy number of 4 for Patient 2. Fluorescent in situ hybridization analysis of Patient 2 showed two different populations of cells with different marker chromosomes. Methylation analysis of the amplified region showed that the extra copies of small nuclear ribonucleoprotein polypeptide N gene were of maternal origin. Phenotypic severity did not correlate with the size and dosage of 15q, or whether the amplification is interstitial or in the form of a supernumerary marker. Pathway analysis showed that in Patient 2, the main functional networks that are affected by the genes from the duplicated/triplicated regions are developmental disorder, neurological disease and hereditary disease. Conclusions The 15q11-q13 gains that were found in both patients could explain their phenotypic presentations. This report expands the cohort of patients for which 15q11-q13 duplications are molecularly characterized.
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Affiliation(s)
- Ee-Shien Tan
- Genetics Service, KK Women's & Children's Hospital, 100 Bukit Timah Road 229899 Singapore, Singapore
| | - Min-Hwee Yong
- Cytogenetics Laboratory, KK Women's & Children's Hospital, 100 Bukit Timah Road 229899 Singapore, Singapore
| | - Eileen Cp Lim
- KK Research Laboratory, KK Women's & Children's Hospital, 100 Bukit Timah Road 229899 Singapore, Singapore
| | - Zhi-Hui Li
- Genomax Technologies Pte Ltd, 51 Science Park Road, #04-15 117586 Singapore, Singapore
| | - Maggie Sy Brett
- KK Research Laboratory, KK Women's & Children's Hospital, 100 Bukit Timah Road 229899 Singapore, Singapore
| | - Ene-Choo Tan
- KK Research Laboratory, KK Women's & Children's Hospital, 100 Bukit Timah Road 229899 Singapore, Singapore ; Office of Clinical Sciences, Duke-NUS Graduate Medical School, 8 College Road 169857 Singapore, Singapore
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29
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Rees E, Walters JT, Chambert KD, O'Dushlaine C, Szatkiewicz J, Richards AL, Georgieva L, Mahoney-Davies G, Legge SE, Moran JL, Genovese G, Levinson D, Morris DW, Cormican P, Kendler KS, O'Neill FA, Riley B, Gill M, Corvin A, Sklar P, Hultman C, Pato C, Pato M, Sullivan PF, Gejman PV, McCarroll SA, O'Donovan MC, Owen MJ, Kirov G. CNV analysis in a large schizophrenia sample implicates deletions at 16p12.1 and SLC1A1 and duplications at 1p36.33 and CGNL1. Hum Mol Genet 2014; 23:1669-76. [PMID: 24163246 PMCID: PMC3929090 DOI: 10.1093/hmg/ddt540] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/26/2013] [Accepted: 10/24/2013] [Indexed: 12/29/2022] Open
Abstract
Large and rare copy number variants (CNVs) at several loci have been shown to increase risk for schizophrenia. Aiming to discover novel susceptibility CNV loci, we analyzed 6882 cases and 11 255 controls genotyped on Illumina arrays, most of which have not been used for this purpose before. We identified genes enriched for rare exonic CNVs among cases, and then attempted to replicate the findings in additional 14 568 cases and 15 274 controls. In a combined analysis of all samples, 12 distinct loci were enriched among cases with nominal levels of significance (P < 0.05); however, none would survive correction for multiple testing. These loci include recurrent deletions at 16p12.1, a locus previously associated with neurodevelopmental disorders (P = 0.0084 in the discovery sample and P = 0.023 in the replication sample). Other plausible candidates include non-recurrent deletions at the glutamate transporter gene SLC1A1, a CNV locus recently suggested to be involved in schizophrenia through linkage analysis, and duplications at 1p36.33 and CGNL1. A burden analysis of large (>500 kb), rare CNVs showed a 1.2% excess in cases after excluding known schizophrenia-associated loci, suggesting that additional susceptibility loci exist. However, even larger samples are required for their discovery.
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Affiliation(s)
- Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK,
| | - James T.R. Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK,
| | - Kimberly D. Chambert
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA,
| | - Colm O'Dushlaine
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA,
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA,
| | - Alexander L. Richards
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK,
| | - Lyudmila Georgieva
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK,
| | - Gerwyn Mahoney-Davies
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK,
| | - Sophie E. Legge
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK,
| | - Jennifer L. Moran
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA,
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA,
| | - Douglas Levinson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA,
| | - Derek W. Morris
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland,
| | - Paul Cormican
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland,
| | - Kenneth S. Kendler
- Department of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA,
| | - Francis A. O'Neill
- Department of Psychiatry, Queen's University, BelfastBT71NN, Northern Ireland,
| | - Brien Riley
- Department of Psychiatry and Human Genetics, Virginia Institute of Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, USA,
| | - Michael Gill
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland,
| | - Aiden Corvin
- Department of Psychiatry and Neuropsychiatric Genetics Research Group, Institute of Molecular Medicine, Trinity College Dublin, Dublin 2, Ireland,
| | | | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY, USA,
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,
| | - Carlos Pato
- Department of Psychiatry and Behavioral Science, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033-0121, USA,
| | - Michele Pato
- Department of Psychiatry and Behavioral Science, Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033-0121, USA,
| | - Patrick F. Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA,
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA,
| | - Pablo V. Gejman
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston, IL 60201, USA and
- Department of Psychiatry and Behavioral Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Steven A. McCarroll
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA,
| | - Michael C. O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK,
| | - Michael J. Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK,
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff CF24 4HQ, UK,
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30
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Mulle JG, Pulver AE, McGrath JA, Wolyniec PS, Dodd AF, Cutler DJ, Sebat J, Malhotra D, Nestadt G, Conrad DF, Hurles M, Barnes CP, Ikeda M, Iwata N, Levinson DF, Gejman PV, Sanders AR, Duan J, Mitchell AA, Peter I, Sklar P, O'Dushlaine CT, Grozeva D, O'Donovan MC, Owen MJ, Hultman CM, Kähler AK, Sullivan PF, Kirov G, Warren ST. Reciprocal duplication of the Williams-Beuren syndrome deletion on chromosome 7q11.23 is associated with schizophrenia. Biol Psychiatry 2014; 75:371-7. [PMID: 23871472 PMCID: PMC3838485 DOI: 10.1016/j.biopsych.2013.05.040] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 05/03/2013] [Accepted: 05/07/2013] [Indexed: 01/10/2023]
Abstract
BACKGROUND Several copy number variants (CNVs) have been implicated as susceptibility factors for schizophrenia (SZ). Some of these same CNVs also increase risk for autism spectrum disorders, suggesting an etiologic overlap between these conditions. Recently, de novo duplications of a region on chromosome 7q11.23 were associated with autism spectrum disorders. The reciprocal deletion of this region causes Williams-Beuren syndrome. METHODS We assayed an Ashkenazi Jewish cohort of 554 SZ cases and 1014 controls for genome-wide CNV. An excess of large rare and de novo CNVs were observed, including a 1.4 Mb duplication on chromosome 7q11.23 identified in two unrelated patients. To test whether this 7q11.23 duplication is also associated with SZ, we obtained data for 14,387 SZ cases and 28,139 controls from seven additional studies with high-resolution genome-wide CNV detection. We performed a meta-analysis, correcting for study population of origin, to assess whether the duplication is associated with SZ. RESULTS We found duplications at 7q11.23 in 11 of 14,387 SZ cases with only 1 in 28,139 control subjects (unadjusted odds ratio 21.52, 95% confidence interval: 3.13-922.6, p value 5.5 × 10(-5); adjusted odds ratio 10.8, 95% confidence interval: 1.46-79.62, p value .007). Of three SZ duplication carriers with detailed retrospective data, all showed social anxiety and language delay premorbid to SZ onset, consistent with both human studies and animal models of the 7q11.23 duplication. CONCLUSIONS We have identified a new CNV associated with SZ. Reciprocal duplication of the Williams-Beuren syndrome deletion at chromosome 7q11.23 confers an approximately tenfold increase in risk for SZ.
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Affiliation(s)
- Jennifer Gladys Mulle
- Department of Epidemiology, Rollins School of Public Health, Emory University; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - John A McGrath
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine
| | - Paula S Wolyniec
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine
| | - Anne F Dodd
- Department of Epidemiology, Rollins School of Public Health, Emory University
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases; Department of PsychiatryUniversity of California, San Diego, La Jolla, California; Department of Cellular Molecular and Molecular Medicine, University of California, San Diego, La Jolla, California; Institute for Genomic Medicine, University of California, San Diego, La Jolla, California
| | - Dheeraj Malhotra
- Beyster Center for Genomics of Psychiatric Diseases; Department of PsychiatryUniversity of California, San Diego, La Jolla, California
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine
| | - Donald F Conrad
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge
| | - Matthew Hurles
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Masashi Ikeda
- Fujita Health University School of Medicine, Toyake, Aichi, Japan
| | - Nakao Iwata
- Fujita Health University School of Medicine, Toyake, Aichi, Japan
| | - Douglas F Levinson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California
| | - Pablo V Gejman
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston; Department of Psychiatry and Behavioral Sciences, University of Chicago, Chicago, Illinois
| | - Alan R Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston; Department of Psychiatry and Behavioral Sciences, University of Chicago, Chicago, Illinois
| | - Jubao Duan
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem, Evanston; Department of Psychiatry and Behavioral Sciences, University of Chicago, Chicago, Illinois
| | - Adele A Mitchell
- Department of Forensic Biology, Office of Chief Medical Examiner of the City of New York
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York
| | - Pamela Sklar
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston; Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts; Division of Psychiatric Genomics, Department of Psychiatry, Mount Sinai School of Medicine, New York, New York
| | - Colm T O'Dushlaine
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston; Stanley Center for Psychiatric Research, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Detelina Grozeva
- Department of Psychological Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael C O'Donovan
- Department of Psychological Medicine, Cardiff University, Cardiff, United Kingdom
| | - Michael J Owen
- Department of Psychological Medicine, Cardiff University, Cardiff, United Kingdom
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Anna K Kähler
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina
| | - George Kirov
- Department of Psychological Medicine, Cardiff University, Cardiff, United Kingdom
| | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia; Departments of Biochemistry and Pediatrics, Emory University School of Medicine, Atlanta, Georgia
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Influencing the Social Group. EPIGENETIC SHAPING OF SOCIOSEXUAL INTERACTIONS - FROM PLANTS TO HUMANS 2014; 86:107-34. [DOI: 10.1016/b978-0-12-800222-3.00006-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Warburton D, Ronemus M, Kline J, Jobanputra V, Williams I, Anyane-Yeboa K, Chung W, Yu L, Wong N, Awad D, Yu CY, Leotta A, Kendall J, Yamrom B, Lee YH, Wigler M, Levy D. The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease. Hum Genet 2014; 133:11-27. [PMID: 23979609 PMCID: PMC3880624 DOI: 10.1007/s00439-013-1353-9] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/21/2013] [Indexed: 12/25/2022]
Abstract
Congenital heart disease (CHD) is the most common congenital malformation, with evidence of a strong genetic component. We analyzed data from 223 consecutively ascertained families, each consisting of at least one child affected by a conotruncal defect (CNT) or hypoplastic left heart disease (HLHS) and both parents. The NimbleGen HD2-2.1 comparative genomic hybridization platform was used to identify de novo and rare inherited copy number variants (CNVs). Excluding 10 cases with 22q11.2 DiGeorge deletions, we validated de novo CNVs in 8 % of 148 probands with CNTs, 12.7 % of 71 probands with HLHS and none in 4 probands with both. Only 2 % of control families showed a de novo CNV. We also identified a group of ultra-rare inherited CNVs that occurred de novo in our sample, contained a candidate gene for CHD, recurred in our sample or were present in an affected sibling. We confirmed the contribution to CHD of copy number changes in genes such as GATA4 and NODAL and identified several genes in novel recurrent CNVs that may point to novel CHD candidate loci. We also found CNVs previously associated with highly variable phenotypes and reduced penetrance, such as dup 1q21.1, dup 16p13.11, dup 15q11.2-13, dup 22q11.2, and del 2q23.1. We found that the presence of extra-cardiac anomalies was not related to the frequency of CNVs, and that there was no significant difference in CNV frequency or specificity between the probands with CNT and HLHS. In agreement with other series, we identified likely causal CNVs in 5.6 % of our total sample, half of which were de novo.
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Affiliation(s)
- Dorothy Warburton
- Departments of Pediatrics and Genetics and Development, Columbia University, New York, NY, USA,
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Dosage-sensitivity of imprinted genes expressed in the brain: 15q11-q13 and neuropsychiatric illness. Biochem Soc Trans 2013; 41:721-6. [PMID: 23697931 DOI: 10.1042/bst20130008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Imprinted genes, those genes subject to parent-of-origin-specific epigenetic marking resulting in monoallelic parent-specific expression, are sensitive to subtle changes in expression dosage. This has been illustrated in a number of experimental models and the fact that both decreased (or complete loss) and increased imprinted gene expression can lead to human diseases. In the present paper, we discuss the consequence of increased dosage of imprinted genes for brain function, focusing on the PWS (Prader-Willi syndrome) locus on human chromosome 15q11-q13 and how predicted increases in dosage of maternally expressed imprinted genes from this interval are associated with a higher risk of developing psychotic illness. The evidence for this comes from individuals with PWS itself and also non-syndromic cases of psychosis in carriers of a maternally derived copy number variant spanning this locus. Of the known imprinted genes in this region, the prime candidate is maternally expressed UBE3A, which encodes E6-AP (E6-associated protein) ubiquitin ligase and has an influence on a number of important neurotransmitter systems. Furthermore, these findings point to the fact that brain function is exquisitely sensitive to both decreases and increases in the expression of imprinted genes.
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Amiet C, Gourfinkel-An I, Laurent C, Bodeau N, Génin B, Leguern E, Tordjman S, Cohen D. Does epilepsy in multiplex autism pedigrees define a different subgroup in terms of clinical characteristics and genetic risk? Mol Autism 2013; 4:47. [PMID: 24289166 PMCID: PMC4176303 DOI: 10.1186/2040-2392-4-47] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 09/13/2013] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Autism spectrum disorders (ASD) and epilepsy frequently occur together. Prevalence rates are variable, and have been attributed to age, gender, comorbidity, subtype of pervasive developmental disorder (PDD) and risk factors. Recent studies have suggested disparate clinical and genetic settings depending on simplex or multiplex autism. The aim of this study was to assess: 1) the prevalence of epilepsy in multiplex autism and its association with genetic and non-genetic risk factors of major effect, intellectual disability and gender; and 2) whether autism and epilepsy cosegregate within multiplex autism families. METHODS We extracted from the Autism Genetic Resource Exchange (AGRE) database (n = 3,818 children from 1,264 families) all families with relevant medical data (n = 664 children from 290 families). The sample included 478 children with ASD and 186 siblings without ASD. We analyzed the following variables: seizures, genetic and non-genetic risk factors, gender, and cognitive functioning as assessed by Raven's Colored Progressive Matrices (RCPM) and Vineland Adaptive Behavior Scales (VABS). RESULTS The prevalence of epilepsy was 12.8% in cases with ASD and 2.2% in siblings without ASD (P <10-5). With each RCPM or VABS measure, the risk of epilepsy in multiplex autism was significantly associated with intellectual disability, but not with gender. Identified risk factors (genetic or non-genetic) of autism tended to be significantly associated with epilepsy (P = 0.052). When children with prematurity, pre- or perinatal insult, or cerebral palsy were excluded, a genetic risk factor was reported for 6/59 (10.2%) of children with epilepsy and 12/395 (3.0%) of children without epilepsy (P = 0.002). Finally, using a permutation test, there was significant evidence that the epilepsy phenotype co-segregated within families (P <10-4). CONCLUSIONS Epilepsy in multiplex autism may define a different subgroup in terms of clinical characteristics and genetic risk.
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Affiliation(s)
| | | | | | | | | | | | | | - David Cohen
- Department of Child and Adolescent Psychiatry, Assistance Publique-Hôpitaux de Paris (AP-HP), Groupe Hospitalier Pitié-Salpêtrière, Université Pierre et Marie Curie, 47 bd de l'Hôpital, 75013 Paris, France.
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Zhu L, Wang X, Li XL, Towers A, Cao X, Wang P, Bowman R, Yang H, Goldstein J, Li YJ, Jiang YH. Epigenetic dysregulation of SHANK3 in brain tissues from individuals with autism spectrum disorders. Hum Mol Genet 2013; 23:1563-78. [PMID: 24186872 DOI: 10.1093/hmg/ddt547] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The molecular basis for the majority of cases of autism spectrum disorders (ASD) remains unknown. We tested the hypothesis that ASD have an epigenetic cause by performing DNA methylation profiling of five CpG islands (CGI-1 to CGI-5) in the SHANK3 gene in postmortem brain tissues from 54 ASD patients and 43 controls. We found significantly increased overall DNA methylation (epimutation) in three intragenic CGIs (CGI-2, CGI-3 and CGI-4). The increased methylation was clustered in the CGI-2 and CGI-4 in ∼15% of ASD brain tissues. SHANK3 has an extensive array of mRNA splice variants resulting from combinations of five intragenic promoters and alternative splicing of coding exons. Altered expression and alternative splicing of SHANK3 isoforms were observed in brain tissues with increased methylation of SHANK3 CGIs in ASD brain tissues. A DNA methylation inhibitor modified the methylation of CGIs and altered the isoform-specific expression of SHANK3 in cultured cells. This study is the first to find altered methylation patterns in SHANK3 in ASD brain samples. Our finding provides evidence to support an alternative approach to investigating the molecular basis of ASD. The ability to alter the epigenetic modification and expression of SHANK3 by environmental factors suggests that SHANK3 may be a valuable biomarker for dissecting the role of gene and environment interaction in the etiology of ASD.
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Coppola A, Ruosi P, Santulli L, Striano S, Zara F, Striano P, Sisodiya SM. Neurological features and long-term follow-up in 15q11.2-13.1 duplication. Eur J Med Genet 2013; 56:614-8. [PMID: 24075935 DOI: 10.1016/j.ejmg.2013.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/01/2013] [Indexed: 11/19/2022]
Abstract
Various rearrangements occurring in the 15q11-q13 region have been reported in association with epilepsy. Deletions are the most frequent and are associated with Angelman or Prader-Willi syndrome. Duplications feature complex phenotypes including developmental delay, autistic-like behaviour and seizures. Among these, trisomy has been described as a milder phenotype compared to tetrasomy, but reports are rare and the phenotype is not yet defined. Here we report two adult cases with a 15q11.2-13.1 duplication showing a complex and similar epileptic phenotype.
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Affiliation(s)
- Antonietta Coppola
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK; Epilepsy Society, Chesham Lane, Chalfont St Peter, Bucks, UK.
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Città S, Buono S, Greco D, Barone C, Alfei E, Bulgheroni S, Usilla A, Pantaleoni C, Romano C. 3q29 microdeletion syndrome: Cognitive and behavioral phenotype in four patients. Am J Med Genet A 2013; 161A:3018-22. [DOI: 10.1002/ajmg.a.36142] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 06/24/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Santina Città
- Unit of Psychology; IRCCS Associazione Oasi Maria Santissima; Troina Italy
| | - Serafino Buono
- Unit of Psychology; IRCCS Associazione Oasi Maria Santissima; Troina Italy
| | - Donatella Greco
- Unit of Pediatrics and Medical Genetics; IRCCS Associazione Oasi Maria Santissima; Troina Italy
| | - Concetta Barone
- Unit of Pediatrics and Medical Genetics; IRCCS Associazione Oasi Maria Santissima; Troina Italy
| | - Enrico Alfei
- Fondazione IRCCS Istituto Neurologico Carlo Besta; Milano Italy
| | - Sara Bulgheroni
- Fondazione IRCCS Istituto Neurologico Carlo Besta; Milano Italy
| | - Arianna Usilla
- Fondazione IRCCS Istituto Neurologico Carlo Besta; Milano Italy
| | | | - Corrado Romano
- Unit of Pediatrics and Medical Genetics; IRCCS Associazione Oasi Maria Santissima; Troina Italy
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Costain G, Lionel AC, Merico D, Forsythe P, Russell K, Lowther C, Yuen T, Husted J, Stavropoulos DJ, Speevak M, Chow EWC, Marshall CR, Scherer SW, Bassett AS. Pathogenic rare copy number variants in community-based schizophrenia suggest a potential role for clinical microarrays. Hum Mol Genet 2013; 22:4485-501. [PMID: 23813976 DOI: 10.1093/hmg/ddt297] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Individually rare, large copy number variants (CNVs) contribute to genetic vulnerability for schizophrenia. Unresolved questions remain, however, regarding the anticipated yield of clinical microarray testing in schizophrenia. Using high-resolution genome-wide microarrays and rigorous methods, we investigated rare CNVs in a prospectively recruited community-based cohort of 459 unrelated adults with schizophrenia and estimated the minimum prevalence of clinically significant CNVs that would be detectable on a clinical microarray. A blinded review by two independent clinical cytogenetic laboratory directors of all large (>500 kb) rare CNVs in cases and well-matched controls showed that those deemed to be clinically significant were highly enriched in schizophrenia (16.4-fold increase, P < 0.0001). In a single community catchment area, the prevalence of individuals with these CNVs was 8.1%. Rare 1.7 Mb CNVs at 2q13 were found to be significantly associated with schizophrenia for the first time, compared with the prevalence in 23 838 population-based controls (42.9-fold increase, P = 0.0002). Additional novel findings that will facilitate the future clinical interpretation of smaller CNVs in schizophrenia include: (i) a greater proportion of individuals with two or more rare exonic CNVs >10 kb in size (1.5-fold increase, P = 0.0109) in schizophrenia; (ii) the systematic discovery of new candidate genes for schizophrenia; and, (iii) functional gene enrichment mapping highlighting a differential impact in schizophrenia of rare exonic deletions involving diverse functions, including neurodevelopmental and synaptic processes (4.7-fold increase, P = 0.0060). These findings suggest consideration of a potential role for clinical microarray testing in schizophrenia, as is now the suggested standard of care for related developmental disorders like autism.
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Affiliation(s)
- Gregory Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada M5S 2S1
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Béna F, Bruno DL, Eriksson M, van Ravenswaaij-Arts C, Stark Z, Dijkhuizen T, Gerkes E, Gimelli S, Ganesamoorthy D, Thuresson AC, Labalme A, Till M, Bilan F, Pasquier L, Kitzis A, Dubourgm C, Rossi M, Bottani A, Gagnebin M, Sanlaville D, Gilbert-Dussardier B, Guipponi M, van Haeringen A, Kriek M, Ruivenkamp C, Antonarakis SE, Anderlid BM, Slater HR, Schoumans J. Molecular and clinical characterization of 25 individuals with exonic deletions of NRXN1 and comprehensive review of the literature. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:388-403. [PMID: 23533028 DOI: 10.1002/ajmg.b.32148] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 02/22/2013] [Indexed: 11/12/2022]
Abstract
This study aimed to elucidate the observed variable phenotypic expressivity associated with NRXN1 (Neurexin 1) haploinsufficiency by analyses of the largest cohort of patients with NRXN1 exonic deletions described to date and by comprehensively reviewing all comparable copy number variants in all disease cohorts that have been published in the peer reviewed literature (30 separate papers in all). Assessment of the clinical details in 25 previously undescribed individuals with NRXN1 exonic deletions demonstrated recurrent phenotypic features consisting of moderate to severe intellectual disability (91%), severe language delay (81%), autism spectrum disorder (65%), seizures (43%), and hypotonia (38%). These showed considerable overlap with previously reported NRXN1-deletion associated phenotypes in terms of both spectrum and frequency. However, we did not find evidence for an association between deletions involving the β-isoform of neurexin-1 and increased head size, as was recently published in four cases with a deletion involving the C-terminus of NRXN1. We identified additional rare copy number variants in 20% of cases. This study supports a pathogenic role for heterozygous exonic deletions of NRXN1 in neurodevelopmental disorders. The additional rare copy number variants identified may act as possible phenotypic modifiers as suggested in a recent digenic model of neurodevelopmental disorders.
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Affiliation(s)
- Frédérique Béna
- Service of Genetic Medicine, Geneva University Hospital, Geneva, Switzerland
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Shin R, Kobayashi K, Hagihara H, Kogan JH, Miyake S, Tajinda K, Walton NM, Gross AK, Heusner CL, Chen Q, Tamura K, Miyakawa T, Matsumoto M. The immature dentate gyrus represents a shared phenotype of mouse models of epilepsy and psychiatric disease. Bipolar Disord 2013; 15:405-21. [PMID: 23560889 PMCID: PMC3752967 DOI: 10.1111/bdi.12064] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/13/2013] [Indexed: 01/08/2023]
Abstract
OBJECTIVES There is accumulating evidence to suggest psychiatric disorders, such as bipolar disorder and schizophrenia, share common etiologies, pathophysiologies, genetics, and drug responses with many of the epilepsies. Here, we explored overlaps in cellular/molecular, electrophysiological, and behavioral phenotypes between putative mouse models of bipolar disorder/schizophrenia and epilepsy. We tested the hypothesis that an immature dentate gyrus (iDG), whose association with psychosis in patients has recently been reported, represents a common phenotype of both diseases. METHODS Behaviors of calcium/calmodulin-dependent protein kinase II alpha (α-CaMKII) heterozygous knock-out (KO) mice, which are a representative bipolar disorder/schizophrenia model displaying iDG, and pilocarpine-treated mice, which are a representative epilepsy model, were tested followed by quantitative polymerase chain reaction (qPCR)/immunohistochemistry for mRNA/protein expression associated with an iDG phenotype. In vitro electrophysiology of dentate gyrus granule cells (DG GCs) was examined in pilocarpine-treated epileptic mice. RESULTS The two disease models demonstrated similar behavioral deficits, such as hyperactivity, poor working memory performance, and social withdrawal. Significant reductions in mRNA expression and immunoreactivity of the mature neuronal marker calbindin and concomitant increases in mRNA expression and immunoreactivity of the immature neuronal marker calretinin represent iDG signatures that are present in both mice models. Electrophysiologically, we have confirmed that DG GCs from pilocarpine-treated mice represent an immature state. A significant decrease in hippocampal α-CaMKII protein levels was also found in both models. CONCLUSIONS Our data have shown iDG signatures from mouse models of both bipolar disorder/schizophrenia and epilepsy. The evidence suggests that the iDG may, in part, be responsible for the abnormal behavioral phenotype, and that the underlying pathophysiologies in epilepsy and bipolar disorder/schizophrenia are strikingly similar.
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Affiliation(s)
- Rick Shin
- CNS, Astellas Research Institute of America LLCSkokie, IL, USA
| | - Katsunori Kobayashi
- Department of Pharmacology, Graduate School of Medicine, Nippon Medical SchoolTokyo, Japan,Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
| | - Hideo Hagihara
- Institute for Comprehensive Medical Science, Fujita Health UniversityAichi, Japan
| | - Jeffrey H Kogan
- CNS, Astellas Research Institute of America LLCSkokie, IL, USA
| | - Shinichi Miyake
- CNS, Astellas Research Institute of America LLCSkokie, IL, USA
| | | | - Noah M Walton
- CNS, Astellas Research Institute of America LLCSkokie, IL, USA
| | - Adam K Gross
- CNS, Astellas Research Institute of America LLCSkokie, IL, USA
| | | | - Qian Chen
- CNS, Astellas Research Institute of America LLCSkokie, IL, USA
| | - Kouichi Tamura
- CNS, Astellas Research Institute of America LLCSkokie, IL, USA
| | - Tsuyoshi Miyakawa
- Institute for Comprehensive Medical Science, Fujita Health UniversityAichi, Japan
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Marini C, Cecconi A, Contini E, Pantaleo M, Metitieri T, Guarducci S, Giglio S, Guerrini R, Genuardi M. Clinical and genetic study of a family with a paternally inherited 15q11-q13 duplication. Am J Med Genet A 2013; 161A:1459-64. [PMID: 23633446 DOI: 10.1002/ajmg.a.35907] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/25/2013] [Indexed: 01/19/2023]
Abstract
Interstitial chromosome 15q11-q13 duplications are associated with developmental delay, behavioral problems and additional manifestations, including epilepsy. In most affected individuals the duplicated chromosome is maternally derived, whereas paternal inheritance is more often associated with a normal phenotype. Seizures have not been described in patients with paternal dup 15q11-q13. We describe a family with five individuals in three generations with a paternally-inherited 15q11-q13 duplication, four of whom exhibited abnormal phenotypic characteristics, including seizures. The 18-year-old female proband presented with moderate intellectual disability, obesity, and epilepsy. Her brother manifested learning disability and behavioral problems. They both inherited the 15q11-q13 dup from their father who had a normal phenotype. Their paternal uncle and grandfather also had the duplication and were reported to have had seizures. Array-CGH and MLPA analyses showed that the duplication included the TUBGCP5, CYFIP1, MKRN3, MAGEL2, NDN, SNRPN, UBE3A, ATP10A, GABRB3, GABRA5, GABRG3, and OCA2 genes. This report provides evidence for intrafamilial phenotypic variability of paternal dup 15q11-q13, ranging from normal to intellectual disability and seizures, and potentially expanding the phenotype of paternal 15q11-q13 interstitial duplications.
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Affiliation(s)
- Carla Marini
- Pediatric Neurology Unit and Laboratories, Pediatric Hospital A. Meyer, Department of Clinical Pathophysiology, University of Florence, Florence, Italy
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Dabell MP, Rosenfeld JA, Bader P, Escobar LF, El-Khechen D, Vallee SE, Dinulos MBP, Curry C, Fisher J, Tervo R, Hannibal MC, Siefkas K, Wyatt PR, Hughes L, Smith R, Ellingwood S, Lacassie Y, Stroud T, Farrell SA, Sanchez-Lara PA, Randolph LM, Niyazov D, Stevens CA, Schoonveld C, Skidmore D, MacKay S, Miles JH, Moodley M, Huillet A, Neill NJ, Ellison JW, Ballif BC, Shaffer LG. Investigation ofNRXN1deletions: Clinical and molecular characterization. Am J Med Genet A 2013; 161A:717-31. [DOI: 10.1002/ajmg.a.35780] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 10/29/2012] [Indexed: 01/01/2023]
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Beaudet AL. The utility of chromosomal microarray analysis in developmental and behavioral pediatrics. Child Dev 2013; 84:121-32. [PMID: 23311723 DOI: 10.1111/cdev.12050] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chromosomal microarray analysis (CMA) has emerged as a powerful new tool to identify genomic abnormalities associated with a wide range of developmental disabilities including congenital malformations, cognitive impairment, and behavioral abnormalities. CMA includes array comparative genomic hybridization (CGH) and single nucleotide polymorphism (SNP) arrays, both of which are useful for detection of genomic copy number variants (CNV) such as microdeletions and microduplications. The frequency of disease-causing CNVs is highest (20%-25%) in children with moderate to severe intellectual disability accompanied by malformations or dysmorphic features. Disease-causing CNVs are found in 5%-10% of cases of autism, being more frequent in severe phenotypes. CMA has replaced Giemsa-banded karyotype as the first-tier test for genetic evaluation of children with developmental and behavioral disabilities.
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Coughlin CR, Scharer GH, Shaikh TH. Clinical impact of copy number variation analysis using high-resolution microarray technologies: advantages, limitations and concerns. Genome Med 2012; 4:80. [PMID: 23114084 PMCID: PMC3580449 DOI: 10.1186/gm381] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Copy number variation (CNV) analysis has had a major impact on the field of medical genetics, providing a mechanism to identify disease-causing genomic alterations in an unprecedented number of diseases and phenotypes. CNV analysis is now routinely used in the clinical diagnostic laboratory, and has led to a significant increase in the detection of chromosomal abnormalities. These findings are used for prenatal decision making, clinical management and genetic counseling. Although a powerful tool to identify genomic alterations, CNV analysis may also result in the detection of genomic alterations that have unknown clinical significance or reveal unintended information. This highlights the importance of informed consent and genetic counseling for clinical CNV analysis. This review examines the advantages and limitations of CNV discovery in the clinical diagnostic laboratory, as well as the impact on the clinician and family.
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Affiliation(s)
- Curtis R Coughlin
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045, USA
| | - Gunter H Scharer
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045, USA ; Intellectual and Developmental Disabilities Research Center, University of Colorado Denver, Aurora, CO 80045, USA
| | - Tamim H Shaikh
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado Denver, Aurora, CO 80045, USA ; Intellectual and Developmental Disabilities Research Center, University of Colorado Denver, Aurora, CO 80045, USA
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Is genomics bad for you? Behav Brain Sci 2012; 35:364-5. [PMID: 23095385 DOI: 10.1017/s0140525x12000994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The plasticity of the genome complicates genetic causation but should be investigated from a functional perspective. Specific adaptive hypotheses are referenced in the target article, but it is also necessary to explain how the integrity of the genome is maintained despite processes that tend towards its diversification and degradation. These include the accumulation of deleterious changes and intragenomic conflict.
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15q11.2 proximal imbalances associated with a diverse array of neuropsychiatric disorders and mild dysmorphic features. J Dev Behav Pediatr 2012; 33:570-6. [PMID: 22922608 DOI: 10.1097/dbp.0b013e31826052ae] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Deletion within the proximal region of chromosome 15q11.2 between breakpoints 1 and 2 (BP1-BP2) has been proposed to be a risk factor for intellectual disability, seizure, and schizophrenia. However, the clinical significance of its reciprocal duplication is not clearly defined yet. We evaluated 1654 consecutive pediatric patients with various neurological disorders by high-resolution microarray-based comparative genomic hybridization. We identified 21 patients carrying 15q11.2 BP1-BP2 deletion and 12 patients carrying 15q11.2 BP1-BP2 duplication in this cohort, which represent 1.27% (21/1,654) and 0.7% (12/1,654) of the patients analyzed, respectively. Approximately 87.5% of the patients carrying the deletion and 80% of the patients carrying the duplication have developmental delay or intellectual disability. Other recurrent clinical features in these patients include mild dysmorphic features, autistic spectrum disorders, and epilepsy. Our observations provide further evidence in favor of a strong association of 15q11.2 BP1-BP2 deletion with a variety of neuropsychiatric disorders. The diversity of clinical findings in these patients expands the phe-notypic spectrum of individuals carrying the deletion. In addition, possible etiological effects of 15q11.2 BP1-BP2 duplication in neuropsychiatric disorders are proposed.
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Liao HM, Chao YL, Huang AL, Cheng MC, Chen YJ, Lee KF, Fang JS, Hsu CH, Chen CH. Identification and characterization of three inherited genomic copy number variations associated with familial schizophrenia. Schizophr Res 2012; 139:229-36. [PMID: 22682706 DOI: 10.1016/j.schres.2012.05.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 04/26/2012] [Accepted: 05/15/2012] [Indexed: 12/23/2022]
Abstract
Schizophrenia is a complex mental disorder with high degree of genetic influence in its etiology. Several recent studies revealed that copy number variations (CNVs) of genomic DNA contributed significantly to the genetic architecture of sporadic schizophrenia. This study aimed to investigate whether CNVs also contribute to the familial forms of schizophrenia. Using array-based comparative genomic hybridization technology, we searched for pathogenic CNV associated with schizophrenia in a sample of 60 index cases from multiplex schizophrenia families. We detected three inherited CNVs that were associated with schizophrenia in three families, including a microdeletion of ~4.4Mb at chromosome 6q12-q13, a microduplication of ~1Mb at chromosome 18q12.3, and an interstitial duplication of ~5Mb at chromosome 15q11.2-q13.1. Our data indicate that CNVs contribute to the genetic underpinnings of the familial forms of schizophrenia as well as of the sporadic form. As 15q11-13 duplication is a well-known recurrent CNV associated with autism in the literature, the detection of the 15q11.2-q13.1 duplication in our schizophrenia patients provides additional support to other studies reporting that schizophrenia is part of the clinical spectrum of 15q11-q13 duplication syndrome.
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Affiliation(s)
- Hsiao-Mei Liao
- Institute of Biotechnology and Graduate Program of Biotechnology in Medicine, National Tsing-Hua University, Hsinchu, Taiwan
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Vargas H, Beldia G, Korosh W, Sudhalter V, Iqbal A, Sanchez-Lacay JA, Velinov M. A 4.5 Mb terminal deletion of chromosome 12p helps further define a psychosis-associated locus. Eur J Med Genet 2012; 55:573-6. [PMID: 22669037 DOI: 10.1016/j.ejmg.2012.04.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 04/13/2012] [Indexed: 01/01/2023]
Abstract
A 12 year-old girl presented with cognitive disability and dysmorphic features. Chromosome microarray analysis revealed a de novo, approximately 4.5 Mb terminal deletion of the short arm of chromosome 12 at 12p13.33 region: chr12:100712-4607067. At 13 years this patient developed psychotic manifestations and was admitted to a psychiatric department for treatment. She started hearing voices, talking to herself and laughing without reason. We have previously reported a male individual with psychotic manifestations and a larger (6.2 Mb) terminal deletion in the same chromosomal region. The present case along with previous reports, define a 2 Mb region on chromosome 12p, where a psychosis-associated gene may be located. Included in this psychosis-associated area are 18 OMIM listed genes.
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