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Hong H, Wang Y, Menard M, Buckley J, Zhou L, Volpicelli-Daley L, Standaert D, Qin H, Benveniste E. Suppression of the JAK/STAT Pathway Inhibits Neuroinflammation in the Line 61-PFF Mouse Model of Parkinson's Disease. RESEARCH SQUARE 2024:rs.3.rs-4307273. [PMID: 38766241 PMCID: PMC11100885 DOI: 10.21203/rs.3.rs-4307273/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Parkinson's disease (PD) is characterized by neuroinflammation, progressive loss of dopaminergic neurons, and accumulation of a-synuclein (a-Syn) into insoluble aggregates called Lewy pathology. The Line 61 a-Syn mouse is an established preclinical model of PD; Thy-1 is used to promote human a-Syn expression, and features of sporadic PD develop at 9-18 months of age. To accelerate the PD phenotypes, we injected sonicated human a-Syn preformed fibrils (PFFs) into the striatum, which produced phospho-Syn (p-a-Syn) inclusions in the substantia nigra pars compacta and significantly increased MHC Class II-positive immune cells. Additionally, there was enhanced infiltration and activation of innate and adaptive immune cells in the midbrain. We then used this new model, Line 61-PFF, to investigate the effect of inhibiting the JAK/STAT signaling pathway, which is critical for regulation of innate and adaptive immune responses. After administration of the JAK1/2 inhibitor AZD1480, immunofluorescence staining showed a significant decrease in p-a-Syn inclusions and MHC Class II expression. Flow cytometry showed reduced infiltration of CD4+ T-cells, CD8+ T-cells, CD19+ B-cells, dendritic cells, macrophages, and endogenous microglia into the midbrain. Importantly, single-cell RNA-Sequencing analysis of CD45+ cells from the midbrain identified 9 microglia clusters, 5 monocyte/macrophage (MM) clusters, and 5 T-cell (T) clusters, in which potentially pathogenic MM4 and T3 clusters were associated with neuroinflammatory responses in Line 61-PFF mice. AZD1480 treatment reduced cell numbers and cluster-specific expression of the antigen-presentation genes H2-Eb1, H2-Aa, H2-Ab1, and Cd74 in the MM4 cluster and proinflammatory genes such as Tnf, Il1b, C1qa, and C1qc in the T3 cluster. Together, these results indicate that inhibiting the JAK/STAT pathway suppresses the activation and infiltration of innate and adaptive cells, reducing neuroinflammation in the Line 61-PFF mouse model.
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Wu J, Wu T, Xie X, Niu Q, Zhao Z, Zhu B, Chen Y, Zhang L, Gao X, Niu X, Gao H, Li J, Xu L. Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle. Foods 2023; 12:3986. [PMID: 37959106 PMCID: PMC10647706 DOI: 10.3390/foods12213986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Meat quality is an economically important trait for global food production. Copy number variations (CNVs) have been previously implicated in elucidating the genetic basis of complex traits. In this article, we detected a total of 112,198 CNVs and 10,102 CNV regions (CNVRs) based on the Bovine HD SNP array. Next, we performed a CNV-based genome-wide association analysis (GWAS) of six meat quality traits and identified 12 significant CNV segments corresponding to eight candidate genes, including PCDH15, CSMD3, etc. Using region-based association analysis, we further identified six CNV segments relevant to meat quality in beef cattle. Among these, TRIM77 and TRIM64 within CNVR4 on BTA29 were detected as candidate genes for backfat thickness (BFT). Notably, we identified a 34 kb duplication for meat color (MC) which was supported by read-depth signals, and this duplication was embedded within the keratin gene family including KRT4, KRT78, and KRT79. Our findings will help to dissect the genetic architecture of meat quality traits from the aspects of CNVs, and subsequently improve the selection process in breeding programs.
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Affiliation(s)
- Jiayuan Wu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Tianyi Wu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xueyuan Xie
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Qunhao Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Zhida Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Bo Zhu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Yan Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Lupei Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xue Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Xiaoyan Niu
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Jinzhong 030801, China
| | - Huijiang Gao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Junya Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
| | - Lingyang Xu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (J.W.); (B.Z.); (L.Z.); (J.L.)
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Xi K, Cai SQ, Yan HF, Tian Y, Cai J, Yang XM, Wang JM, Xing GG. CSMD3 Deficiency Leads to Motor Impairments and Autism-Like Behaviors via Dysfunction of Cerebellar Purkinje Cells in Mice. J Neurosci 2023; 43:3949-3969. [PMID: 37037606 PMCID: PMC10219040 DOI: 10.1523/jneurosci.1835-22.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 03/18/2023] [Accepted: 04/05/2023] [Indexed: 04/12/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with highly heritable heterogeneity. Mutations of CUB and sushi multiple domains 3 (CSMD3) gene have been reported in individuals with ASD. However, the underlying mechanisms of CSMD3 for the onset of ASD remain unexplored. Here, using male CSMD3 knock-out (CSMD3 -/-) mice, we found that genetic deletion of CSMD3 produced core autistic-like symptoms (social interaction deficits, restricted interests, and repetitive and stereotyped behaviors) and motor dysfunction in mice, indicating that the CSMD3 gene can be considered as a candidate for ASD. Moreover, we discovered that the ablation of CSMD3 in mice led to abnormal cerebellar Purkinje cell (PC) morphology in Crus I/II lobules, including aberrant developmental dendritogenesis and spinogenesis of PCs. Furthermore, combining in vivo fiber photometry calcium imaging and ex vivo electrophysiological recordings, we showed that the CSMD3 -/- mice exhibited an increased neuronal activity (calcium fluorescence signals) in PCs of Crus I/II lobules in response to movement activity, as well as an enhanced intrinsic excitability of PCs and an increase of excitatory rather than inhibitory synaptic input to the PCs, and an impaired long-term depression at the parallel fiber-PC synapse. These results suggest that CSMD3 plays an important role in the development of cerebellar PCs. Loss of CSMD3 causes abnormal PC morphology and dysfunction in the cerebellum, which may underlie the pathogenesis of motor deficits and core autistic-like symptoms in CSMD3 -/- mice. Our findings provide novel insight into the pathophysiological mechanisms by which CSMD3 mutations cause impairments in cerebellar function that may contribute to ASD.SIGNIFICANCE STATEMENT Autism spectrum disorder (ASD) is a neurodevelopmental disorder with highly heritable heterogeneity. Advances in genomic analysis have contributed to numerous candidate genes for the risk of ASD. Recently, a novel giant gene CSMD3 encoding a protein with CUB and sushi multiple domains (CSMDs) has been identified as a candidate gene for ASD. However, the underlying mechanisms of CSMD3 for the onset of ASD remain largely unknown. Here, we unravel that loss of CSMD3 results in abnormal morphology, increased intrinsic excitabilities, and impaired synaptic plasticity in cerebellar PCs, subsequently leading to motor deficits and ASD-like behaviors in mice. These results provide novel insight into the pathophysiological mechanisms by which CSMD3 mutations cause impairments in cerebellar function that may contribute to ASD.
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Affiliation(s)
- Ke Xi
- Neuroscience Research Institute, Peking University, Beijing 100191, People's Republic of China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University, Beijing 100191, People's Republic of China
- Health Science Center, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of China, Beijing 100191, People's Republic of China
| | - Si-Qing Cai
- Neuroscience Research Institute, Peking University, Beijing 100191, People's Republic of China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University, Beijing 100191, People's Republic of China
- Health Science Center, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of China, Beijing 100191, People's Republic of China
| | - Hui-Fang Yan
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, People's Republic of China
| | - Yue Tian
- Neuroscience Research Institute, Peking University, Beijing 100191, People's Republic of China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University, Beijing 100191, People's Republic of China
- Health Science Center, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of China, Beijing 100191, People's Republic of China
| | - Jie Cai
- Neuroscience Research Institute, Peking University, Beijing 100191, People's Republic of China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University, Beijing 100191, People's Republic of China
- Health Science Center, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of China, Beijing 100191, People's Republic of China
| | - Xiao-Mei Yang
- Department of Human Anatomy and Embryology, School of Basic Medical Sciences, Peking University, Beijing 100191, People's Republic of China
| | - Jing-Min Wang
- Department of Pediatrics, Peking University First Hospital, Beijing 100034, People's Republic of China
| | - Guo-Gang Xing
- Neuroscience Research Institute, Peking University, Beijing 100191, People's Republic of China
- Department of Neurobiology, School of Basic Medical Sciences, Peking University, Beijing 100191, People's Republic of China
- Health Science Center, Key Laboratory for Neuroscience, Ministry of Education of China and National Health Commission of China, Beijing 100191, People's Republic of China
- Second Affiliated Hospital of Xinxiang Medical University, Henan 453002, People's Republic of China
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Sennsfelder L, Guilly S, Leruste S, Hoareau L, Léocadie W, Beuvain P, Nekaa M, Bagard M, Robin S, Lanneaux J, Etchebarren L, Tallot M, Spodenkiewicz M, Alessandri JL, Morel G, Blanluet M, Gueguen P, Roy-Doray B. Description of Copy Number Variations in a Series of Children and Adolescents with FASD in Reunion Island. CHILDREN (BASEL, SWITZERLAND) 2023; 10:children10040694. [PMID: 37189943 DOI: 10.3390/children10040694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Fetal Alcohol Spectrum Disorders (FASD) are the most common cause of neurocognitive impairment and social inadaptation, affecting 1 birth in 100. Despite the existence of precise diagnostic criteria, the diagnosis remains difficult, often confounded with other genetic syndromes or neurodevelopmental disorders. Since 2016, Reunion Island has been a pilot region for the identification, diagnosis, and care of FASD in France. OBJECTIVE To evaluate the prevalence and the types of Copy Number Variations (CNV) in FASD patients. METHODS A retrospective chart review of 101 patients diagnosed with FASD in the Reference Center for developmental anomalies and in the FASD Diagnostic Center of the University Hospital was performed. Records of all patients were reviewed to obtain their medical history, family history, clinical phenotype, and investigations, including genetic testing (CGH- or SNP-array). RESULTS A rate of 20.8% (n = 21) of CNVs was found including 57% (12/21) of pathogenic variants and 29% (6/21) of variants of uncertain signification (VUS). CONCLUSION A particularly high number of CNVs was found in children and adolescents with FASD. It reinforces the plea for a multidisciplinary approach for developmental disorders to explore both environmental factors, such as avoidable teratogens and intrinsic vulnerabilities, especially genetic determinants.
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Affiliation(s)
- Laëtitia Sennsfelder
- Laboratoire EPI (Etudes pharmaco-immunologiques), UFR Santé, Université de La Réunion, CHU (Centre Hospitalier Universitaire) de La Réunion, 97400 Saint-Denis, France
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
| | - Susie Guilly
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
| | - Sébastien Leruste
- CIC 1410 (Centre d'Investigation Clinique), CHU (Centre Hospitalier Universitaire) de La Réunion, 97400 Saint-Denis, France
- UFR Santé, Université de La Réunion, 97410 Saint-Pierre, France
| | - Ludovic Hoareau
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
| | - Willy Léocadie
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
| | - Pauline Beuvain
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
| | - Meïssa Nekaa
- Centre Ressources TSAF (Troubles du Spectre de l'Alcoolisation Fœtale), Fondation Père Favron, CHU (Centre Hospitalier Universitaire) de La Réunion, 97546 Saint-Pierre, France
| | - Maïté Bagard
- Centre Ressources TSAF (Troubles du Spectre de l'Alcoolisation Fœtale), Fondation Père Favron, CHU (Centre Hospitalier Universitaire) de La Réunion, 97546 Saint-Pierre, France
| | - Stéphanie Robin
- Centre Diagnostic TSAF (Troubles du Spectre de l'Alcoolisation Fœtale), CHU (Centre Hospitalier Universitaire) de La Réunion, 97400 Saint-Denis, France
| | - Justine Lanneaux
- Centre Diagnostic TSAF (Troubles du Spectre de l'Alcoolisation Fœtale), CHU (Centre Hospitalier Universitaire) de La Réunion, 97400 Saint-Denis, France
| | - Léa Etchebarren
- Centre Diagnostic TSAF (Troubles du Spectre de l'Alcoolisation Fœtale), CHU (Centre Hospitalier Universitaire) de La Réunion, 97400 Saint-Denis, France
| | - Marilyn Tallot
- Centre Diagnostic TSAF (Troubles du Spectre de l'Alcoolisation Fœtale), CHU (Centre Hospitalier Universitaire) de La Réunion, 97400 Saint-Denis, France
| | - Michel Spodenkiewicz
- CIC 1410 (Centre d'Investigation Clinique), CHU (Centre Hospitalier Universitaire) de La Réunion, 97400 Saint-Denis, France
- Pôle de Santé Mentale, CHU (Centre Hospitalier Universitaire) de La Réunion, 97448 Saint-Pierre, France
| | - Jean-Luc Alessandri
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Ouest Occitanie Réunion, Site Constitutif de La Réunion, 97400 Saint-Denis, France
| | - Godelieve Morel
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Ouest Occitanie Réunion, Site Constitutif de La Réunion, 97400 Saint-Denis, France
| | - Maud Blanluet
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
| | - Paul Gueguen
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
| | - Bérénice Roy-Doray
- Laboratoire EPI (Etudes pharmaco-immunologiques), UFR Santé, Université de La Réunion, CHU (Centre Hospitalier Universitaire) de La Réunion, 97400 Saint-Denis, France
- Service de Génétique, CHU (Centre Hospitalier Universitaire) de La Réunion, La Réunion, 97400 Saint-Denis, France
- CIC 1410 (Centre d'Investigation Clinique), CHU (Centre Hospitalier Universitaire) de La Réunion, 97400 Saint-Denis, France
- Centre Ressources TSAF (Troubles du Spectre de l'Alcoolisation Fœtale), Fondation Père Favron, CHU (Centre Hospitalier Universitaire) de La Réunion, 97546 Saint-Pierre, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Sud-Ouest Occitanie Réunion, Site Constitutif de La Réunion, 97400 Saint-Denis, France
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5
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Mohajeri K, Yadav R, D'haene E, Boone PM, Erdin S, Gao D, Moyses-Oliveira M, Bhavsar R, Currall BB, O'Keefe K, Burt ND, Lowther C, Lucente D, Salani M, Larson M, Redin C, Dudchenko O, Aiden EL, Menten B, Tai DJC, Gusella JF, Vergult S, Talkowski ME. Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models. Am J Hum Genet 2022; 109:2049-2067. [PMID: 36283406 PMCID: PMC9674968 DOI: 10.1016/j.ajhg.2022.09.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 01/26/2023] Open
Abstract
Point mutations and structural variants that directly disrupt the coding sequence of MEF2C have been associated with a spectrum of neurodevelopmental disorders (NDDs). However, the impact of MEF2C haploinsufficiency on neurodevelopmental pathways and synaptic processes is not well understood, nor are the complex mechanisms that govern its regulation. To explore the functional changes associated with structural variants that alter MEF2C expression and/or regulation, we generated an allelic series of 204 isogenic human induced pluripotent stem cell (hiPSC)-derived neural stem cells and glutamatergic induced neurons. These neuronal models harbored CRISPR-engineered mutations that involved direct deletion of MEF2C or deletion of the boundary points for topologically associating domains (TADs) and chromatin loops encompassing MEF2C. Systematic profiling of mutation-specific alterations, contrasted to unedited controls that were exposed to the same guide RNAs for each edit, revealed that deletion of MEF2C caused differential expression of genes associated with neurodevelopmental pathways and synaptic function. We also discovered significant reduction in synaptic activity measured by multielectrode arrays (MEAs) in neuronal cells. By contrast, we observed robust buffering against MEF2C regulatory disruption following deletion of a distal 5q14.3 TAD and loop boundary, whereas homozygous loss of a proximal loop boundary resulted in down-regulation of MEF2C expression and reduced electrophysiological activity on MEA that was comparable to direct gene disruption. Collectively, these studies highlight the considerable functional impact of MEF2C deletion in neuronal cells and systematically characterize the complex interactions that challenge a priori predictions of regulatory consequences from structural variants that disrupt three-dimensional genome organization.
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Affiliation(s)
- Kiana Mohajeri
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Rachita Yadav
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Philip M Boone
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Serkan Erdin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dadi Gao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mariana Moyses-Oliveira
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Riya Bhavsar
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas D Burt
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Monica Salani
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mathew Larson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Claire Redin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA; UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, China
| | - Björn Menten
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Derek J C Tai
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.
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6
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Song W, Li Q, Wang T, Li Y, Fan T, Zhang J, Wang Q, Pan J, Dong Q, Sun ZS, Wang Y. Putative complement control protein CSMD3 dysfunction impairs synaptogenesis and induces neurodevelopmental disorders. Brain Behav Immun 2022; 102:237-250. [PMID: 35245678 DOI: 10.1016/j.bbi.2022.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/10/2022] [Accepted: 02/26/2022] [Indexed: 12/23/2022] Open
Abstract
Recent studies have reported that complement-related proteins modulate brain development through regulating synapse processes in the cortex. CSMD3 belongs to a group of putative complement control proteins. However, its role in the central nervous system and synaptogenesis remains largely unknown. Here we report that CSMD3 deleterious mutations occur frequently in patients with neurodevelopmental disorders (NDDs). Csmd3 is predominantly expressed in cortical neurons of the developing cortex. In mice, Csmd3 disruption induced retarded development and NDD-related behaviors. Csmd3 deficiency impaired synaptogenesis and neurogenesis, allowing fewer neurons reaching the cortical plate. Csmd3 deficiency also induced perturbed functional networks in the developing cortex, involving a number of downregulated synapse-associated genes that influence early synaptic organization and upregulated genes related to immune activity. Our study provides mechanistic insights into the endogenous regulation of complement-related proteins in synaptic development and supports the pathological role of CSMD3 in NDDs.
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Affiliation(s)
- Wei Song
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan Li
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Tao Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanyuan Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianda Fan
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Jianghong Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingqing Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinrong Pan
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiwen Dong
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Sciences, Hebei University, Baoding 071002, China; Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yan Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Cooley Coleman JA, Sarasua SM, Boccuto L, Moore HW, Skinner SA, DeLuca JM. Comprehensive investigation of the phenotype of MEF2C-related disorders in human patients: A systematic review. Am J Med Genet A 2021; 185:3884-3894. [PMID: 34184825 DOI: 10.1002/ajmg.a.62412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/31/2022]
Abstract
MEF2C-related disorders (aka MEF2C-haploinsufficiency) are caused by variations in or involving the MEF2C gene and are characterized by intellectual disability, developmental delay, lack of speech, limited walking, and seizures. Despite these findings, the disorder is not easily recognized clinically. We performed a systematic review following Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines to assemble the most comprehensive list of patients and their phenotypes. Through searching PubMed, Web of Science, and MEDLINE, 43 articles met the inclusion criteria and were fully reviewed. One hundred and seventeen patients were identified from these publications with most having a phenotype of intellectual disability, developmental delay, seizures, hypotonia, absent speech, inability to walk, stereotypic movements, and MRI abnormalities. Nonclassical findings included one patient with a question mark ear, two patients with a jugular pit, one patient with a unique neuroendocrine finding, and nine patients that did not have MEF2C deletions or disruptions but may be affected due to a positional effect on MEF2C. This systematic review characterizes the phenotype of MEF2C-related disorders, documents the severity of this condition, and will help providers to better diagnose and care for patients and their families. Additionally, this compiled information provides a comprehensive resource for investigators interested in pursuing specific genotype-phenotype correlations.
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Affiliation(s)
- Jessica A Cooley Coleman
- School of Nursing, Clemson University, Clemson, South Carolina, USA.,Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Sara M Sarasua
- School of Nursing, Clemson University, Clemson, South Carolina, USA
| | - Luigi Boccuto
- School of Nursing, Clemson University, Clemson, South Carolina, USA
| | | | | | - Jane M DeLuca
- School of Nursing, Clemson University, Clemson, South Carolina, USA.,Greenwood Genetic Center, Greenwood, South Carolina, USA
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8
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Raviglione F, Douzgou S, Scala M, Mingarelli A, D'Arrigo S, Freri E, Darra F, Giglio S, Bonaglia MC, Pantaleoni C, Mastrangelo M, Epifanio R, Elia M, Saletti V, Morlino S, Vari MS, De Liso P, Pavaine J, Spaccini L, Cattaneo E, Gardella E, Møller RS, Marchese F, Colonna C, Gandioli C, Gobbi G, Ram D, Palumbo O, Carella M, Germano M, Tonduti D, De Angelis D, Caputo D, Bergonzini P, Novara F, Zuffardi O, Verrotti A, Orsini A, Bonuccelli A, De Muto MC, Trivisano M, Vigevano F, Granata T, Bernardina BD, Tranchina A, Striano P. Electroclinical features of MEF2C haploinsufficiency-related epilepsy: A multicenter European study. Seizure 2021; 88:60-72. [PMID: 33831796 DOI: 10.1016/j.seizure.2021.03.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Epilepsy is a main manifestation in the autosomal dominant mental retardation syndrome caused by heterozygous variants in MEF2C. We aimed to delineate the electro-clinical features and refine the genotype-phenotype correlations in patients with MEF2C haploinsufficiency. METHODS We thoroughly investigated 25 patients with genetically confirmed MEF2C-syndrome across 12 different European Genetics and Epilepsy Centers, focusing on the epileptic phenotype. Clinical features (seizure types, onset, evolution, and response to therapy), EEG recordings during waking/sleep, and neuroimaging findings were analyzed. We also performed a detailed literature review using the terms "MEF2C", "seizures", and "epilepsy". RESULTS Epilepsy was diagnosed in 19 out of 25 (~80%) subjects, with age at onset <30 months. Ten individuals (40%) presented with febrile seizures and myoclonic seizures occurred in ~50% of patients. Epileptiform abnormalities were observed in 20/25 patients (80%) and hypoplasia/partial agenesis of the corpus callosum was detected in 12/25 patients (~50%). Nine patients harbored a 5q14.3 deletion encompassing MEF2C and at least one other gene. In 7 out of 10 patients with myoclonic seizures, MIR9-2 and LINC00461 were also deleted, whereas ADGRV1 was involved in 3/4 patients with spasms. CONCLUSION The epileptic phenotype of MEF2C-syndrome is variable. Febrile and myoclonic seizures are the most frequent, usually associated with a slowing of the background activity and irregular diffuse discharges of frontally dominant, symmetric or asymmetric, slow theta waves with interposed spike-and-waves complexes. The haploinsufficiency of ADGRV1, MIR9-2, and LINC00461 likely contributes to myoclonic seizures and spasms in patients with MEF2C syndrome.
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Affiliation(s)
| | - Sofia Douzgou
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK; Member of ERN-ITHACA
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Stefano D'Arrigo
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Elena Freri
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Member of ERN EpiCARE
| | - Francesca Darra
- Child Neuropsychiatry Unit, Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | - Sabrina Giglio
- Department of Biomedical Experimental and Clinical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Maria C Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Chiara Pantaleoni
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Massimo Mastrangelo
- Paediatric Neurology Unit, Department of Pediatrics, Children's Hospital Vittore Buzzi, Milan, Italy
| | - Roberta Epifanio
- Clinical Neurophysiology Unit, IRCCS, E Medea Scientific Institute, Bosisio Parini, Lecco, Italy
| | | | - Veronica Saletti
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Silvia Morlino
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Poliambulatorio "Giovanni Paolo II", Viale Padre Pio, snc, San Giovanni Rotondo 71013, Italy
| | - Maria Stella Vari
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Paola De Liso
- Department of Neuroscience, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy; Member of ERN EpiCARE
| | - Julija Pavaine
- Academic Unit of Paediatric Radiology, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, University of Manchester, Manchester, UK
| | - Luigina Spaccini
- Clinical Genetics Service, Department of Pediatrics, Vittore Buzzi Hospital, Milan, Italy
| | - Elisa Cattaneo
- Clinical Genetics Service, Department of Pediatrics, Vittore Buzzi Hospital, Milan, Italy
| | - Elena Gardella
- The Danish Epilepsy Centre Filadelfia, Dianalund, Denmark; Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark; Member of ERN EpiCARE
| | - Rikke S Møller
- The Danish Epilepsy Centre Filadelfia, Dianalund, Denmark; Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark; Member of ERN EpiCARE
| | - Francesca Marchese
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Clara Colonna
- Hospital Neuropsychiatry Service, ASST Rhodense, Rho, Milan, Italy
| | - Claudia Gandioli
- Hospital Neuropsychiatry Service, ASST Rhodense, Rho, Milan, Italy
| | - Giuseppe Gobbi
- Child Neurology Unit, IRCCS Istituto delle Scienze Neurologiche, Bologna, Italy
| | - Dipak Ram
- Department of Paediatric Neurology, Royal Manchester Children's Hospital, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Orazio Palumbo
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Poliambulatorio "Giovanni Paolo II", Viale Padre Pio, snc, San Giovanni Rotondo 71013, Italy
| | - Massimo Carella
- Division of Medical Genetics, Fondazione IRCCS Casa Sollievo della Sofferenza, Poliambulatorio "Giovanni Paolo II", Viale Padre Pio, snc, San Giovanni Rotondo 71013, Italy
| | - Michele Germano
- Maternal and Pediatric Department, Fondazione IRCCS Casa Sollievo della Sofferenza, Poliambulatorio "Giovanni Paolo II", Viale Padre Pio, snc, San Giovanni Rotondo (FG) 71013, Italy
| | - Davide Tonduti
- Paediatric Neurology Unit, Department of Pediatrics, Children's Hospital Vittore Buzzi, Milan, Italy
| | - Diego De Angelis
- Pediatric Department, "Sapienza" University of Rome, Rome 00185, Italy
| | - Davide Caputo
- Department of Health Sciences, Child Neuropsychiatry Unit - Epilepsy Center, San Paolo Hospital, University of Medicine, Milan, Italy; Member of ERN EpiCARE
| | | | - Francesca Novara
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Orsetta Zuffardi
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Alberto Verrotti
- Department of Pediatrics, San Salvatore Hospital, University of L'Aquila, L'Aquila, Italy
| | - Alessandro Orsini
- Pediatric Neurology Santa Chiara Hospital, University of Pisa, Pisa, Italy
| | - Alice Bonuccelli
- Pediatric Neurology Santa Chiara Hospital, University of Pisa, Pisa, Italy
| | | | - Marina Trivisano
- Department of Neuroscience, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy; Member of ERN EpiCARE
| | - Federico Vigevano
- Department of Neuroscience, Bambino Gesù Children's Hospital, IRRCS, Rome, Italy; Member of ERN EpiCARE
| | - Tiziana Granata
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Member of ERN EpiCARE
| | - Bernardo Dalla Bernardina
- Child Neuropsychiatry Unit, Department of Life and Reproduction Sciences, University of Verona, Verona, Italy
| | - Antonia Tranchina
- Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy; Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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9
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Longo JF, Brosius SN, Znoyko I, Alers VA, Jenkins DP, Wilson RC, Carroll AJ, Wolff DJ, Roth KA, Carroll SL. Establishment and genomic characterization of a sporadic malignant peripheral nerve sheath tumor cell line. Sci Rep 2021; 11:5690. [PMID: 33707600 PMCID: PMC7952412 DOI: 10.1038/s41598-021-85055-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 02/17/2021] [Indexed: 12/19/2022] Open
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive Schwann cell-derived neoplasms that occur sporadically or in patients with neurofibromatosis type 1 (NF1). Preclinical research on sporadic MPNSTs has been limited as few cell lines exist. We generated and characterized a new sporadic MPNST cell line, 2XSB, which shares the molecular and genomic features of the parent tumor. These cells have a highly complex karyotype with extensive chromothripsis. 2XSB cells show robust invasive 3-dimensional and clonogenic culture capability and form solid tumors when xenografted into immunodeficient mice. High-density single nucleotide polymorphism array and whole exome sequencing analyses indicate that, unlike NF1-associated MPNSTs, 2XSB cells have intact, functional NF1 alleles with no evidence of mutations in genes encoding components of Polycomb Repressor Complex 2. However, mutations in other genes implicated in MPNST pathogenesis were identified in 2XSB cells including homozygous deletion of CDKN2A and mutations in TP53 and PTEN. We also identified mutations in genes not previously associated with MPNSTs but associated with the pathogenesis of other human cancers. These include DNMT1, NUMA1, NTRK1, PDE11A, CSMD3, LRP5 and ACTL9. This sporadic MPNST-derived cell line provides a useful tool for investigating the biology and potential treatment regimens for sporadic MPNSTs.
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Affiliation(s)
- Jody Fromm Longo
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Stephanie N Brosius
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA.,Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA.,Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Iya Znoyko
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Victoria A Alers
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Dorea P Jenkins
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Robert C Wilson
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA.,Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC, 29425-9080, USA
| | - Andrew J Carroll
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA
| | - Daynna J Wolff
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA
| | - Kevin A Roth
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Steven L Carroll
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, 171 Ashley Avenue, MSC 908, Charleston, SC, 29425-9080, USA. .,Center for Genomic Medicine, Medical University of South Carolina, Charleston, SC, 29425-9080, USA. .,Department of Pathology, University of Alabama at Birmingham, Birmingham, AL, 35294-0017, USA.
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10
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Huang Y, Li Y, Wang X, Yu J, Cai Y, Zheng Z, Li R, Zhang S, Chen N, Asadollahpour Nanaei H, Hanif Q, Chen Q, Fu W, Li C, Cao X, Zhou G, Liu S, He S, Li W, Chen Y, Chen H, Lei C, Liu M, Jiang Y. An atlas of CNV maps in cattle, goat and sheep. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1747-1764. [PMID: 33486588 DOI: 10.1007/s11427-020-1850-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 11/16/2020] [Indexed: 11/26/2022]
Abstract
Copy number variation (CNV) is the most prevalent type of genetic structural variation that has been recognized as an important source of phenotypic variation in humans, animals and plants. However, the mechanisms underlying the evolution of CNVs and their function in natural or artificial selection remain unknown. Here, we generated CNV region (CNVR) datasets which were diverged or shared among cattle, goat, and sheep, including 886 individuals from 171 diverse populations. Using 9 environmental factors for genome-wide association study (GWAS), we identified a series of candidate CNVRs, including genes relating to immunity, tick resistance, multi-drug resistance, and muscle development. The number of CNVRs shared between species is significantly higher than expected (P<0.00001), and these CNVRs may be more persist than the single nucleotide polymorphisms (SNPs) shared between species. We also identified genomic regions under long-term balancing selection and uncovered the potential diversity of the selected CNVRs close to the important functional genes. This study provides the evidence that balancing selection might be more common in mammals than previously considered, and might play an important role in the daily activities of these ruminant species.
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Affiliation(s)
- Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yunjia Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xihong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jiantao Yu
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Yudong Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ran Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shunjin Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | | | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Punjab, 577, Pakistan
- Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, 45650, Islamabad, Pakistan
| | - Qiuming Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Weiwei Fu
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Xiukai Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Shudong Liu
- College of Information Engineering, Northwest A&F University, Yangling, 712100, China
| | - Sangang He
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Biotechnology Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, 830026, China
| | - Wenrong Li
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Biotechnology Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, 830026, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Mingjun Liu
- Key Laboratory of Genetics Breeding and Reproduction of Grass feeding Livestock, Ministry of Agriculture, Biotechnology Research Institute, Xinjiang Academy of Animal Sciences, Urumqi, 830026, China
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
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11
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D'haene E, Bar-Yaacov R, Bariah I, Vantomme L, Van Loo S, Cobos FA, Verboom K, Eshel R, Alatawna R, Menten B, Birnbaum RY, Vergult S. A neuronal enhancer network upstream of MEF2C is compromised in patients with Rett-like characteristics. Hum Mol Genet 2020; 28:818-827. [PMID: 30445463 PMCID: PMC6381311 DOI: 10.1093/hmg/ddy393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 01/06/2023] Open
Abstract
Mutations in myocyte enhancer factor 2C (MEF2C), an important transcription factor in neurodevelopment, are associated with a Rett-like syndrome. Structural variants (SVs) upstream of MEF2C, which do not disrupt the gene itself, have also been found in patients with a similar phenotype, suggesting that disruption of MEF2C regulatory elements can also cause a Rett-like phenotype. To characterize those elements that regulate MEF2C during neural development and that are affected by these SVs, we used genomic tools coupled with both in vitro and in vivo functional assays. Through circularized chromosome conformation capture sequencing
(4C-seq) and the assay for transposase-accessible chromatin using sequencing
(ATAC-seq), we revealed a complex interaction network in which the MEF2C promoter physically contacts several distal enhancers that are deleted or translocated by disease-associated SVs. A total of 16 selected candidate regulatory sequences were tested for enhancer activity in vitro, with 14 found to be functional enhancers. Further analyses of their in vivo activity in zebrafish showed that each of these enhancers has a distinct activity pattern during development, with eight enhancers displaying neuronal activity. In summary, our results disentangle a complex regulatory network governing neuronal MEF2C expression that involves multiple distal enhancers. In addition, the characterized neuronal enhancers pose as novel candidates to screen for mutations in neurodevelopmental disorders, such as Rett-like syndrome.
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Affiliation(s)
- Eva D'haene
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Reut Bar-Yaacov
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Inbar Bariah
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Lies Vantomme
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Sien Van Loo
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Francisco Avila Cobos
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium.,Bioinformatics Institute Ghent from Nucleotides to Networks (BIG N2N), Ghent, Belgium
| | - Karen Verboom
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), 9000 Ghent, Belgium
| | - Reut Eshel
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Rawan Alatawna
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Björn Menten
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
| | - Ramon Y Birnbaum
- Department of Life Sciences, Faculty of Natural Sciences, The Ben-Gurion University of the Negev, Beersheba, Israel.,Center of Evolutionary Genomics and Medicine, The Ben-Gurion University of the Negev, Beersheba, Israel
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University, 9000 Ghent, Belgium
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12
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Csmd2 Is a Synaptic Transmembrane Protein that Interacts with PSD-95 and Is Required for Neuronal Maturation. eNeuro 2019; 6:ENEURO.0434-18.2019. [PMID: 31068362 PMCID: PMC6506821 DOI: 10.1523/eneuro.0434-18.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 12/21/2022] Open
Abstract
Mutations and copy number variants of the CUB and Sushi multiple domains 2 (CSMD2) gene are associated with neuropsychiatric disease. CSMD2 encodes a single-pass transmembrane protein with a large extracellular domain comprising repeats of CUB and Sushi domains. High expression of CSMD2 in the developing and mature brain suggests possible roles in neuron development or function, but the cellular functions of CSMD2 are not known. In this study, we show that mouse Csmd2 is expressed in excitatory and inhibitory neurons in the forebrain. Csmd2 protein exhibits a somatodendritic localization in the neocortex and hippocampus, with smaller puncta localizing to the neuropil. Using immunohistochemical and biochemical methods, we demonstrate that Csmd2 localizes to dendritic spines and is enriched in the postsynaptic density (PSD). Accordingly, we show that the cytoplasmic tail domain of Csmd2 interacts with synaptic scaffolding proteins of the membrane-associated guanylate kinase (MAGUK) family. The association between Csmd2 and MAGUK member PSD-95 is dependent on a PDZ-binding domain on the Csmd2 tail, which is also required for synaptic targeting of Csmd2. Finally, we show that knock-down of Csmd2 expression in hippocampal neuron cultures results in reduced complexity of dendritic arbors and deficits in dendritic spine density. Knock-down of Csmd2 in immature developing neurons results in reduced filopodia density, whereas Csmd2 knock-down in mature neurons causes significant reductions in dendritic spine density and dendrite complexity. Together, these results point toward a function for Csmd2 in development and maintenance of dendrites and synapses, which may account for its association with certain psychiatric disorders.
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13
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Thyme SB, Pieper LM, Li EH, Pandey S, Wang Y, Morris NS, Sha C, Choi JW, Herrera KJ, Soucy ER, Zimmerman S, Randlett O, Greenwood J, McCarroll SA, Schier AF. Phenotypic Landscape of Schizophrenia-Associated Genes Defines Candidates and Their Shared Functions. Cell 2019; 177:478-491.e20. [PMID: 30929901 PMCID: PMC6494450 DOI: 10.1016/j.cell.2019.01.048] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/15/2018] [Accepted: 01/27/2019] [Indexed: 01/25/2023]
Abstract
Genomic studies have identified hundreds of candidate genes near loci associated with risk for schizophrenia. To define candidates and their functions, we mutated zebrafish orthologs of 132 human schizophrenia-associated genes. We created a phenotype atlas consisting of whole-brain activity maps, brain structural differences, and profiles of behavioral abnormalities. Phenotypes were diverse but specific, including altered forebrain development and decreased prepulse inhibition. Exploration of these datasets identified promising candidates in more than 10 gene-rich regions, including the magnesium transporter cnnm2 and the translational repressor gigyf2, and revealed shared anatomical sites of activity differences, including the pallium, hypothalamus, and tectum. Single-cell RNA sequencing uncovered an essential role for the understudied transcription factor znf536 in the development of forebrain neurons implicated in social behavior and stress. This phenotypic landscape of schizophrenia-associated genes prioritizes more than 30 candidates for further study and provides hypotheses to bridge the divide between genetic association and biological mechanism.
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Affiliation(s)
- Summer B Thyme
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Lindsey M Pieper
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Eric H Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shristi Pandey
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yiqun Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Nathan S Morris
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Carrie Sha
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joo Won Choi
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kristian J Herrera
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Edward R Soucy
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Steve Zimmerman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Owen Randlett
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joel Greenwood
- Center for Brain Science, Harvard University, Cambridge, MA 02138, USA
| | - Steven A McCarroll
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Cambridge, MA 02142, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Center for Brain Science, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Biozentrum, University of Basel, CH-4056 Basel, Switzerland; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; FAS Center for Systems Biology, Harvard University, MA 02138, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98104, USA.
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Gilman JL, Newman HA, Freeman R, Singh KE, Puckett RL, Morohashi DK, Stein C, Palomino K, Lebel RR, Kimonis VE. Two cases of Legg-Perthes and intellectual disability in Tricho-Rhino-Phalangeal syndrome type 1 associated with novel TRPS1 mutations. Am J Med Genet A 2017; 173:1663-1667. [PMID: 28256045 DOI: 10.1002/ajmg.a.38204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 12/18/2016] [Accepted: 02/02/2017] [Indexed: 11/06/2022]
Abstract
Tricho-Rhino-Phalangeal syndrome is a rare autosomal dominant genetic disorder caused by mutations in the TRPS1 gene. This malformation syndrome is characterized by distinctive craniofacial features including sparse scalp hair, bulbous tip of the nose, long flat philtrum, thin upper vermilion border, and protruding ears. Skeletal abnormalities include cone-shaped epiphyses at the phalanges, hip malformations, and short stature. In this report, we describe two patients with the physical manifestations and genotype of TRPS type I but with learning/intellectual disability not typically described as part of the syndrome. The first patient has a novel heterozygous two-base-pair deletion of nucleotides at 3198-3199 (c.3198-3199delAT) in the TRPS1 gene causing a translational frameshift and subsequent alternate stop codon. The second patient has a 3.08 million base-pair interstitial deletion at 8q23.3 (113,735,487-116,818,578), which includes the TRPS1 gene and CSMD3. Our patients have characteristic craniofacial features, Legg-Perthes syndrome, various skeletal abnormalities including cone shaped epiphyses, anxiety (first patient), and intellectual disability, presenting unusual phenotypes that add to the clinical spectrum of the disease.
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Affiliation(s)
- Jordana L Gilman
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, New York
| | - Heather A Newman
- Department of Pediatrics, Division of Genetic and Genomic Medicine, University of California, Irvine, Orange, California
| | - Rebecca Freeman
- Department of Pediatrics, Division of Genetic and Genomic Medicine, University of California, Irvine, Orange, California
| | - Kathryn E Singh
- Department of Pediatrics, Division of Genetic and Genomic Medicine, University of California, Irvine, Orange, California
| | - Rebecca L Puckett
- Department of Pediatrics, Division of Genetic and Genomic Medicine, University of California, Irvine, Orange, California
| | - David K Morohashi
- Division of Family Medicine, School of Medicine, University of California, Irvine, California
| | - Constance Stein
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, New York
| | - Kathryn Palomino
- Department of Orthopedic Surgery, SUNY Upstate Medical University, Syracuse, New York
| | - Robert Roger Lebel
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, New York
| | - Virginia E Kimonis
- Department of Pediatrics, Division of Genetic and Genomic Medicine, University of California, Irvine, Orange, California
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15
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The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. Nat Genet 2016; 49:36-45. [PMID: 27841880 DOI: 10.1038/ng.3720] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/17/2016] [Indexed: 12/16/2022]
Abstract
Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyotypes and demonstrated complexity that was cryptic to karyotyping in 21% of BCAs, highlighting the limitations of conventional cytogenetic approaches. At least 33.9% of BCAs resulted in gene disruption that likely contributed to the developmental phenotype, 5.2% were associated with pathogenic genomic imbalances, and 7.3% disrupted topologically associated domains (TADs) encompassing known syndromic loci. Remarkably, BCA breakpoints in eight subjects altered a single TAD encompassing MEF2C, a known driver of 5q14.3 microdeletion syndrome, resulting in decreased MEF2C expression. We propose that sequence-level resolution dramatically improves prediction of clinical outcomes for balanced rearrangements and provides insight into new pathogenic mechanisms, such as altered regulation due to changes in chromosome topology.
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16
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Naseer MI, Chaudhary AG, Rasool M, Kalamegam G, Ashgan FT, Assidi M, Ahmed F, Ansari SA, Zaidi SK, Jan MM, Al-Qahtani MH. Copy number variations in Saudi family with intellectual disability and epilepsy. BMC Genomics 2016; 17:757. [PMID: 27766957 PMCID: PMC5073808 DOI: 10.1186/s12864-016-3091-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Background Epilepsy is genetically complex but common brain disorder of the world affecting millions of people with almost of all age groups. Novel Copy number variations (CNVs) are considered as important reason for the numerous neurodevelopmental disorders along with intellectual disability and epilepsy. DNA array based studies contribute to explain a more severe clinical presentation of the disease but interoperation of many detected CNVs are still challenging. Results In order to study novel CNVs with epilepsy related genes in Saudi family with six affected and two normal individuals with several forms of epileptic seizures, intellectual disability (ID), and minor dysmorphism, we performed the high density whole genome Agilent sure print G3 Hmn CGH 2x 400 K array-CGH chips analysis. Our results showed de novo deletions, duplications and deletion plus duplication on differential chromosomal regions in the affected individuals that were not shown in the normal fathe and normal kids by using Agilent CytoGenomics 3.0.6.6 softwear. Copy number gain were observed in the chromosome 1, 16 and 22 with LCE3C, HPR, GSTT2, GSTTP2, DDT and DDTL genes respectively whereas the deletions observed in the chromosomal regions 8p23-p21 (4303127–4337759) and the potential gene in this region is CSMD1 (OMIM: 612279). Moreover, the array CGH results deletions and duplication were also validated by using primer design of deleted regions utilizing the flanked SNPs using simple PCR and also by using quantitative real time PCR. Conclusions We found some of the de novo deletions and duplication in our study in Saudi family with intellectual disability and epilepsy. Our results suggest that array-CGH should be used as a first line of genetic test for epilepsy except there is a strong indication for a monogenic syndrome. The advanced high through put array-CGH technique used in this study aim to collect the data base and to identify new mechanisms describing epileptic disorder, may help to improve the clinical management of individual cases in decreasing the burden of epilepsy in Saudi Arabia.
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Affiliation(s)
- Muhammad I Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
| | - Adeel G Chaudhary
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Gauthaman Kalamegam
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Fai T Ashgan
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Mourad Assidi
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Farid Ahmed
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Shakeel A Ansari
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Syed Kashif Zaidi
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Mohammed M Jan
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Box 80215, Jeddah, 21589, Saudi Arabia
| | - Mohammad H Al-Qahtani
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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17
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CUB and Sushi multiple domains 3 regulates dendrite development. Neurosci Res 2016; 110:11-7. [DOI: 10.1016/j.neures.2016.03.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 01/08/2023]
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19q13.32 microdeletion syndrome: three new cases. Eur J Med Genet 2014; 57:654-8. [PMID: 25230004 DOI: 10.1016/j.ejmg.2014.08.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 08/29/2014] [Indexed: 11/22/2022]
Abstract
A previous report described a unique phenotype associated with an apparently de novo 732 kb 19q13.32 microdeletion, consisting of intellectual disability, facial asymmetry, ptosis, oculomotor abnormalities, orofacial clefts, cardiac defects, scoliosis and chronic constipation. We report three unrelated patients with developmental delay and dysmorphic features, who were all found to have interstitial 19q13.32 microdeletions of varying sizes. Both the previously reported patient and our Patient 1 with a larger, 1.3-Mb deletion have distinctive dysmorphic features and medical problems, allowing us to define a recognizable 19q13.32 microdeletion syndrome. Patient 1 was hypotonic and dysmorphic at birth, with aplasia of the posterior corpus callosum, bilateral ptosis, oculomotor paralysis, down-slanting palpebral fissures, facial asymmetry, submucosal cleft palate, micrognathia, wide-spaced nipples, right-sided aortic arch, hypospadias, bilateral inguinal hernias, double toenail of the left second toe, partial 2-3 toe syndactyly, kyphoscoliosis and colonic atony. Therefore, the common features of the 19q13.32 microdeletion syndrome include facial asymmetry, ptosis, oculomotor paralysis, orofacial clefting, micrognathia, kyphoscoliosis, aortic defects and colonic atony. These findings are probably related to a deletion of some combination of the 20-23 genes in common between these two patients, especially NPAS1, NAPA, ARHGAP35, SLC8A2, DHX34, MEIS3, and ZNF541. These candidate genes are expressed in the brain parenchyma, glia, heart, gastrointestinal tract and musculoskeletal system and likely play a fundamental role in the expression of this phenotype. This report delineates the phenotypic spectrum associated with the haploinsufficiency of genes found in 19q13.32.
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19
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Combined analysis with copy number variation identifies risk loci in lung cancer. BIOMED RESEARCH INTERNATIONAL 2014; 2014:469103. [PMID: 25093167 PMCID: PMC4100386 DOI: 10.1155/2014/469103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/11/2014] [Accepted: 06/11/2014] [Indexed: 12/26/2022]
Abstract
Background. Lung cancer is the most important cause of cancer mortality worldwide, but the underlying mechanisms of this disease are not fully understood. Copy number variations (CNVs) are promising genetic variations to study because of their potential effects on cancer.
Methodology/Principal Findings. Here we conducted a pilot study in which we systematically analyzed the association of CNVs in two lung cancer datasets: the Environment And Genetics in Lung cancer Etiology (EAGLE) and the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial datasets. We used a preestablished association method to test the datasets separately and conducted a combined analysis to test the association accordance between the two datasets. Finally, we identified 167 risk SNP loci and 22 CNVs associated with lung cancer and linked them with recombination hotspots. Functional annotation and biological relevance analyses implied that some of our predicted risk loci were supported by other studies and might be potential candidate loci for lung cancer studies. Conclusions/Significance. Our results further emphasized the importance of copy number variations in cancer and might be a valuable complement to current genome-wide association studies on cancer.
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20
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Lossie AC, Muir WM, Lo CL, Timm F, Liu Y, Gray W, Zhou FC. Implications of genomic signatures in the differential vulnerability to fetal alcohol exposure in C57BL/6 and DBA/2 mice. Front Genet 2014; 5:173. [PMID: 24966868 PMCID: PMC4052096 DOI: 10.3389/fgene.2014.00173] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/22/2014] [Indexed: 12/12/2022] Open
Abstract
Maternal alcohol consumption inflicts a multitude of phenotypic consequences that range from undetectable changes to severe dysmorphology. Using tightly controlled murine studies that deliver precise amounts of alcohol at discrete developmental stages, our group and other labs demonstrated in prior studies that the C57BL/6 and DBA/2 inbred mouse strains display differential susceptibility to the teratogenic effects of alcohol. Since the phenotypic diversity extends beyond the amount, dosage and timing of alcohol exposure, it is likely that an individual's genetic background contributes to the phenotypic spectrum. To identify the genomic signatures associated with these observed differences in alcohol-induced dysmorphology, we conducted a microarray-based transcriptome study that also interrogated the genomic signatures between these two lines based on genetic background and alcohol exposure. This approach is called a gene x environment (GxE) analysis; one example of a GxE interaction would be a gene whose expression level increases in C57BL/6, but decreases in DBA/2 embryos, following alcohol exposure. We identified 35 candidate genes exhibiting GxE interactions. To identify cis-acting factors that mediated these interactions, we interrogated the proximal promoters of these 35 candidates and found 241 single nucleotide variants (SNVs) in 16 promoters. Further investigation indicated that 186 SNVs (15 promoters) are predicted to alter transcription factor binding. In addition, 62 SNVs created, removed or altered the placement of a CpG dinucleotide in 13 of the proximal promoters, 53 of which overlapped putative transcription factor binding sites. These 53 SNVs are also our top candidates for future studies aimed at examining the effects of alcohol on epigenetic gene regulation.
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Affiliation(s)
- Amy C Lossie
- Department of Animal Sciences, Purdue University West Lafayette, IN, USA
| | - William M Muir
- Department of Animal Sciences, Purdue University West Lafayette, IN, USA ; Department of Medicine, Indiana University School of Medicine Indianapolis, IN, USA
| | - Chiao-Ling Lo
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Floyd Timm
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Yunlong Liu
- Department of Molecular and Medical Genetics, Indiana University School of Medicine Indianapolis, IN, USA
| | - Whitney Gray
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA
| | - Feng C Zhou
- Department of Anatomy and Cell Biology, Indiana University School of Medicine Indianapolis, IN, USA ; Stark Neuroscience Research Institute, Indiana University School of Medicine Indianapolis, IN, USA
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Functionally enigmatic genes: a case study of the brain ignorome. PLoS One 2014; 9:e88889. [PMID: 24523945 PMCID: PMC3921226 DOI: 10.1371/journal.pone.0088889] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 01/14/2014] [Indexed: 12/26/2022] Open
Abstract
What proportion of genes with intense and selective expression in specific tissues, cells, or systems are still almost completely uncharacterized with respect to biological function? In what ways do these functionally enigmatic genes differ from well-studied genes? To address these two questions, we devised a computational approach that defines so-called ignoromes. As proof of principle, we extracted and analyzed a large subset of genes with intense and selective expression in brain. We find that publications associated with this set are highly skewed--the top 5% of genes absorb 70% of the relevant literature. In contrast, approximately 20% of genes have essentially no neuroscience literature. Analysis of the ignorome over the past decade demonstrates that it is stubbornly persistent, and the rapid expansion of the neuroscience literature has not had the expected effect on numbers of these genes. Surprisingly, ignorome genes do not differ from well-studied genes in terms of connectivity in coexpression networks. Nor do they differ with respect to numbers of orthologs, paralogs, or protein domains. The major distinguishing characteristic between these sets of genes is date of discovery, early discovery being associated with greater research momentum--a genomic bandwagon effect. Finally we ask to what extent massive genomic, imaging, and phenotype data sets can be used to provide high-throughput functional annotation for an entire ignorome. In a majority of cases we have been able to extract and add significant information for these neglected genes. In several cases--ELMOD1, TMEM88B, and DZANK1--we have exploited sequence polymorphisms, large phenome data sets, and reverse genetic methods to evaluate the function of ignorome genes.
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22
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Zhang R, Song C. Loss of CSMD1 or 2 may contribute to the poor prognosis of colorectal cancer patients. Tumour Biol 2014; 35:4419-23. [DOI: 10.1007/s13277-013-1581-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/17/2013] [Indexed: 10/25/2022] Open
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Hotz A, Hellenbroich Y, Sperner J, Linder-Lucht M, Tacke U, Walter C, Caliebe A, Nagel I, Saunders DE, Wolff G, Martin P, Morris-Rosendahl DJ. Microdeletion 5q14.3 and anomalies of brain development. Am J Med Genet A 2013; 161A:2124-33. [DOI: 10.1002/ajmg.a.36020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 03/31/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Alrun Hotz
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | | | | | - Michaela Linder-Lucht
- Zentrum für Kinder- und Jugendmedizin; Albert-Ludwigs-Universitätsklinikum Freiburg; Freiburg Germany
| | - Uta Tacke
- Zentrum für Kinder- und Jugendmedizin; Albert-Ludwigs-Universitätsklinikum Freiburg; Freiburg Germany
| | - Caren Walter
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | - Almuth Caliebe
- Institut für Humangenetik; Christian-Albrechts-Universität Kiel; Kiel Germany
| | - Inga Nagel
- Institut für Humangenetik; Christian-Albrechts-Universität Kiel; Kiel Germany
| | - Dawn E. Saunders
- Department of Radiology; Great Ormond Street Hospital; London United Kingdom
| | - Gerhard Wolff
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
| | - Peter Martin
- Séguin Klinik; Epilepsiezentrum Kehl-Kork; Kork Germany
| | - Deborah J. Morris-Rosendahl
- Institute of Human Genetics; Albert-Ludwigs University Medical Centre Freiburg; Freiburg Germany
- National Heart and Lung Institute; Imperial College, London; London United Kingdom
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Curran S, Ahn JW, Grayton H, Collier DA, Ogilvie CM. NRXN1 deletions identified by array comparative genome hybridisation in a clinical case series - further understanding of the relevance of NRXN1 to neurodevelopmental disorders. J Mol Psychiatry 2013; 1:4. [PMID: 25408897 PMCID: PMC4223877 DOI: 10.1186/2049-9256-1-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 11/29/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Microdeletions in the NRXN1 gene have been associated with a range of neurodevelopmental disorders, including autism spectrum disorders, schizophrenia, intellectual disability, speech and language delay, epilepsy and hypotonia. RESULTS In the present study we performed array CGH analysis on 10,397 individuals referred for diagnostic cytogenetic analysis, using a custom oligonucleotide array, which included 215 NRXN1 probes (median spacing 4.9 kb). We found 34 NRXN1 deletions (0.33% of referrals) ranging from 9 to 942 kb in size, of which 18 were exonic (0.17%). Three deletions affected exons also in the beta isoform of NRXN1. No duplications were found. Patients had a range of phenotypes including developmental delay, learning difficulties, attention deficit hyperactivity disorder (ADHD), autism, speech delay, social communication difficulties, epilepsy, behaviour problems and microcephaly. Five patients who had deletions in NRXN1 had a second CNV implicated in neurodevelopmental disorder: a CNTNAP2 and CSMD3 deletion in patients with exonic NRXN1 deletions, and a Williams-Beuren syndrome deletion and two 22q11.2 duplications in patients with intronic NRXN1 deletions. CONCLUSIONS Exonic deletions in the NRXN1 gene, predominantly affecting the alpha isoform, were found in patients with a range of neurodevelopmental disorders referred for diagnostic cytogenetic analysis. The targeting of dense oligonucleotide probes to the NRXN1 locus on array comparative hybridisation platforms provides detailed characterisation of deletions in this gene, and is likely to add to understanding of the importance of NRXN1 in neural development.
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Affiliation(s)
- Sarah Curran
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Kings College London, De Crespigny Park, Denmark Hill, London, SE5 8AF UK
| | - Joo Wook Ahn
- Cytogenetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Hannah Grayton
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, Denmark Hill, London, SE5 8AF UK
| | - David A Collier
- MRC Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, De Crespigny Park, Denmark Hill, London, SE5 8AF UK
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25
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Lionel AC, Vaags AK, Sato D, Gazzellone MJ, Mitchell EB, Chen HY, Costain G, Walker S, Egger G, Thiruvahindrapuram B, Merico D, Prasad A, Anagnostou E, Fombonne E, Zwaigenbaum L, Roberts W, Szatmari P, Fernandez BA, Georgieva L, Brzustowicz LM, Roetzer K, Kaschnitz W, Vincent JB, Windpassinger C, Marshall CR, Trifiletti RR, Kirmani S, Kirov G, Petek E, Hodge JC, Bassett AS, Scherer SW. Rare exonic deletions implicate the synaptic organizer Gephyrin (GPHN) in risk for autism, schizophrenia and seizures. Hum Mol Genet 2013; 22:2055-66. [DOI: 10.1093/hmg/ddt056] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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Cabras V, Milia A, Montaldo C, Nucaro A. Cryptic chromosome rearrangements in five patients, with normal and/or abnormal karyotypes, associated with mental retardation, autism and/or epilepsy, detected by BAC genome array-CGH. Prague Med Rep 2012; 113:279-88. [PMID: 23249659 DOI: 10.14712/23362936.2015.11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
This report describes the usefulness of the BAC genome array-CGH platform in the detection of cryptic rearrangements. We examined ten patients with normal and/or abnormal karyotypes and dysmorphic features, associated with mental retardation, autism and/or epilepsy. This approach led us to discover further cryptic chromosomal rearrangements, not previously detected by conventional cytogenetic procedures, and allowed us to better delineate genotype/phenotype correlation. Our experience shows the validity of the BAC platform as a reliable method for genome-wide screening of chromosomal aberrations in patient with idiopathic mental retardation and/or in association with autism and epilepsy.
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Affiliation(s)
- V Cabras
- Department of Experimental Medical Pathology, Faculty of Medicine and Surgery, University of Cagliari, Cagliari, Italy
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Toral-López J, Buentello-Volante B, Balderas-Minor MM, Amezcua-Herrera C, Valdes-Miranda JM, González-Huerta LM, Gudiño M, Cuevas-Covarrubias SA, Zenteno JC. An intellectually disabled patient with the 5q14.3q15 microdeletion syndrome associated with an apparently de novo t(2;5)(q13;q14). Am J Med Genet A 2012; 158A:942-6. [PMID: 22419405 DOI: 10.1002/ajmg.a.35262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 12/23/2011] [Indexed: 12/22/2022]
Affiliation(s)
- Jaime Toral-López
- Department of Genetics, Centro Médico Ecatepec, ISSEMYM, Mexico, Mexico
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Saitsu H, Igarashi N, Kato M, Okada I, Kosho T, Shimokawa O, Sasaki Y, Nishiyama K, Tsurusaki Y, Doi H, Miyake N, Harada N, Hayasaka K, Matasumoto N. De novo 5q14.3 translocation 121.5-kb upstream of MEF2C in a patient with severe intellectual disability and early-onset epileptic encephalopathy. Am J Med Genet A 2011; 155A:2879-84. [PMID: 21990267 DOI: 10.1002/ajmg.a.34289] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/27/2011] [Indexed: 01/18/2023]
Abstract
Recent studies have shown that haploinsufficiency of MEF2C causes severe intellectual disability, epilepsy, hypotonia, and cerebral malformations. We report on a female patient with severe intellectual disability, early-onset epileptic encephalopathy, and hypoplastic corpus callosum, possessing a de novo balanced translocation, t(5;15)(q13.3;q26.1). The patient showed upward gazing and tonic seizure of lower extremities followed by generalized clonic seizures at 4 months of age. Electroencephalogram showed hypsarrhythmia when asleep. By using fluorescent in situ hybridization (FISH), southern hybridization and inverse PCR, the translocation breakpoints were determined at the nucleotide level. The 5q14.3 breakpoint was localized 121.5-kb upstream of MEF2C. The 15q26.2 breakpoint was mapped 119-kb downstream of LOC91948 non-coding RNA. We speculate that the translocation may disrupt the proper regulation of MEF2C expression in the developing brain, resulting in severe intellectual disability and early-onset epileptic encephalopathy.
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Affiliation(s)
- Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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Nucaro A, Pisano T, Chillotti I, Montaldo C, Pruna D. Chromosome 8p23.2-pter: a critical region for mental retardation, autism and epilepsy? Clin Genet 2011; 79:394-5; author reply 396. [DOI: 10.1111/j.1399-0004.2010.01548.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Levinson DF, Duan J, Oh S, Wang K, Sanders AR, Shi J, Zhang N, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, Kendler KS, Freedman R, Dudbridge F, Pe’er I, Hakonarson H, Bergen SE, Fanous AH, Holmans PA, Gejman PV. Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications. Am J Psychiatry 2011; 168:302-16. [PMID: 21285140 PMCID: PMC4441324 DOI: 10.1176/appi.ajp.2010.10060876] [Citation(s) in RCA: 332] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To evaluate previously reported associations of copy number variants (CNVs) with schizophrenia and to identify additional associations, the authors analyzed CNVs in the Molecular Genetics of Schizophrenia study (MGS) and additional available data. METHOD After quality control, MGS data for 3,945 subjects with schizophrenia or schizoaffective disorder and 3,611 screened comparison subjects were available for analysis of rare CNVs (<1% frequency). CNV detection thresholds were chosen that maximized concordance in 151 duplicate assays. Pointwise and genewise analyses were carried out, as well as analyses of previously reported regions. Selected regions were visually inspected and confirmed with quantitative polymerase chain reaction. RESULTS In analyses of MGS data combined with other available data sets, odds ratios of 7.5 or greater were observed for previously reported deletions in chromosomes 1q21.1, 15q13.3, and 22q11.21, duplications in 16p11.2, and exon-disrupting deletions in NRXN1. The most consistently supported candidate associations across data sets included a 1.6-Mb deletion in chromosome 3q29 (21 genes, TFRC to BDH1) that was previously described in a mild-moderate mental retardation syndrome, exonic duplications in the gene for vasoactive intestinal peptide receptor 2 (VIPR2), and exonic duplications in C16orf72. The case subjects had a modestly higher genome-wide number of gene-containing deletions (>100 kb and >1 Mb) but not duplications. CONCLUSIONS The data strongly confirm the association of schizophrenia with 1q21.1, 15q13.3, and 22q11.21 deletions, 16p11.2 duplications, and exonic NRXN1 deletions. These CNVs, as well as 3q29 deletions, are also associated with mental retardation, autism spectrum disorders, and epilepsy. Additional candidate genes and regions, including VIPR2, were identified. Study of the mechanisms underlying these associations should shed light on the pathophysiology of schizophrenia.
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Magri C, Sacchetti E, Traversa M, Valsecchi P, Gardella R, Bonvicini C, Minelli A, Gennarelli M, Barlati S. New copy number variations in schizophrenia. PLoS One 2010; 5:e13422. [PMID: 20967226 PMCID: PMC2954184 DOI: 10.1371/journal.pone.0013422] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 09/19/2010] [Indexed: 12/18/2022] Open
Abstract
Genome-wide screenings for copy number variations (CNVs) in patients with schizophrenia have demonstrated the presence of several CNVs that increase the risk of developing the disease and a growing number of large rare CNVs; the contribution of these rare CNVs to schizophrenia remains unknown. Using Affymetrix 6.0 arrays, we undertook a systematic search for CNVs in 172 patients with schizophrenia and 160 healthy controls, all of Italian origin, with the aim of confirming previously identified loci and identifying novel schizophrenia susceptibility genes. We found five patients with a CNV occurring in one of the regions most convincingly implicated as risk factors for schizophrenia: NRXN1 and the 16p13.1 regions were found to be deleted in single patients and 15q11.2 in 2 patients, whereas the 15q13.3 region was duplicated in one patient. Furthermore, we found three distinct patients with CNVs in 2q12.2, 3q29 and 17p12 loci, respectively. These loci were previously reported to be deleted or duplicated in patients with schizophrenia but were never formally associated with the disease. We found 5 large CNVs (>900 kb) in 4q32, 5q14.3, 8q23.3, 11q25 and 17q12 in five different patients that could include some new candidate schizophrenia susceptibility genes. In conclusion, the identification of previously reported CNVs and of new, rare, large CNVs further supports a model of schizophrenia that includes the effect of multiple, rare, highly penetrant variants.
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Affiliation(s)
- Chiara Magri
- Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnology, Brescia University School of Medicine, Brescia, Italy
| | - Emilio Sacchetti
- Department of Mental Health, Brescia Spedali Civili, Brescia, Italy
- University Psychiatric Unit, Brescia University School of Medicine, Brescia, Italy
- Centre on Behavioural and Neurodegenerative Disorders, Brescia University and EULO, Brescia, Italy
- * E-mail: (ES); (SB)
| | - Michele Traversa
- Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnology, Brescia University School of Medicine, Brescia, Italy
| | - Paolo Valsecchi
- Department of Mental Health, Brescia Spedali Civili, Brescia, Italy
- University Psychiatric Unit, Brescia University School of Medicine, Brescia, Italy
| | - Rita Gardella
- Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnology, Brescia University School of Medicine, Brescia, Italy
| | - Cristian Bonvicini
- Genetics Unit, IRCCS San Giovanni di Dio, Fatebenefratelli, Brescia, Italy
| | - Alessandra Minelli
- Genetics Unit, IRCCS San Giovanni di Dio, Fatebenefratelli, Brescia, Italy
| | - Massimo Gennarelli
- Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnology, Brescia University School of Medicine, Brescia, Italy
- Genetics Unit, IRCCS San Giovanni di Dio, Fatebenefratelli, Brescia, Italy
| | - Sergio Barlati
- Division of Biology and Genetics, Department of Biomedical Sciences and Biotechnology, Brescia University School of Medicine, Brescia, Italy
- Centre on Behavioural and Neurodegenerative Disorders, Brescia University and EULO, Brescia, Italy
- * E-mail: (ES); (SB)
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Le Meur N, Holder-Espinasse M, Jaillard S, Goldenberg A, Joriot S, Amati-Bonneau P, Guichet A, Barth M, Charollais A, Journel H, Auvin S, Boucher C, Kerckaert JP, David V, Manouvrier-Hanu S, Saugier-Veber P, Frébourg T, Dubourg C, Andrieux J, Bonneau D. MEF2C haploinsufficiency caused by either microdeletion of the 5q14.3 region or mutation is responsible for severe mental retardation with stereotypic movements, epilepsy and/or cerebral malformations. J Med Genet 2009; 47:22-9. [PMID: 19592390 DOI: 10.1136/jmg.2009.069732] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Over the last few years, array-comparative genomic hybridisation (CGH) has considerably improved our ability to detect cryptic unbalanced rearrangements in patients with syndromic mental retardation. METHOD Molecular karyotyping of six patients with syndromic mental retardation was carried out using whole-genome oligonucleotide array-CGH. RESULTS 5q14.3 microdeletions ranging from 216 kb to 8.8 Mb were detected in five unrelated patients with the following phenotypic similarities: severe mental retardation with absent speech, hypotonia and stereotypic movements. Facial dysmorphic features, epilepsy and/or cerebral malformations were also present in most of these patients. The minimal common deleted region of these 5q14 microdeletions encompassed only MEF2C, the gene for a protein known to act in brain as a neurogenesis effector, which regulates excitatory synapse number. In a patient with a similar phenotype, an MEF2C nonsense mutation was subsequently identified. CONCLUSION Taken together, these results strongly suggest that haploinsufficiency of MEF2C is responsible for severe mental retardation with stereotypic movements, seizures and/or cerebral malformations.
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Affiliation(s)
- N Le Meur
- Service de Génétique, CHU de Rouen, France.
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Abstract
Autism is a severe neurodevelopmental disorder that is typically diagnosed by 3 years of age. Core symptoms of autism include profound deficits in social interaction and communication, restricted interests, stereotyped responses, and other repetitive patterns of behavior. Other abnormalities include mental retardation and comorbid epilepsy. These symptoms underscore the consequences of genetic inheritance for brain function and behavior. The etiology of autism may involve an interaction between genetic susceptibility (mediated by multiple genes) and environmental factors influencing brain development.
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Mutations may make humans walk on all fours. Nature 2008. [DOI: 10.1038/news.2008.868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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