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Duński E, Pękowska A. Keeping the balance: Trade-offs between human brain evolution, autism, and schizophrenia. Front Genet 2022; 13:1009390. [DOI: 10.3389/fgene.2022.1009390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/12/2022] [Indexed: 11/22/2022] Open
Abstract
The unique qualities of the human brain are a product of a complex evolutionary process. Evolution, famously described by François Jacob as a “tinkerer,” builds upon existing genetic elements by modifying and repurposing them for new functions. Genetic changes in DNA may lead to the emergence of new genes or cause altered gene expression patterns. Both gene and regulatory element mutations may lead to new functions. Yet, this process may lead to side-effects. An evolutionary trade-off occurs when an otherwise beneficial change, which is important for evolutionary success and is under strong positive selection, concurrently results in a detrimental change in another trait. Pleiotropy occurs when a gene affects multiple traits. Antagonistic pleiotropy is a phenomenon whereby a genetic variant leads to an increase in fitness at one life-stage or in a specific environment, but simultaneously decreases fitness in another respect. Therefore, it is conceivable that the molecular underpinnings of evolution of highly complex traits, including brain size or cognitive ability, under certain conditions could result in deleterious effects, which would increase the susceptibility to psychiatric or neurodevelopmental diseases. Here, we discuss possible trade-offs and antagonistic pleiotropies between evolutionary change in a gene sequence, dosage or activity and the susceptibility of individuals to autism spectrum disorders and schizophrenia. We present current knowledge about genes and alterations in gene regulatory landscapes, which have likely played a role in establishing human-specific traits and have been implicated in those diseases.
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2
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Ji F, Zhu X, Liao H, Ouyang L, Huang Y, Syeda MZ, Ying S. New Era of Mapping and Understanding Common Fragile Sites: An Updated Review on Origin of Chromosome Fragility. Front Genet 2022; 13:906957. [PMID: 35669181 PMCID: PMC9164283 DOI: 10.3389/fgene.2022.906957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Common fragile sites (CFSs) are specific genomic loci prone to forming gaps or breakages upon replication perturbation, which correlate well with chromosomal rearrangement and copy number variation. CFSs have been actively studied due to their important pathophysiological relevance in different diseases such as cancer and neurological disorders. The genetic locations and sequences of CFSs are crucial to understanding the origin of such unstable sites, which require reliable mapping and characterizing approaches. In this review, we will inspect the evolving techniques for CFSs mapping, especially genome-wide mapping and sequencing of CFSs based on current knowledge of CFSs. We will also revisit the well-established hypotheses on the origin of CFSs fragility, incorporating novel findings from the comprehensive analysis of finely mapped CFSs regarding their locations, sequences, and replication/transcription, etc. This review will present the most up-to-date picture of CFSs and, potentially, a new framework for future research of CFSs.
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Affiliation(s)
- Fang Ji
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinli Zhu
- Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Liao
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Liujian Ouyang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingfei Huang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Madiha Zahra Syeda
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Songmin Ying
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
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3
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Li J, Sun X, You Y, Li Q, Wei C, Zhao L, Sun M, Meng H, Zhang T, Yue W, Wang L, Zhang D. Auts2 deletion involves in DG hypoplasia and social recognition deficit: The developmental and neural circuit mechanisms. SCIENCE ADVANCES 2022; 8:eabk1238. [PMID: 35235353 PMCID: PMC8890717 DOI: 10.1126/sciadv.abk1238] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/06/2022] [Indexed: 05/30/2023]
Abstract
The involvement of genetic risk and the underlying developmental and neural circuit mechanisms in autism-related social deficit are largely unclear. Here, we report that deletion of AUTS2, a high-susceptibility gene of ASDs, caused postnatal dentate gyrus (DG) hypoplasia, which was closely relevant to social recognition deficit. Furthermore, a previously unknown mechanism for neural cell migration in postnatal DG development was identified, in which Auts2-related signaling played a vital role as the transcription repressor. Moreover, the supramammillary nucleus (SuM)-DG-CA3 neural circuit was found to be involved in social recognition and affected in Auts2-deleted mice due to DG hypoplasia. Correction of DG-CA3 synaptic transmission by using a pharmacological approach or chemo/optogenetic activation of the SuM-DG circuit restored the social recognition deficit in Auts2-deleted mice. Our findings demonstrated the vital role of Auts2 in postnatal DG development, and this role was critical for SuM-DG-CA3 neural circuit-mediated social recognition behavior.
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Affiliation(s)
- Jun Li
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Xiaoxuan Sun
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Yang You
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Qiongwei Li
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Chengwen Wei
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Linnan Zhao
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Mengwen Sun
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Hu Meng
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Tian Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Weihua Yue
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Lifang Wang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
| | - Dai Zhang
- Peking University Sixth Hospital, Peking University Institute of Mental Health, NHC Key Laboratory of Mental Health (Peking University), National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China
- Chinese Institute for Brain Research, Beijing, China
- Institute for Brain Research and Rehabilitation (IBRR), Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
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4
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Kanlayaprasit S, Thongkorn S, Panjabud P, Jindatip D, Hu VW, Kikkawa T, Osumi N, Sarachana T. Autism-Related Transcription Factors Underlying the Sex-Specific Effects of Prenatal Bisphenol A Exposure on Transcriptome-Interactome Profiles in the Offspring Prefrontal Cortex. Int J Mol Sci 2021; 22:13201. [PMID: 34947998 PMCID: PMC8708761 DOI: 10.3390/ijms222413201] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 11/16/2022] Open
Abstract
Bisphenol A (BPA) is an environmental risk factor for autism spectrum disorder (ASD). BPA exposure dysregulates ASD-related genes in the hippocampus and neurological functions of offspring. However, whether prenatal BPA exposure has an impact on genes in the prefrontal cortex, another brain region highly implicated in ASD, and through what mechanisms have not been investigated. Here, we demonstrated that prenatal BPA exposure disrupts the transcriptome-interactome profiles of the prefrontal cortex of neonatal rats. Interestingly, the list of BPA-responsive genes was significantly enriched with known ASD candidate genes, as well as genes that were dysregulated in the postmortem brain tissues of ASD cases from multiple independent studies. Moreover, several differentially expressed genes in the offspring's prefrontal cortex were the targets of ASD-related transcription factors, including AR, ESR1, and RORA. The hypergeometric distribution analysis revealed that BPA may regulate the expression of such genes through these transcription factors in a sex-dependent manner. The molecular docking analysis of BPA and ASD-related transcription factors revealed novel potential targets of BPA, including RORA, SOX5, TCF4, and YY1. Our findings indicated that prenatal BPA exposure disrupts ASD-related genes in the offspring's prefrontal cortex and may increase the risk of ASD through sex-dependent molecular mechanisms, which should be investigated further.
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Grants
- FRB65_hea(80)_175_37_05 Fundamental Fund, Chulalongkorn University
- AHS-CU 61004 Faculty of Allied Health Sciences Research Fund, Chulalongkorn University
- GRU 6300437001-1 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- GRU_64_033_37_004 Ratchadapisek Somphot Fund for Supporting Research Unit, Chulalongkorn University
- The 100th Anniversary Chulalongkorn University Fund for Doctoral Scholarship, Graduate School, Chulalongkorn University
- The Overseas Research Experience Scholarship for Graduate Students from Graduate School, Chulalongkorn University
- PHD/0029/2561 The Royal Golden Jubilee Ph.D. Programme Scholarship, Thailand Research Fund and National Research Council of Thailand
- National Research Council of Thailand (NRCT)
- GCUGR1125623067D-67 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- GCUGR1125632108D-108 The 90th Anniversary Chulalongkorn University Fund (Ratchadaphiseksomphot Endowment Fund), Graduate School, Chulalongkorn University
- 2073011 Chulalongkorn University Laboratory Animal Center (CULAC) Grant
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Affiliation(s)
- Songphon Kanlayaprasit
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (S.T.); (P.P.)
| | - Surangrat Thongkorn
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (S.T.); (P.P.)
| | - Pawinee Panjabud
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand; (S.K.); (S.T.); (P.P.)
| | - Depicha Jindatip
- Systems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand;
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Valerie W. Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC 20052, USA;
| | - Takako Kikkawa
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai 980-8577, Miyagi, Japan; (T.K.); (N.O.)
| | - Noriko Osumi
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai 980-8577, Miyagi, Japan; (T.K.); (N.O.)
| | - Tewarit Sarachana
- Systems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand;
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Genetic determinants of autism spectrum disorders - a review. CURRENT PROBLEMS OF PSYCHIATRY 2021. [DOI: 10.2478/cpp-2021-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Abstract
Introduction: It is estimated that various types of abnormalities from the autistic spectrum disorder occur in up to 2% of the population. These include difficulties in maintaining relationships, communication, and repetitive behaviours. Literature describes them quite well, in contrast to the causes of these disorders, which include both environmental factors and a very long list of genetic aberrations.
Materials and methods: The papers available on the PubMed platform and other sources were reviewed to describe the most important genetic factors responsible for the development of autism spectrum disorders.
Results: There are many genes and their mutations associated with the prevalence of autism spectrum disorders in patients. One of the main factors is the SHANK gene family, with the type and degree of abnormality in patients depending on the damage to particular genes: SHANK1-SHANK3. Research also shows the potential of targeted symptom-relieving therapies in patients with SHANK3 mutations. A correlation with the occurrence of autism has also been demonstrated for genes responsible for calcium signaling - especially the group of IP3R calcium channels. Their calcium transmission is abnormal in the majority of patients with autism spectrum disorders. A number of mutations in the 7q region were discovered - including the AUTS2, GNAI1, RELN, KMT2E, BRAF genes - the occurrence of which is associated with the presence of symptoms of autism. Autism spectrum disorders occur in about 10% of patients suffering from monogenic syndromes such as fragile X chromosome syndrome, Timothy syndrome, tuberous sclerosis, Rett syndrome or hamartomatic tumor syndrome.
Conclusions: Research shows that many mutations can contribute to the development of autism spectrum disorders. Further studies are necessary to discover their therapeutic and diagnostic potential for autism.
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Pauli S, Berger H, Ufartes R, Borchers A. Comparing a Novel Malformation Syndrome Caused by Pathogenic Variants in FBRSL1 to AUTS2 Syndrome. Front Cell Dev Biol 2021; 9:779009. [PMID: 34805182 PMCID: PMC8602103 DOI: 10.3389/fcell.2021.779009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 11/13/2022] Open
Abstract
Truncating variants in specific exons of Fibrosin-like protein 1 (FBRSL1) were recently reported to cause a novel malformation and intellectual disability syndrome. The clinical spectrum includes microcephaly, facial dysmorphism, cleft palate, skin creases, skeletal anomalies and contractures, postnatal growth retardation, global developmental delay as well as respiratory problems, hearing impairment and heart defects. The function of FBRSL1 is largely unknown, but pathogenic variants in the FBRSL1 paralog Autism Susceptibility Candidate 2 (AUTS2) are causative for an intellectual disability syndrome with microcephaly (AUTS2 syndrome). Some patients with AUTS2 syndrome also show additional symptoms like heart defects and contractures overlapping with the phenotype presented by patients with FBRSL1 mutations. For AUTS2, a dual function, depending on different isoforms, was described and suggested for FBRSL1. Both, nuclear FBRSL1 and AUTS2 are components of the Polycomb subcomplexes PRC1.3 and PRC1.5. These complexes have essential roles in developmental processes, cellular differentiation and proliferation by regulating gene expression via histone modification. In addition, cytoplasmic AUTS2 controls neural development, neuronal migration and neurite extension by regulating the cytoskeleton. Here, we review recent data on FBRSL1 in respect to previously published data on AUTS2 to gain further insights into its molecular function, its role in development as well as its impact on human genetics.
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Affiliation(s)
- Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Hanna Berger
- Faculty of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
| | - Roser Ufartes
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Annette Borchers
- Faculty of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
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Sanchez-Jimeno C, Blanco-Kelly F, López-Grondona F, Losada-Del Pozo R, Moreno B, Rodrigo-Moreno M, Martinez-Cayuelas E, Riveiro-Alvarez R, Fenollar-Cortés M, Ayuso C, Rodríguez de Alba M, Lorda-Sanchez I, Almoguera B. Attention Deficit Hyperactivity and Autism Spectrum Disorders as the Core Symptoms of AUTS2 Syndrome: Description of Five New Patients and Update of the Frequency of Manifestations and Genotype-Phenotype Correlation. Genes (Basel) 2021; 12:genes12091360. [PMID: 34573342 PMCID: PMC8471078 DOI: 10.3390/genes12091360] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 12/14/2022] Open
Abstract
Haploinsufficiency of AUTS2 has been associated with a syndromic form of neurodevelopmental delay characterized by intellectual disability, autistic features, and microcephaly, also known as AUTS2 syndrome. While the phenotype associated with large deletions and duplications of AUTS2 is well established, clinical features of patients harboring AUTS2 sequence variants have not been extensively described. In this study, we describe the phenotype of five new patients with AUTS2 pathogenic variants, three of them harboring loss-of-function sequence variants. The phenotype of the patients was characterized by attention deficit/hyperactivity disorder (ADHD) and autism spectrum disorder (ASD) or autistic features and mild global developmental delay (GDD) or intellectual disability (ID), all in 4/5 patients (80%), a frequency higher than previously reported for ADHD and autistic features. Microcephaly and short stature were found in 60% of the patients; and feeding difficulties, generalized hypotonia, and ptosis, were each found in 40%. We also provide the aggregated frequency of the 32 items included in the AUTS2 syndrome severity score (ASSS) in patients currently reported in the literature. The main characteristics of the syndrome are GDD/ID in 98% of patients, microcephaly in 65%, feeding difficulties in 62%, ADHD or hyperactivity in 54%, and autistic traits in 52%. Finally, using the location of 31 variants from the literature together with variants from the five patients, we found significantly higher ASSS values in patients with pathogenic variants affecting the 3′ end of the gene, confirming the genotype-phenotype correlation initially described.
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Affiliation(s)
- Carolina Sanchez-Jimeno
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Fermina López-Grondona
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Rebeca Losada-Del Pozo
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - Beatriz Moreno
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - María Rodrigo-Moreno
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - Elena Martinez-Cayuelas
- Department of Pediatrics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (R.L.-D.P.); (B.M.); (M.R.-M.); (E.M.-C.)
| | - Rosa Riveiro-Alvarez
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - María Fenollar-Cortés
- Clinical Genetics Unit, Department of Clinical Analysis, Clínico San Carlos University Hospital, 28040 Madrid, Spain;
- IIS-Clínico San Carlos University Hospital (IsISSC), 28040 Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Marta Rodríguez de Alba
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Isabel Lorda-Sanchez
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
| | - Berta Almoguera
- Department of Genetics and Genomics, IIS–Fundación Jiménez Díaz University Hospital, 28040 Madrid, Spain; (C.S.-J.); (F.B.-K.); (F.L.-G.); (R.R.-A.); (C.A.); (M.R.d.A.); (I.L.-S.)
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28040 Madrid, Spain
- Correspondence:
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Erotomania and phenotypic continuum in a family frameshift variant of AUTS2: a case report and review. BMC Psychiatry 2021; 21:360. [PMID: 34273950 PMCID: PMC8285776 DOI: 10.1186/s12888-021-03342-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 06/25/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Pathogenic variants of the AUTS2 (Autism Susceptibility candidate 2) gene predispose to intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, facial dysmorphism and short stature. This phenotype is therefore associated with neurocognitive disturbances and social cognition, indicating potential functional maladjustment in the affected subjects, and a potentially significant impact on quality of life. Although many isolated cases have been reported in the literature, to date no families have been described. This case reports on a family (three generations) with a frameshift variant in the AUTS2 gene. CASE PRESENTATION The proband is 13 years old with short stature, dysmorphic features, moderate intellectual disability and autism spectrum disorder. His mother is 49 years old and also has short stature and similar dysmorphic features. She does not have autism disorder but presents an erotomaniac delusion. Her cognitive performance is heterogeneous. The two aunts are also of short stature. The 50-year-old aunt has isolated social cognition disorders. The 45-year-old aunt has severe cognitive impairment and autism spectrum disorder. The molecular analysis of the three sisters and the proband shows the same AUTS2 heterozygous duplication leading to a frame shift expected to produce a premature stop codon, p.(Met593Tyrfs*85). Previously reported isolated cases revealed phenotypic and cognitive impairment variability. In this case report, these variabilities are present within the same family, presenting the same variant. CONCLUSIONS The possibility of a phenotypic spectrum within the same family highlights the need for joint psychiatry and genetics research.
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9
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Mossink B, Negwer M, Schubert D, Nadif Kasri N. The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective. Cell Mol Life Sci 2021; 78:2517-2563. [PMID: 33263776 PMCID: PMC8004494 DOI: 10.1007/s00018-020-03714-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID) and autism spectrum disorders (ASD), are a large group of disorders in which early insults during brain development result in a wide and heterogeneous spectrum of clinical diagnoses. Mutations in genes coding for chromatin remodelers are overrepresented in NDD cohorts, pointing towards epigenetics as a convergent pathogenic pathway between these disorders. In this review we detail the role of NDD-associated chromatin remodelers during the developmental continuum of progenitor expansion, differentiation, cell-type specification, migration and maturation. We discuss how defects in chromatin remodelling during these early developmental time points compound over time and result in impaired brain circuit establishment. In particular, we focus on their role in the three largest cell populations: glutamatergic neurons, GABAergic neurons, and glia cells. An in-depth understanding of the spatiotemporal role of chromatin remodelers during neurodevelopment can contribute to the identification of molecular targets for treatment strategies.
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Affiliation(s)
- Britt Mossink
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Moritz Negwer
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
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10
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Gieldon L, Jauch A, Obeid K, Kaufmann L, Hinderhofer K, Haug U, Moog U. Germ cell mosaicism for AUTS2 exon 6 deletion. Am J Med Genet A 2021; 185:1261-1265. [PMID: 33577136 DOI: 10.1002/ajmg.a.62091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/07/2021] [Accepted: 01/09/2021] [Indexed: 11/11/2022]
Abstract
Haploinsufficiency of AUTS2 has been associated with neurodevelopmental disorders and dysmorphic features (MIM # 615834). More than 50 patients have been described, mostly carrying de novo deletions of one or more exons, including eight patients with exon 6 deletions. We report on two siblings, a girl and a boy aged 11 and 13 years, in whom the same pathogenic 85 kb deletion on 7q11.22 encompassing exon 6 of AUTS2 by SNP array analysis was identified. Both children had typical symptoms of AUTS2 syndrome such as intellectual impairment and behavioral problems, but with markedly different expression. SNP array analysis excluded the deletion in blood samples of both parents and a healthy brother. Conventional karyotyping of both parents and additional FISH analyses, marking the flanking regions of the deletion, did not show any structural rearrangements involving 7q11.22. A germ cell mosaicism was suggested as the most probable explanation for occurrence of the same deletion in these two siblings. To our knowledge this is the first report of germ cell mosaicism for AUTS2 syndrome. It additionally provides further evidence of intrafamilial phenotypic variability in AUTS2 syndrome and adds clinical information to the phenotypic spectrum of patients with AUTS2 exon 6 deletions.
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Affiliation(s)
- Laura Gieldon
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Katharina Obeid
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Lilian Kaufmann
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | - Ulrich Haug
- Center for Child Neurology and Social Pediatrics Maulbronn, Maulbronn, Germany
| | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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11
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Martinez-Delgado B, Lopez-Martin E, Lara-Herguedas J, Monzon S, Cuesta I, Juliá M, Aquino V, Rodriguez-Martin C, Damian A, Gonzalo I, Gomez-Mariano G, Baladron B, Cazorla R, Iglesias G, Roman E, Ros P, Tutor P, Mellor S, Jimenez C, Cabrejas MJ, Gonzalez-Vioque E, Alonso J, Bermejo-Sánchez E, Posada M. De novo small deletion affecting transcription start site of short isoform of AUTS2 gene in a patient with syndromic neurodevelopmental defects. Am J Med Genet A 2020; 185:877-883. [PMID: 33346930 DOI: 10.1002/ajmg.a.62017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/03/2020] [Accepted: 11/22/2020] [Indexed: 12/15/2022]
Abstract
Disruption of the autism susceptibility candidate 2 (AUTS2) gene through genomic rearrangements, copy number variations (CNVs), and intragenic deletions and mutations, has been recurrently involved in syndromic forms of developmental delay and intellectual disability, known as AUTS2 syndrome. The AUTS2 gene plays an important role in regulation of neuronal migration, and when altered, associates with a variable phenotype from severely to mildly affected patients. The more severe phenotypes significantly correlate with the presence of defects affecting the C-terminus part of the gene. This article reports a new patient with a syndromic neurodevelopmental disorder, who presents a deletion of 30 nucleotides in the exon 9 of the AUTS2 gene. Importantly, this deletion includes the transcription start site for the AUTS2 short transcript isoform, which has an important role in brain development. Gene expression analysis of AUTS2 full-length and short isoforms revealed that the deletion found in this patient causes a remarkable reduction in the expression level, not only of the short isoform, but also of the full AUTS2 transcripts. This report adds more evidence for the role of mutated AUTS2 short transcripts in the development of a severe phenotype in the AUTS2 syndrome.
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Affiliation(s)
- Beatriz Martinez-Delgado
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain.,Consortium for Biomedical Research in Rare Diseases (CIBER de Enfermedades Raras/CIBERER) (CB06/07/1009), ISCIII, Madrid, Spain.,Undiagnosed Diseases Network International, Madrid, Spain
| | - Estrella Lopez-Martin
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain.,Consortium for Biomedical Research in Rare Diseases (CIBER de Enfermedades Raras/CIBERER) (CB06/07/1009), ISCIII, Madrid, Spain.,Undiagnosed Diseases Network International, Madrid, Spain
| | - Julián Lara-Herguedas
- Department of Neuropediatrics, Puerta de Hierro University Teaching Hospital, Madrid, Spain
| | - Sara Monzon
- Undiagnosed Diseases Network International, Madrid, Spain.,Bioinformatics Unit, ISCIII, Madrid, Spain
| | - Isabel Cuesta
- Undiagnosed Diseases Network International, Madrid, Spain.,Bioinformatics Unit, ISCIII, Madrid, Spain
| | - Miguel Juliá
- Undiagnosed Diseases Network International, Madrid, Spain.,Bioinformatics Unit, ISCIII, Madrid, Spain
| | - Virginia Aquino
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain
| | - Carlos Rodriguez-Martin
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain
| | - Alejandra Damian
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain
| | - Irene Gonzalo
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain
| | - Gema Gomez-Mariano
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain.,Undiagnosed Diseases Network International, Madrid, Spain
| | - Beatriz Baladron
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain.,Undiagnosed Diseases Network International, Madrid, Spain
| | - Rosario Cazorla
- Department of Neuropediatrics, Puerta de Hierro University Teaching Hospital, Madrid, Spain
| | - Gema Iglesias
- Department of Neuropediatrics, Puerta de Hierro University Teaching Hospital, Madrid, Spain
| | - Enriqueta Roman
- Department of Neuropediatrics, Puerta de Hierro University Teaching Hospital, Madrid, Spain
| | | | - Pablo Tutor
- Department of Internal Medicine, Puerta de Hierro University Teaching Hospital, Madrid, Spain
| | - Susana Mellor
- Department of Internal Medicine, Puerta de Hierro University Teaching Hospital, Madrid, Spain
| | - Carlos Jimenez
- Department of Neurology, Puerta de Hierro University Teaching Hospital, Madrid, Spain
| | - Maria Jose Cabrejas
- Department of Clinical Biochemistry, Puerta de Hierro University Teaching Hospital, Madrid, Spain
| | - Emiliano Gonzalez-Vioque
- Department of Clinical Biochemistry, Puerta de Hierro University Teaching Hospital, Madrid, Spain
| | - Javier Alonso
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain.,Consortium for Biomedical Research in Rare Diseases (CIBER de Enfermedades Raras/CIBERER) (CB06/07/1009), ISCIII, Madrid, Spain.,Undiagnosed Diseases Network International, Madrid, Spain
| | - Eva Bermejo-Sánchez
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain.,Undiagnosed Diseases Network International, Madrid, Spain
| | - Manuel Posada
- Institute of Rare Diseases Research (Instituto de Investigación de Enfermedades Raras/IIER), Carlos III Institute of Health (Instituto de Salud Carlos III/ISCIII), Madrid, Spain.,Consortium for Biomedical Research in Rare Diseases (CIBER de Enfermedades Raras/CIBERER) (CB06/07/1009), ISCIII, Madrid, Spain.,Undiagnosed Diseases Network International, Madrid, Spain
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12
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A genetic window to auditory-verbal problems in bipolar disorder. Psychiatr Genet 2020; 30:169-173. [PMID: 33165203 DOI: 10.1097/ypg.0000000000000265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Bipolar disorder is a high prevalent psychiatric condition entailing recurrent episodes of elevated mood and depression, but also diverse cognitive problems. One deficit observed in patients concerns to auditory-verbal processing. Being a hereditary condition with a complex genetic architecture, it is not clear which genes contribute to this deficit. We show that candidates for bipolar disorder significantly overlap with candidates for clinical conditions resulting from a deficit in the phonological loop of working memory, particularly, developmental dyslexia and specific language impairment. The overlapping genes are involved in aspects of brain development and function (particularly, brain oscillations) potentially underlying phonological processing and accordingly, emerge as promising candidates for auditory-verbal deficits in bipolar disorder.
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13
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Saeki S, Enokizono T, Imagawa K, Fukushima H, Kajikawa D, Sakai A, Tanaka M, Ohto T, Suzuki H, Uehara T, Takenouchi T, Kenjiro K, Takada H. A case of autism spectrum disorder with cleft lip and palate carrying a mutation in exon 8 of AUTS2. Clin Case Rep 2019; 7:2059-2063. [PMID: 31788251 PMCID: PMC6878208 DOI: 10.1002/ccr3.2377] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/16/2019] [Accepted: 07/13/2019] [Indexed: 11/11/2022] Open
Abstract
We report a patient with autism and cleft lip and palate carrying a de novo heterozygous AUTS2 mutation, c.1464_1467del ACTC (p.Tyr488*). Although the causal relationship between cleft lip and palate and this mutation is unclear, this case report may expand the clinical phenotype of AUTS2 syndrome.
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Affiliation(s)
- Saki Saeki
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Takashi Enokizono
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Kazuo Imagawa
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Hiroko Fukushima
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Daigo Kajikawa
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Aiko Sakai
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Mai Tanaka
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Tatsuyuki Ohto
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
| | - Hisato Suzuki
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
| | - Tomoko Uehara
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
| | | | - Kosaki Kenjiro
- Center for Medical GeneticsKeio University School of MedicineTokyoJapan
| | - Hidetoshi Takada
- Department of Pediatrics, Faculty of MedicineUniversity of TsukubaTsukubaJapan
- Department of Child Health, Faculty of MedicineUniversity of TsukubaTsukubaJapan
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14
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Maya I, Singer A, Yonath H, Reches A, Rienstein S, Zeligson S, Ben Shachar S, Sagi-Dain L. What have we learned from 691 prenatal chromosomal microarrays for ventricular septal defects? Acta Obstet Gynecol Scand 2019; 99:757-764. [PMID: 31424084 DOI: 10.1111/aogs.13708] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/09/2019] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Ventricular septal defect (VSD) represents the most common type of congenital cardiac anomaly, affecting more than 1 in 300 live births. The objective of this study was to examine the incidence and nature of abnormal chromosomal microarray analysis (CMA) results in a large cohort of pregnancies with VSD. MATERIAL AND METHODS Data acquisition was performed through the Ministry of Health computerized database. All CMA results performed due to VSD during 2013-2017 were included. The rates of clinically significant CMA results of cases with isolated and non-isolated VSD were compared with two control populations-a systematic review of 9272 pregnancies and a local cohort of 5541 fetuses with normal ultrasound. RESULTS Overall, 691 CMA analyses performed due to a sonographic indication of VSD were detected. Of 568 pregnancies with isolated VSD, eight (1.4%) clinically significant copy number variants were detected, a nonsignificant difference compared with low risk pregnancies. Of the 123 pregnancies with non-isolated VSDs, 18 (14.6%) clinically significant CMA results were detected, a considerably increased risk compared with control pregnancies. Karyotype-detectable anomalies constituted 12 of the 18 abnormal CMA results in non-isolated VSD group (66.7%), a significantly higher proportion compared with 2 of 8 (25%) in isolated VSD cohort. CONCLUSIONS The outcomes of our study, representing the largest number of CMA results in pregnancies with VSD, suggest that the rate of abnormal CMA findings in isolated VSD does not differ from pregnancies with normal ultrasound. This observation is true for populations undergoing routine common trisomy screening tests and early sonographic evaluation, as well as widely available non-invasive prenatal screening. Conversely, CMA analysis yields a high detection rate in pregnancies with non-isolated VSD. Our results question the recommendation to perform invasive prenatal testing for CMA in pregnancies with isolated VSD.
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Affiliation(s)
- Idit Maya
- Rabin Medical Center, Recanati Genetics Institute, Beilinson Hospital, Petach Tikva, Israel
| | - Amihood Singer
- Community Genetics, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Hagith Yonath
- Sheba Medical Center, Genetics Institute, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Adi Reches
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Tel Aviv Sourasky Medical Center, Genetics Institute, Tel Aviv, Israel
| | - Shlomit Rienstein
- Danek Gertner Institute of Human Genetics, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Zeligson
- Shaare Zedek Medical Center, Medical Genetics Institute, Jerusalem, Israel
| | - Shay Ben Shachar
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Tel Aviv Sourasky Medical Center, Genetics Institute, Tel Aviv, Israel.,Clalit Research Institute, Ramat Gan, Israel
| | - Lena Sagi-Dain
- Carmel Medical Center, Genetics Institute, Haifa, Israel.,Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
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15
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Murphy E, Benítez-Burraco A. Toward the Language Oscillogenome. Front Psychol 2018; 9:1999. [PMID: 30405489 PMCID: PMC6206218 DOI: 10.3389/fpsyg.2018.01999] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/28/2018] [Indexed: 12/20/2022] Open
Abstract
Language has been argued to arise, both ontogenetically and phylogenetically, from specific patterns of brain wiring. We argue that it can further be shown that core features of language processing emerge from particular phasal and cross-frequency coupling properties of neural oscillations; what has been referred to as the language ‘oscillome.’ It is expected that basic aspects of the language oscillome result from genetic guidance, what we will here call the language ‘oscillogenome,’ for which we will put forward a list of candidate genes. We have considered genes for altered brain rhythmicity in conditions involving language deficits: autism spectrum disorders, schizophrenia, specific language impairment and dyslexia. These selected genes map on to aspects of brain function, particularly on to neurotransmitter function. We stress that caution should be adopted in the construction of any oscillogenome, given the range of potential roles particular localized frequency bands have in cognition. Our aim is to propose a set of genome-to-language linking hypotheses that, given testing, would grant explanatory power to brain rhythms with respect to language processing and evolution.
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Affiliation(s)
- Elliot Murphy
- Division of Psychology and Language Sciences, University College London, London, United Kingdom.,Department of Psychology, University of Westminster, London, United Kingdom
| | - Antonio Benítez-Burraco
- Department of Spanish Language, Linguistics and Literary Theory, University of Seville, Seville, Spain
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16
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The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:306-327. [PMID: 29309830 DOI: 10.1016/j.pnpbp.2017.12.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/13/2022]
Abstract
The complexity of the human brain emerges from a long and finely tuned developmental process orchestrated by the crosstalk between genome and environment. Vis à vis other species, the human brain displays unique functional and morphological features that result from this extensive developmental process that is, unsurprisingly, highly vulnerable to both genetically and environmentally induced alterations. One of the most striking outcomes of the recent surge of sequencing-based studies on neurodevelopmental disorders (NDDs) is the emergence of chromatin regulation as one of the two domains most affected by causative mutations or Copy Number Variations besides synaptic function, whose involvement had been largely predicted for obvious reasons. These observations place chromatin dysfunction at the top of the molecular pathways hierarchy that ushers in a sizeable proportion of NDDs and that manifest themselves through synaptic dysfunction and recurrent systemic clinical manifestation. Here we undertake a conceptual investigation of chromatin dysfunction in NDDs with the aim of systematizing the available evidence in a new framework: first, we tease out the developmental vulnerabilities in human corticogenesis as a structuring entry point into the causation of NDDs; second, we provide a much needed clarification of the multiple meanings and explanatory frameworks revolving around "epigenetics", highlighting those that are most relevant for the analysis of these disorders; finally we go in-depth into paradigmatic examples of NDD-causing chromatin dysregulation, with a special focus on human experimental models and datasets.
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17
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Gao K, Zhang Y, Zhang L, Kong W, Xie H, Wang J, Wu Y, Wu X, Liu X, Zhang Y, Zhang F, Yu ACH, Jiang Y. Large De Novo Microdeletion in Epilepsy with Intellectual and Developmental Disabilities, with a Systems Biology Analysis. ADVANCES IN NEUROBIOLOGY 2018; 21:247-266. [DOI: 10.1007/978-3-319-94593-4_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Gambin T, Yuan B, Bi W, Liu P, Rosenfeld JA, Coban-Akdemir Z, Pursley AN, Nagamani SCS, Marom R, Golla S, Dengle L, Petrie HG, Matalon R, Emrick L, Proud MB, Treadwell-Deering D, Chao HT, Koillinen H, Brown C, Urraca N, Mostafavi R, Bernes S, Roeder ER, Nugent KM, Bader PI, Bellus G, Cummings M, Northrup H, Ashfaq M, Westman R, Wildin R, Beck AE, Immken L, Elton L, Varghese S, Buchanan E, Faivre L, Lefebvre M, Schaaf CP, Walkiewicz M, Yang Y, Kang SHL, Lalani SR, Bacino CA, Beaudet AL, Breman AM, Smith JL, Cheung SW, Lupski JR, Patel A, Shaw CA, Stankiewicz P. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med 2017; 9:83. [PMID: 28934986 PMCID: PMC5607840 DOI: 10.1186/s13073-017-0472-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association. RESULTS In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses. CONCLUSIONS Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Amber N Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sailaja Golla
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lauren Dengle
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Reuben Matalon
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Lisa Emrick
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica B Proud
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Treadwell-Deering
- Department of Psychiatry and Behavioral Sciences, Child and Adolescent Psychiatry Division, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Hannele Koillinen
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Chester Brown
- Genetics Division, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38105, USA.,Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | - Nora Urraca
- Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | | | | | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Patricia I Bader
- Northeast Indiana Genetic Counseling Center, Wayne, IN, 46804, USA
| | - Gary Bellus
- Section of Clinical Genetics & Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael Cummings
- Department of Psychiatry Erie County Medical Center, Buffalo, NY, 14215, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Myla Ashfaq
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | | | - Robert Wildin
- St. Luke's Children's Hospital, Boise, ID, 83702, USA.,The National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Anita E Beck
- Seattle Children's Hospital, Seattle, WA, 98105, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | | | - Lindsay Elton
- Child Neurology Consultants of Austin, Austin, TX, 78731, USA
| | - Shaun Varghese
- THINK Neurology for Kids/Children's Memorial Hermann Hospital, The Woodlands, TX, 77380, USA
| | - Edward Buchanan
- Division of Plastic Surgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Mathilde Lefebvre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sung-Hae L Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, 77021, USA.
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19
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Srivastava A, McGrath B, Bielas SL. Histone H2A Monoubiquitination in Neurodevelopmental Disorders. Trends Genet 2017; 33:566-578. [PMID: 28669576 PMCID: PMC5562288 DOI: 10.1016/j.tig.2017.06.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/05/2017] [Indexed: 11/21/2022]
Abstract
Covalent histone modifications play an essential role in gene regulation and cellular specification required for multicellular organism development. Monoubiquitination of histone H2A (H2AUb1) is a reversible transcriptionally repressive mark. Exchange of histone H2A monoubiquitination and deubiquitination reflects the succession of transcriptional profiles during development required to produce cellular diversity from pluripotent cells. Germ-line pathogenic variants in components of the H2AUb1 regulatory axis are being identified as the genetic basis of congenital neurodevelopmental disorders. Here, we review the human genetics findings coalescing on molecular mechanisms that alter the genome-wide distribution of this histone modification required for development.
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Affiliation(s)
- Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Brian McGrath
- Cell and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA; Cell and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, USA.
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20
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Abstract
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics; the Department of Pathology; and the Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics; and the Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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21
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Chen XS, Reader RH, Hoischen A, Veltman JA, Simpson NH, Francks C, Newbury DF, Fisher SE. Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. Sci Rep 2017; 7:46105. [PMID: 28440294 PMCID: PMC5404330 DOI: 10.1038/srep46105] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 03/08/2017] [Indexed: 12/22/2022] Open
Abstract
A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential “multiple-hit” cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affecting STARD9, while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation.
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Affiliation(s)
- Xiaowei Sylvia Chen
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Rose H Reader
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Clinical Genetics, University of Maastricht, Maastricht, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Nuala H Simpson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Clyde Francks
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Dianne F Newbury
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
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22
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The Correlation-Base-Selection Algorithm for Diagnostic Schizophrenia Based on Blood-Based Gene Expression Signatures. BIOMED RESEARCH INTERNATIONAL 2017; 2017:7860506. [PMID: 28280741 PMCID: PMC5322573 DOI: 10.1155/2017/7860506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/30/2016] [Indexed: 11/20/2022]
Abstract
Microarray analysis of gene expression is often used to diagnose different types of disease. Many studies report remarkable achievements in nervous system disease. Clinical diagnosis of schizophrenia (SCZ) still depends on doctors' experience, which is unreliable and needs to be more objective and quantified. To solve this problem, we collected whole blood gene expression data from four studies, including 152 individuals with schizophrenia (SCZ) and 138 normal controls in different regions. The correlation-based feature selection (CFS, one of the machine learning methods) algorithm was applied in this study, and 103 significantly differentially expressed genes between patients and controls, called “feature genes,” were selected; then, a model for SCZ diagnosis was built. The samples were subdivided into 10 groups, and cross-validation showed that the model we constructed achieved nearly 100% classification accuracy. Mathematical evaluation of the datasets before and after data processing proved the effectiveness of our algorithm. Feature genes were enriched in Parkinson's disease, oxidative phosphorylation, and TGF-beta signaling pathways, which were previously reported to be associated with SCZ. These results suggest that the analysis of gene expression in whole blood by our model could be a useful tool for diagnosing SCZ.
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23
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Sapkota Y, Narasimhan A, Kumaran M, Sehrawat BS, Damaraju S. A Genome-Wide Association Study to Identify Potential Germline Copy Number Variants for Sporadic Breast Cancer Susceptibility. Cytogenet Genome Res 2016; 149:156-164. [PMID: 27668787 DOI: 10.1159/000448558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 11/19/2022] Open
Abstract
Breast cancer (BC) predisposition in populations arises from both genetic and nongenetic risk factors. Structural variations such as copy number variations (CNVs) are heritable determinants for disease susceptibility. The primary objectives of this study are (1) to identify CNVs associated with sporadic BC using a genome-wide association study (GWAS) design; (2) to utilize 2 distinct CNV calling algorithms to identify concordant CNVs as a strategy to reduce false positive associations in the hypothesis-generating GWAS discovery phase, and (3) to identify potential candidate CNVs for follow-up replication studies. We used Affymetrix SNP Array 6.0 data profiled on Caucasian subjects (422 cases/348 controls) to call CNVs using algorithms implemented in Nexus Copy Number and Partek Genomics Suite software. Nexus algorithm identified CNVs associated with BC (731 autosomal CNVs with >5% frequency in the total sample and Q < 0.05). Thirteen CNVs were identified when Partek algorithm-called CNVs were overlapped with Nexus-identified CNVs; these CNVs showed concordances for frequency, effect size, and direction. Coding genes present within BC-associated CNVs were known to play a role in disease etiology and prognosis. Long noncoding RNAs identified within CNVs showed tissue-specific expression, indicating potential functional relevance of the findings. The identified candidate CNVs warrant independent replication.
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Affiliation(s)
- Yadav Sapkota
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, Tenn., USA
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24
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Sengun E, Yararbas K, Kasakyan S, Alanay Y. AUTS2 Syndrome in a 68-year-old female: Natural history and further delineation of the phenotype. Am J Med Genet A 2016; 170:3231-3236. [DOI: 10.1002/ajmg.a.37882] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 07/15/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Ece Sengun
- Department of Pediatrics; Acibadem University School of Medicine; Istanbul Turkey
| | - Kanay Yararbas
- Duzen Laboratories Group; Istanbul Turkey
- Maltepe University School of Medicine; Istanbul Turkey
| | | | - Yasemin Alanay
- Pediatric Genetics Unit; Department of Pediatrics; Acibadem University School of Medicine; Istanbul Turkey
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25
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Beunders G, van de Kamp J, Vasudevan P, Morton J, Smets K, Kleefstra T, de Munnik SA, Schuurs-Hoeijmakers J, Ceulemans B, Zollino M, Hoffjan S, Wieczorek S, So J, Mercer L, Walker T, Velsher L, Parker MJ, Magee AC, Elffers B, Kooy RF, Yntema HG, Meijers-Heijboer EJ, Sistermans EA. A detailed clinical analysis of 13 patients with AUTS2 syndrome further delineates the phenotypic spectrum and underscores the behavioural phenotype. J Med Genet 2016; 53:523-32. [DOI: 10.1136/jmedgenet-2015-103601] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/09/2016] [Indexed: 12/31/2022]
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26
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Erickson RP. The importance of de novo mutations for pediatric neurological disease--It is not all in utero or birth trauma. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 767:42-58. [PMID: 27036065 DOI: 10.1016/j.mrrev.2015.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 01/30/2023]
Abstract
The advent of next generation sequencing (NGS, which consists of massively parallel sequencing to perform TGS (total genome sequencing) or WES (whole exome sequencing)) has abundantly discovered many causative mutations in patients with pediatric neurological disease. A surprisingly high number of these are de novo mutations which have not been inherited from either parent. For epilepsy, autism spectrum disorders, and neuromotor disorders, including cerebral palsy, initial estimates put the frequency of causative de novo mutations at about 15% and about 10% of these are somatic. There are some shared mutated genes between these three classes of disease. Studies of copy number variation by comparative genomic hybridization (CGH) proceded the NGS approaches but they also detect de novo variation which is especially important for ASDs. There are interesting differences between the mutated genes detected by CGS and NGS. In summary, de novo mutations cause a very significant proportion of pediatric neurological disease.
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Affiliation(s)
- Robert P Erickson
- Dept. of Pediatrics, University of Arizona College of Medicine, Tucson, AZ 85724, United States.
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27
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Srivastava A, Ritesh KC, Tsan YC, Liao R, Su F, Cao X, Hannibal MC, Keegan CE, Chinnaiyan AM, Martin DM, Bielas SL. De novo dominant ASXL3 mutations alter H2A deubiquitination and transcription in Bainbridge-Ropers syndrome. Hum Mol Genet 2015; 25:597-608. [PMID: 26647312 DOI: 10.1093/hmg/ddv499] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/01/2015] [Indexed: 12/22/2022] Open
Abstract
De novo truncating mutations in Additional sex combs-like 3 (ASXL3) have been identified in individuals with Bainbridge-Ropers syndrome (BRS), characterized by failure to thrive, global developmental delay, feeding problems, hypotonia, dysmorphic features, profound speech delays and intellectual disability. We identified three novel de novo heterozygous truncating variants distributed across ASXL3, outside the original cluster of ASXL3 mutations previously described for BRS. Primary skin fibroblasts established from a BRS patient were used to investigate the functional impact of pathogenic variants. ASXL3 mRNA transcripts from the mutated allele are prone to nonsense-mediated decay, and expression of ASXL3 is reduced. We found that ASXL3 interacts with BAP1, a hydrolase that removes mono-ubiquitin from histone H2A lysine 119 (H2AK119Ub1) as a component of the Polycomb repressive deubiquitination (PR-DUB) complex. A significant increase in H2AK119Ub1 was observed in ASXL3 patient fibroblasts, highlighting an important functional role for ASXL3 in PR-DUB mediated deubiquitination. Transcriptomes of ASXL3 patient and control fibroblasts were compared to investigate the impact of chromatin changes on transcriptional regulation. Out of 564 significantly differentially expressed genes (DEGs) in ASXL3 patient fibroblasts, 52% were upregulated and 48% downregulated. DEGs were enriched in molecular processes impacting transcriptional regulation, development and proliferation, consistent with the features of BRS. This is the first single gene disorder linked to defects in deubiquitination of H2AK119Ub1 and suggests an important role for dynamic regulation of H2A mono-ubiquitination in transcriptional regulation and the pathophysiology of BRS.
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Affiliation(s)
| | | | | | | | - Fengyun Su
- Howard Hughes Medical Institute, Department of Pathology, Departments of Urology, Computational Medicine and Bioinformatics, and
| | - Xuhong Cao
- Howard Hughes Medical Institute, Department of Pathology, Departments of Urology, Computational Medicine and Bioinformatics, and
| | - Mark C Hannibal
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Catherine E Keegan
- Department of Human Genetics, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Arul M Chinnaiyan
- Howard Hughes Medical Institute, Department of Pathology, Departments of Urology, Computational Medicine and Bioinformatics, and
| | - Donna M Martin
- Department of Human Genetics, Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, USA
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28
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Reiner O, Karzbrun E, Kshirsagar A, Kaibuchi K. Regulation of neuronal migration, an emerging topic in autism spectrum disorders. J Neurochem 2015; 136:440-56. [PMID: 26485324 DOI: 10.1111/jnc.13403] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/04/2015] [Accepted: 10/09/2015] [Indexed: 12/14/2022]
Abstract
Autism spectrum disorders (ASD) encompass a group of neurodevelopmental diseases that demonstrate strong heritability, however, the inheritance is not simple and many genes have been associated with these disorders. ASD is regarded as a neurodevelopmental disorder, and abnormalities at different developmental stages are part of the disease etiology. This review provides a general background on neuronal migration during brain development and discusses recent advancements in the field connecting ASD and aberrant neuronal migration. We propose that neuronal migration impairment may be an important common pathophysiology in autism spectrum disorders (ASD). This review provides a general background on neuronal migration during brain development and discusses recent advancements in the field connecting ASD and aberrant neuronal migration.
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Affiliation(s)
- Orly Reiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eyal Karzbrun
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Aditya Kshirsagar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Showa, Nagoya, Japan
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29
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Fan Y, Qiu W, Wang L, Gu X, Yu Y. Exonic deletions ofAUTS2in Chinese patients with developmental delay and intellectual disability. Am J Med Genet A 2015; 170A:515-522. [PMID: 26545289 DOI: 10.1002/ajmg.a.37454] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/19/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Yanjie Fan
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research; Shanghai China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research; Shanghai China
| | - Lili Wang
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research; Shanghai China
| | - Xuefan Gu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research; Shanghai China
| | - Yongguo Yu
- Department of Pediatric Endocrinology/Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine; Shanghai Institute for Pediatric Research; Shanghai China
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30
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Schneider A, Puechberty J, Ng BL, Coubes C, Gatinois V, Tournaire M, Girard M, Dumont B, Bouret P, Magnetto J, Baghdadli A, Pellestor F, Geneviève D. Identification of disrupted AUTS2 and EPHA6 genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder. Am J Med Genet A 2015; 167A:3031-7. [PMID: 26333717 DOI: 10.1002/ajmg.a.37350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/12/2015] [Indexed: 11/09/2022]
Abstract
Intellectual disability (ID) is a frequent feature but is highly clinically and genetically heterogeneous. The establishment of the precise diagnosis in patients with ID is challenging due to this heterogeneity but crucial for genetic counseling and appropriate care for the patients. Among the etiologies of patients with ID, apparently balanced de novo rearrangements represent 0.6%. Several mechanisms explain the ID in patients with apparently balanced de novo rearrangement. Among them, disruption of a disease gene at the breakpoint, is frequently evoked. In this context, technologies recently developed are used to characterize precisely such chromosomal rearrangements. Here, we report the case of a boy with ID, facial features and autistic behavior who is carrying a de novo balanced reciprocal translocation t(3;7)(q11.2;q11.22)dn. Using microarray analysis, array painting (AP) technology combined with molecular study, we have identified the interruption of the autism susceptibility candidate 2 gene (AUTS2) and EPH receptor A6 gene (EPHA6). We consider that the disruption of AUTS2 explains the phenotype of the patient; the exact role of EPHA6 in human pathology is not well defined. Based on the observation of recurrent germinal and somatic translocations involving AUTS2 and the molecular environment content, we put forward the hypothesis that the likely chromosomal mechanism responsible for the translocation could be due either to replicative stress or to recombination-based mechanisms.
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Affiliation(s)
- Anouck Schneider
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | | | - Bee Ling Ng
- Cytometry Core Facility, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - Vincent Gatinois
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Magali Tournaire
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Manon Girard
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Bruno Dumont
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Pauline Bouret
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Julia Magnetto
- CRA, Département de Psychiatrie de l'Enfant et de l'Adolescent, Centre de Ressources Autisme, CHRU de Montpellier, France
| | - Amaria Baghdadli
- CRA, Département de Psychiatrie de l'Enfant et de l'Adolescent, Centre de Ressources Autisme, CHRU de Montpellier, France
| | - Franck Pellestor
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - David Geneviève
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France.,Département de Génétique Médicale, CHRU de Montpellier, France
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31
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A genome-wide association study of antidepressant response in Koreans. Transl Psychiatry 2015; 5:e633. [PMID: 26348319 PMCID: PMC5068817 DOI: 10.1038/tp.2015.127] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/20/2015] [Accepted: 07/08/2015] [Indexed: 12/11/2022] Open
Abstract
We conducted a three-stage genome-wide association study (GWAS) of response to antidepressant drugs in an ethnically homogeneous sample of Korean patients in untreated episodes of nonpsychotic unipolar depression, mostly of mature onset. Strict quality control was maintained in case selection, diagnosis, verification of adherence and outcome assessments. Analyzed cases completed 6 weeks of treatment with adequate plasma drug concentrations. The overall successful completion rate was 85.5%. Four candidate single-nucleotide polymorphisms (SNPs) on three chromosomes were identified by genome-wide search in the discovery sample of 481 patients who received one of four allowed selective serotonin reuptake inhibitor (SSRI) antidepressant drugs (Stage 1). In a focused replication study of 230 SSRI-treated patients, two of these four SNP candidates were confirmed (Stage 2). Analysis of the Stage 1 and Stage 2 samples combined (n = 711) revealed GWAS significance (P = 1.60 × 10(-8)) for these two SNP candidates, which were in perfect linkage disequilibrium. These two significant SNPs were confirmed also in a focused cross-replication study of 159 patients treated with the non-SSRI antidepressant drug mirtazapine (Stage 3). Analysis of the Stage 1, Stage 2 and Stage 3 samples combined (n = 870) also revealed GWAS significance for these two SNPs, which was sustained after controlling for gender, age, number of previous episodes, age at onset and baseline severity (P = 3.57 × 10(-8)). For each SNP, the response rate decreased (odds ratio=0.31, 95% confidence interval: 0.20-0.47) as a function of the number of minor alleles (non-response alleles). The two SNPs significantly associated with antidepressant response are rs7785360 and rs12698828 of the AUTS2 gene, located on chromosome 7 in 7q11.22. This gene has multiple known linkages to human psychological functions and neurobehavioral disorders. Rigorous replication efforts in other ethnic populations are recommended.
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32
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Nebel RA, Kirschen J, Cai J, Woo YJ, Cherian K, Abrahams BS. Reciprocal Relationship between Head Size, an Autism Endophenotype, and Gene Dosage at 19p13.12 Points to AKAP8 and AKAP8L. PLoS One 2015; 10:e0129270. [PMID: 26076356 PMCID: PMC4468215 DOI: 10.1371/journal.pone.0129270] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/06/2015] [Indexed: 12/30/2022] Open
Abstract
Microcephaly and macrocephaly are overrepresented in individuals with autism and are thought to be disease-related risk factors or endophenotypes. Analysis of DNA microarray results from a family with a low functioning autistic child determined that the proband and two additional unaffected family members who carry a rare inherited 760 kb duplication of unknown clinical significance at 19p13.12 are macrocephalic. Consideration alongside overlapping deletion and duplication events in the literature provides support for a strong relationship between gene dosage at this locus and head size, with losses and gains associated with microcephaly (p=1.11x10(-11)) and macrocephaly (p=2.47x10(-11)), respectively. Data support A kinase anchor protein 8 and 8-like (AKAP8 and AKAP8L) as candidate genes involved in regulation of head growth, an interesting finding given previous work implicating the AKAP gene family in autism. Towards determination of which of AKAP8 and AKAP8L may be involved in the modulation of head size and risk for disease, we analyzed exome sequencing data for 693 autism families (2591 individuals) where head circumference data were available. No predicted loss of function variants were observed, precluding insights into relationship to head size, but highlighting strong evolutionary conservation. Taken together, findings support the idea that gene dosage at 19p13.12, and AKAP8 and/or AKAP8L in particular, play an important role in modulation of head size and may contribute to autism risk. Exome sequencing of the family also identified a rare inherited variant predicted to disrupt splicing of TPTE / PTEN2, a PTEN homologue, which may likewise contribute to both macrocephaly and autism risk.
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Affiliation(s)
- Rebecca A. Nebel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jill Kirschen
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Jinlu Cai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Young Jae Woo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Koshi Cherian
- Saul R. Korey Department of Neurology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
- Epilepsy Management Center, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
- Department of Pediatrics, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
| | - Brett S. Abrahams
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
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Han Y, Ru GQ, Mou X, Wang HJ, Ma Y, He XL, Yan Z, Huang D. AUTS2 is a potential therapeutic target for pancreatic cancer patients with liver metastases. Med Hypotheses 2015; 85:203-6. [PMID: 25962312 DOI: 10.1016/j.mehy.2015.04.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/26/2015] [Indexed: 10/23/2022]
Abstract
Liver metastasis is a common event at the advanced stage of pancreatic malignancies. Identification of effective therapeutic targets is crucial for the management of pancreatic cancer patients with liver metastases. In this study, we show that (A) AUTS2 is overexpressed in liver metastases of pancreatic cancer and could be a biomarker for defining cancer subtypes. (B) AUTS2 expression is positively correlated with Docetaxel resistance, TGF-beta pathway activation, HEDGEHOG and WNT signaling pathway. (C) By building an AUTS2 centered protein-drug interaction network, we show that AUTS2 might promote chemotherapeutic resistance and metastasis by exerting its effect on epithelial-mesenchymal transition and WNT signaling pathway. (D) Five drugs that could down regulate the expression of AUTS2 were also suggested. These drugs might help in the treatment of pancreatic cancer patients at the stage of liver metastasis. In summary, our results indicate that AUTS2 is a candidate biomarker for defining liver metastasis of pancreatic cancer and directing personalized therapies.
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Affiliation(s)
- Yong Han
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou 310014, Zhejiang, PR China; Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Guo-Qing Ru
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou 310014, Zhejiang, PR China
| | - Xiaozhou Mou
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Hui-ju Wang
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Yingyu Ma
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China
| | - Xiang-Lei He
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou 310014, Zhejiang, PR China
| | - Zhilong Yan
- Department of General Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, Zhejiang, PR China
| | - Dongsheng Huang
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou 310014, PR China; Department of General Surgery, Zhejiang Provincial People's Hospital, Hangzhou 310014, Zhejiang, PR China.
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34
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Liu Y, Zhao D, Dong R, Yang X, Zhang Y, Tammimies K, Uddin M, Scherer SW, Gai Z. De novo exon 1 deletion ofAUTS2gene in a patient with autism spectrum disorder and developmental delay: A case report and a brief literature review. Am J Med Genet A 2015; 167:1381-5. [PMID: 25851617 DOI: 10.1002/ajmg.a.37050] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 02/20/2015] [Indexed: 01/08/2023]
Affiliation(s)
- Yi Liu
- Pediatric Research Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Dongmei Zhao
- Pediatric Health Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Rui Dong
- Pediatric Research Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Xiaomeng Yang
- Pediatric Research Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Yanqing Zhang
- Pediatric Health Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
| | - Kristiina Tammimies
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Canada
| | - Mohammed Uddin
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics; The Hospital for Sick Children; Toronto Canada
- McLaughlin Centre and Department of Molecular Genetics; University of Toronto; Toronto Canada
| | - Zhongtao Gai
- Pediatric Research Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
- Pediatric Health Institute; Qilu Children's Hospital of Shandong University; Ji'nan China
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35
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Zhang B, Xu YH, Wei SG, Zhang HB, Fu DK, Feng ZF, Guan FL, Zhu YS, Li SB. Association study identifying a new susceptibility gene (AUTS2) for schizophrenia. Int J Mol Sci 2014; 15:19406-16. [PMID: 25347278 PMCID: PMC4264119 DOI: 10.3390/ijms151119406] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 09/23/2014] [Accepted: 10/10/2014] [Indexed: 12/11/2022] Open
Abstract
Schizophrenia (SCZ) is a severe and debilitating mental disorder, and the specific genetic factors that underlie the risk for SCZ remain elusive. The autism susceptibility candidate 2 (AUTS2) gene has been reported to be associated with autism, suicide, alcohol consumption, and heroin dependence. We hypothesized that AUTS2 might be associated with SCZ. In the present study, three polymorphisms (rs6943555, rs7459368, and rs9886351) in the AUTS2 gene were genotyped in 410 patients with SCZ and 435 controls using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and forced PCR-RFLP methods. We detected an association between SCZ and the rs6943555 genotype distribution (odds ratio (OR)=1.363, 95% confidence interval (CI): 0.848-2.191, p=0.001). The association remained significant after adjusting for gender, and a significant effect (p=0.001) was observed among the females. In the present study, rs6943555 was determined to be associated with female SCZ. Our results confirm previous reports which have suggested that rs6943555 might elucidate the pathogenesis of schizophrenia and play an important role in its etiology.
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Affiliation(s)
- Bao Zhang
- College of Forensic Science, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Yue-Hong Xu
- College of Forensic Science, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Shu-Guang Wei
- College of Forensic Science, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Hong-Bo Zhang
- College of Forensic Science, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Dong-Ke Fu
- College of Forensic Science, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Zu-Fei Feng
- College of Forensic Science, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Fang-Lin Guan
- College of Forensic Science, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Yong-Sheng Zhu
- College of Forensic Science, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
| | - Sheng-Bin Li
- College of Forensic Science, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
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36
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37
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Jiang YH, Wang Y, Xiu X, Choy KW, Pursley AN, Cheung SW. Genetic diagnosis of autism spectrum disorders: the opportunity and challenge in the genomics era. Crit Rev Clin Lab Sci 2014; 51:249-62. [PMID: 24878448 PMCID: PMC5937018 DOI: 10.3109/10408363.2014.910747] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A genetic etiology for autism spectrum disorders (ASDs) was first suggested from twin studies reported in the 1970s. The identification of gene mutations in syndromic ASDs provided evidence to support a genetic cause of ASDs. More recently, genome-wide copy number variant and sequence analyses have uncovered a list of rare and highly penetrant copy number variants (CNVs) or single nucleotide variants (SNVs) associated with ASDs, which has strengthened the claim of a genetic etiology for ASDs. Findings from research studies in the genetics of ASD now support an important role for molecular diagnostics in the clinical genetics evaluation of ASDs. Various molecular diagnostic assays including single gene tests, targeted multiple gene panels and copy number analysis should all be considered in the clinical genetics evaluation of ASDs. Whole exome sequencing could also be considered in selected clinical cases. However, the challenge that remains is to determine the causal role of genetic variants identified through molecular testing. Variable expressivity, pleiotropic effects and incomplete penetrance associated with CNVs and SNVs also present significant challenges for genetic counseling and prenatal diagnosis.
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Affiliation(s)
- Yong-Hui Jiang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC, USA
- Division of Neurology, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
| | - Yi Wang
- Division of Neurology, The Children’s Hospital of Fudan University, Shanghai, People’s Republic of China
| | - Xu Xiu
- Division of Child Development and Health, The Children’s Hospital of Fudan University Shanghai, People’s Republic of China
| | - Kwong Wai Choy
- Department of Obstetrics and Gynecology, and Joint Centre with Utrecht University Genetic core, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, People’s Republic of China
| | - Amber Nolen Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sau W. Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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38
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Beunders G, de Munnik SA, Van der Aa N, Ceulemans B, Voorhoeve E, Groffen AJ, Nillesen WM, Meijers-Heijboer EJ, Frank Kooy R, Yntema HG, Sistermans EA. Two male adults with pathogenic AUTS2 variants, including a two-base pair deletion, further delineate the AUTS2 syndrome. Eur J Hum Genet 2014; 23:803-7. [PMID: 25205402 DOI: 10.1038/ejhg.2014.173] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 07/04/2014] [Accepted: 07/10/2014] [Indexed: 11/09/2022] Open
Abstract
AUTS2 syndrome is characterized by low birth weight, feeding difficulties, intellectual disability, microcephaly and mild dysmorphic features. All affected individuals thus far were caused by chromosomal rearrangements, variants at the base pair level disrupting AUTS2 have not yet been described. Here we present the full clinical description of two affected men with intragenic AUTS2 variants (one two-base pair deletion in exon 7 and one deletion of exon 6). Both variants are de novo and are predicted to cause a frameshift of the full-length transcript but are unlikely to affect the shorter 3' transcript starting in exon 9. The similarities between the phenotypes of both men are striking and further support that AUTS2 syndrome is a single gene disorder.
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Affiliation(s)
- Gea Beunders
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Sonja A de Munnik
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Nathalie Van der Aa
- Department of Medical Genetics, University Hospital Antwerp, Antwerp, Belgium
| | - Berten Ceulemans
- Department of Neurology-Paediatric Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Els Voorhoeve
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Alexander J Groffen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Willy M Nillesen
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | | | - R Frank Kooy
- Department of Medical Genetics, University Hospital Antwerp, Antwerp, Belgium
| | - Helger G Yntema
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Erik A Sistermans
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
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39
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Oksenberg N, Haliburton GDE, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N. Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. Transl Psychiatry 2014; 4:e431. [PMID: 25180570 PMCID: PMC4199417 DOI: 10.1038/tp.2014.78] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 07/14/2014] [Accepted: 07/26/2014] [Indexed: 12/16/2022] Open
Abstract
The autism susceptibility candidate 2 gene (AUTS2) has been associated with multiple neurological diseases including autism spectrum disorders (ASDs). Previous studies showed that AUTS2 has an important neurodevelopmental function and is a suspected master regulator of genes implicated in ASD-related pathways. However, the regulatory role and targets of Auts2 are not well known. Here, by using ChIP-seq (chromatin immunoprecipitation followed by deep sequencing) and RNA-seq on mouse embryonic day 16.5 forebrains, we elucidated the gene regulatory networks of Auts2. We find that the majority of promoters bound by Auts2 belong to genes highly expressed in the developing forebrain, suggesting that Auts2 is involved in transcriptional activation. Auts2 non-promoter-bound regions significantly overlap developing brain-associated enhancer marks and are located near genes involved in neurodevelopment. Auts2-marked sequences are enriched for binding site motifs of neurodevelopmental transcription factors, including Pitx3 and TCF3. In addition, we characterized two functional brain enhancers marked by Auts2 near NRXN1 and ATP2B2, both ASD-implicated genes. Our results implicate Auts2 as an active regulator of important neurodevelopmental genes and pathways and identify novel genomic regions that could be associated with ASD and other neurodevelopmental diseases.
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Affiliation(s)
- N Oksenberg
- Department of Bioengineering and Therapeutic
Sciences, University of California San Francisco,
San Francisco, CA, USA,Institute for Human Genetics, University of
California San Francisco, San Francisco, CA, USA
| | - G D E Haliburton
- Institute for Human Genetics, University of
California San Francisco, San Francisco, CA, USA,Gladstone Institutes, San
Francisco, CA, USA
| | - W L Eckalbar
- Department of Bioengineering and Therapeutic
Sciences, University of California San Francisco,
San Francisco, CA, USA,Institute for Human Genetics, University of
California San Francisco, San Francisco, CA, USA
| | - I Oren
- Department of Life Sciences, Ben Gurion University of
the Negev, Beer Sheva, Israel
| | - S Nishizaki
- Department of Bioengineering and Therapeutic
Sciences, University of California San Francisco,
San Francisco, CA, USA,Institute for Human Genetics, University of
California San Francisco, San Francisco, CA, USA
| | - K Murphy
- Department of Bioengineering and Therapeutic
Sciences, University of California San Francisco,
San Francisco, CA, USA,Institute for Human Genetics, University of
California San Francisco, San Francisco, CA, USA
| | - K S Pollard
- Institute for Human Genetics, University of
California San Francisco, San Francisco, CA, USA,Gladstone Institutes, San
Francisco, CA, USA,Division of Biostatistics, University of California
San Francisco, San Francisco, CA, USA
| | - R Y Birnbaum
- Department of Bioengineering and Therapeutic
Sciences, University of California San Francisco,
San Francisco, CA, USA,Institute for Human Genetics, University of
California San Francisco, San Francisco, CA, USA,Department of Life Sciences, Ben Gurion University of
the Negev, Beer Sheva, Israel,Department of Bioengineering and Therapeutic Sciences, University of
California San Francisco, 1550 4th Street, Rock Hall, RH584C, San Francisco,
CA
94158, USA. E-mails: or
| | - N Ahituv
- Department of Bioengineering and Therapeutic
Sciences, University of California San Francisco,
San Francisco, CA, USA,Institute for Human Genetics, University of
California San Francisco, San Francisco, CA, USA,Department of Bioengineering and Therapeutic Sciences, University of
California San Francisco, 1550 4th Street, Rock Hall, RH584C, San Francisco,
CA
94158, USA. E-mails: or
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40
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Baumgart A, Spiczak SV, Verhoeven-Duif NM, Møller RS, Boor R, Muhle H, Jähn JA, Klitten LL, Hjalgrim H, Lindhout D, Stephani U, van Kempen MJA, Helbig I. Atypical vitamin B6 deficiency: a rare cause of unexplained neonatal and infantile epilepsies. J Child Neurol 2014; 29:704-7. [PMID: 24114605 DOI: 10.1177/0883073813505354] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
ALDH7A1 and PNPO deficiencies are rare inborn errors of vitamin B6 metabolism causing perinatal seizure disorders. The phenotypic variability, however, is broad. To assess the frequency of these deficiencies in unexplained infantile epilepsy, we screened 113 patients for mutations in both genes. We identified 1 patient with an epilepsy phenotype resembling Dravet syndrome and likely pathogenic mutations in ALDH7A1. Presenting features were highly atypical of pyridoxine-dependent epilepsy, including febrile seizures, response to anticonvulsive drugs, and periods of seizure freedom without pyridoxine treatment. "Hidden" vitamin B6 deficiencies might be rare but treatable causes of unexplained epilepsy extending beyond the classical phenotypes.
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Affiliation(s)
- Anna Baumgart
- 1Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany
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41
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Identification of risk genes for autism spectrum disorder through copy number variation analysis in Austrian families. Neurogenetics 2014; 15:117-27. [DOI: 10.1007/s10048-014-0394-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/25/2014] [Indexed: 12/13/2022]
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42
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Palumbo O, Fichera M, Palumbo P, Rizzo R, Mazzolla E, Cocuzza DM, Carella M, Mattina T. TBR1 is the candidate gene for intellectual disability in patients with a 2q24.2 interstitial deletion. Am J Med Genet A 2014; 164A:828-33. [PMID: 24458984 DOI: 10.1002/ajmg.a.36363] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 10/21/2013] [Indexed: 12/25/2022]
Abstract
Interstitial deletion of 2q24.2 is a rarely described cytogenetic aberration in patients with intellectual disability (ID). Previously reported genotype-phenotype correlation identified a minimum deleted region of 2.65 Mb including 15 genes. Recently, a patient with a de novo 2q24.2 microdeletion of 0.4 Mb encompassing only three genes was described. However, the precise relationship between most deleted genes and the clinical features remains unclear. Here we describe a 12-year-old male patient diagnosed with growth retardation and ID. He also showed microcephaly, right palpebral ptosis, scapular winging, and pectus excavatum. Single nucleotide polymorphisms (SNP) array analysis showed a de novo interstitial deletion of 0.122 Mb at 2q24.2 region harboring only TBR1 (T-box, brain, 1; OMIM: 604616), which encodes a T-box family transcription factor expressed in post-mitotic projection neurons and functionally significant in embryologic corticogenesis. This is the first case of a deletion at 2q24.2 involving only TBR1. This finding narrows the smallest region of overlap (SRO) for deletions in this region and strengthens the previously suggested hypothesis that this gene is a strong candidate for the ID phenotype. The identification of TBR1 as candidate for ID encourages further molecular studies to identify novel mutations to understand the pathogenic effects of its haploinsufficiency. Finally, this report provides a review on 10 2q24.2 microdeletion patients.
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Affiliation(s)
- Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, (FG), Italy
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43
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Amarillo IE, Li WL, Li X, Vilain E, Kantarci S. De novo single exon deletion of AUTS2 in a patient with speech and language disorder: a review of disrupted AUTS2 and further evidence for its role in neurodevelopmental disorders. Am J Med Genet A 2014; 164A:958-65. [PMID: 24459036 DOI: 10.1002/ajmg.a.36393] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 11/09/2013] [Indexed: 01/03/2023]
Abstract
The autism susceptibility candidate 2 (AUTS2) gene is suggested to play a critical role in early brain development, and its association with intellectual disability (ID), autism spectrum disorders, and other neurodevelopmental disorders (NDDs) has recently gained more attention. Genomic rearrangements and copy number variations (CNVs) involving AUTS2 have been implicated in a range of NDDs with or without congenital malformations and dysmorphic features. Here we report a 62 kb de novo deletion encompassing exon 6 of AUTS2 detected by chromosomal microarray analysis (CMA) in a 4.5 year-old female patient with severe speech and language disorder, history of tonic-clonic movements, and pes planus with eversion of the feet. This is one of the smallest de novo intragenic deletions of AUTS2 described in patients with NDDs. We reviewed previously reported small pathogenic CNVs (<300 kb) in 19 cases, and correlated their specific locations within AUTS2 as well as presence of enhancers, regulatory elements, and CpG islands with the clinical findings of these cases and our patient. Our report provides additional insight into the clinical spectrum of AUTS2 disruptions.
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Affiliation(s)
- Ina E Amarillo
- Departments of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
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44
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Poot M. Late breaking chromosomes. Mol Syndromol 2013; 4:255-6. [PMID: 24167459 DOI: 10.1159/000354281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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45
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Oksenberg N, Ahituv N. The role of AUTS2 in neurodevelopment and human evolution. Trends Genet 2013; 29:600-8. [PMID: 24008202 DOI: 10.1016/j.tig.2013.08.001] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 12/31/2022]
Abstract
The autism susceptibility candidate 2 (AUTS2) gene is associated with multiple neurological diseases, including autism, and has been implicated as an important gene in human-specific evolution. Recent functional analysis of this gene has revealed a potential role in neuronal development. Here, we review the literature regarding AUTS2, including its discovery, expression, association with autism and other neurological and non-neurological traits, implication in human evolution, function, regulation, and genetic pathways. Through progress in clinical genomic analysis, the medical importance of this gene is becoming more apparent, as highlighted in this review, but more work needs to be done to discover the precise function and the genetic pathways associated with AUTS2.
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Affiliation(s)
- Nir Oksenberg
- Department of Bioengineering and Therapeutic Sciences, and Institute for Human Genetics, University of California, San Francisco (UCSF), 1550 4th Street, San Francisco, CA 94158, USA
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46
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Cheng Y, Quinn JF, Weiss LA. An eQTL mapping approach reveals that rare variants in the SEMA5A regulatory network impact autism risk. Hum Mol Genet 2013; 22:2960-72. [PMID: 23575222 PMCID: PMC3690972 DOI: 10.1093/hmg/ddt150] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 02/05/2013] [Accepted: 03/29/2013] [Indexed: 01/05/2023] Open
Abstract
To date, genome-wide single nucleotide polymorphism (SNP) and copy number variant (CNV) association studies of autism spectrum disorders (ASDs) have led to promising signals but not to easily interpretable or translatable results. Our own genome-wide association study (GWAS) showed significant association to an intergenic SNP near Semaphorin 5A (SEMA5A) and provided evidence for reduced expression of the same gene. In a novel GWAS follow-up approach, we map an expression regulatory pathway for a GWAS candidate gene, SEMA5A, in silico by using population expression and genotype data sets. We find that the SEMA5A regulatory network significantly overlaps rare autism-specific CNVs. The SEMA5A regulatory network includes previous autism candidate genes and regions, including MACROD2, A2BP1, MCPH1, MAST4, CDH8, CADM1, FOXP1, AUTS2, MBD5, 7q21, 20p, USH2A, KIRREL3, DBF4B and RELN, among others. Our results provide: (i) a novel data-derived network implicated in autism, (ii) evidence that the same pathway seeded by an initial SNP association shows association with rare genetic variation in ASDs, (iii) a potential mechanism of action and interpretation for the previous autism candidate genes and genetic variants that fall in this network, and (iv) a novel approach that can be applied to other candidate genes for complex genetic disorders. We take a step towards better understanding of the significance of SEMA5A pathways in autism that can guide interpretation of many other genetic results in ASDs.
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Affiliation(s)
| | | | - Lauren Anne Weiss
- Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
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Jolley A, Corbett M, McGregor L, Waters W, Brown S, Nicholl J, Yu S. De novo intragenic deletion of the autism susceptibility candidate 2 (AUTS2) gene in a patient with developmental delay: a case report and literature review. Am J Med Genet A 2013; 161A:1508-12. [PMID: 23650183 DOI: 10.1002/ajmg.a.35922] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 01/31/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Alexandra Jolley
- Department of Genetic Medicine, Directorate of Genetics and Molecular Pathology, SA Pathology at Women's and Children's Hospital, and School of Paediatrics and Reproductive Health, The University of Adelaide, North Adelaide, South Australia, Australia
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48
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Beunders G, Voorhoeve E, Golzio C, Pardo L, Rosenfeld J, Talkowski M, Simonic I, Lionel A, Vergult S, Pyatt R, van de Kamp J, Nieuwint A, Weiss M, Rizzu P, Verwer L, van Spaendonk R, Shen Y, Wu BL, Yu T, Yu Y, Chiang C, Gusella J, Lindgren A, Morton C, van Binsbergen E, Bulk S, van Rossem E, Vanakker O, Armstrong R, Park SM, Greenhalgh L, Maye U, Neill N, Abbott K, Sell S, Ladda R, Farber D, Bader P, Cushing T, Drautz J, Konczal L, Nash P, de Los Reyes E, Carter M, Hopkins E, Marshall C, Osborne L, Gripp K, Thrush D, Hashimoto S, Gastier-Foster J, Astbury C, Ylstra B, Meijers-Heijboer H, Posthuma D, Menten B, Mortier G, Scherer S, Eichler E, Girirajan S, Katsanis N, Groffen A, Sistermans E. Exonic deletions in AUTS2 cause a syndromic form of intellectual disability and suggest a critical role for the C terminus. Am J Hum Genet 2013; 92:210-20. [PMID: 23332918 PMCID: PMC3567268 DOI: 10.1016/j.ajhg.2012.12.011] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/06/2012] [Accepted: 12/20/2012] [Indexed: 01/15/2023] Open
Abstract
Genomic rearrangements involving AUTS2 (7q11.22) are associated with autism and intellectual disability (ID), although evidence for causality is limited. By combining the results of diagnostic testing of 49,684 individuals, we identified 24 microdeletions that affect at least one exon of AUTS2, as well as one translocation and one inversion each with a breakpoint within the AUTS2 locus. Comparison of 17 well-characterized individuals enabled identification of a variable syndromic phenotype including ID, autism, short stature, microcephaly, cerebral palsy, and facial dysmorphisms. The dysmorphic features were more pronounced in persons with 3'AUTS2 deletions. This part of the gene is shown to encode a C-terminal isoform (with an alternative transcription start site) expressed in the human brain. Consistent with our genetic data, suppression of auts2 in zebrafish embryos caused microcephaly that could be rescued by either the full-length or the C-terminal isoform of AUTS2. Our observations demonstrate a causal role of AUTS2 in neurocognitive disorders, establish a hitherto unappreciated syndromic phenotype at this locus, and show how transcriptional complexity can underpin human pathology. The zebrafish model provides a valuable tool for investigating the etiology of AUTS2 syndrome and facilitating gene-function analysis in the future.
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Affiliation(s)
- Gea Beunders
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Els Voorhoeve
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Christelle Golzio
- Center for Human Disease Modeling, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Luba M. Pardo
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Jill A. Rosenfeld
- Signature Genomic Laboratories, Perkin Elmer, Spokane, WA 99207, USA
| | - Michael E. Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, affiliated with Departments of Genetics and Neurology, Harvard Medical School, Harvard University, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Ingrid Simonic
- East Anglian Medical Genetics Service, Addenbrooke’s Hospital, Cambridge University Hospitals, National Health Service Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Anath C. Lionel
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
- Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Sarah Vergult
- Center for Medical Genetics, University Hospital Ghent, Ghent 9000, Belgium
| | - Robert E. Pyatt
- Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Jiddeke van de Kamp
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Aggie Nieuwint
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Marjan M. Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Patrizia Rizzu
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Lucilla E.N.I. Verwer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | | | - Yiping Shen
- Center for Human Genetic Research, Massachusetts General Hospital, affiliated with Departments of Genetics and Neurology, Harvard Medical School, Harvard University, Boston, MA 02114, USA
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA 02114, USA
- Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Bai-lin Wu
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA 02114, USA
- Children’s Hospital and Institutes of Biomedical Science, Fudan University, Shanghai 200032, China
| | - Tingting Yu
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA 02114, USA
- Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Yongguo Yu
- Department of Laboratory Medicine, Boston Children’s Hospital, Boston, MA 02114, USA
- Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
| | - Colby Chiang
- Center for Human Genetic Research, Massachusetts General Hospital, affiliated with Departments of Genetics and Neurology, Harvard Medical School, Harvard University, Boston, MA 02114, USA
| | - James F. Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, affiliated with Departments of Genetics and Neurology, Harvard Medical School, Harvard University, Boston, MA 02114, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Amelia M. Lindgren
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Cynthia C. Morton
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen van Binsbergen
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht 3508 AB, The Netherlands
| | - Saskia Bulk
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht 3508 AB, The Netherlands
| | | | - Olivier Vanakker
- Center for Medical Genetics, University Hospital Ghent, Ghent 9000, Belgium
| | - Ruth Armstrong
- East Anglian Medical Genetics Service, Addenbrooke’s Hospital, Cambridge University Hospitals, National Health Service Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Soo-Mi Park
- East Anglian Medical Genetics Service, Addenbrooke’s Hospital, Cambridge University Hospitals, National Health Service Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Lynn Greenhalgh
- Clinical Genetics, Royal Liverpool Children’s Hospital, Eaton Road, Alder Hey, Liverpool L12 2AP, Great Britain
| | - Una Maye
- Clinical Genetics, Royal Liverpool Children’s Hospital, Eaton Road, Alder Hey, Liverpool L12 2AP, Great Britain
| | - Nicholas J. Neill
- Signature Genomic Laboratories, Perkin Elmer, Spokane, WA 99207, USA
| | - Kristin M. Abbott
- East Anglian Medical Genetics Service, Addenbrooke’s Hospital, Cambridge University Hospitals, National Health Service Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Susan Sell
- Penn State Milton S. Hershey Medical Center, Hershey, PA 17033, USA
| | - Roger Ladda
- Penn State Milton S. Hershey Medical Center, Hershey, PA 17033, USA
| | - Darren M. Farber
- Department of Neurology, University of Louisville, Louisville, KY 40222, USA
| | - Patricia I. Bader
- Northeast Indiana Genetic Counseling Center, Ft. Wayne, IN 46804, USA
| | - Tom Cushing
- Pediatric Genetics Division, Department of Pediatrics, University of New Mexico, Albuquerque, NM 87131, USA
| | - Joanne M. Drautz
- Pediatric Genetics Division, Department of Pediatrics, University of New Mexico, Albuquerque, NM 87131, USA
| | - Laura Konczal
- University Hospitals, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Patricia Nash
- Department of Behavioral Pediatrics, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Emily de Los Reyes
- Department of Pediatrics and Neurology, The Ohio State University, Columbus, OH 43210, USA
| | - Melissa T. Carter
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Elizabeth Hopkins
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Christian R. Marshall
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
- Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Lucy R. Osborne
- Departments of Medicine and Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Karen W. Gripp
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Devon Lamb Thrush
- Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Sayaka Hashimoto
- Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Julie M. Gastier-Foster
- Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Caroline Astbury
- Pathology and Laboratory Medicine, Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
| | - Danielle Posthuma
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam 1081 HV, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus University Rotterdam, Rotterdam 3000 CB, The Netherlands
| | - Björn Menten
- Center for Medical Genetics, University Hospital Ghent, Ghent 9000, Belgium
| | - Geert Mortier
- Department of Medical Genetics, Antwerp University, Edegem 2650, Belgium
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 1L7, Canada
- Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Evan E. Eichler
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Santhosh Girirajan
- Department of Genome Sciences and Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
- Department of Biochemistry and Molecular Biology Department of Anthropology, Pennsylvania State University, Pennsylvania, PA 16803, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Alexander J. Groffen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam 1081 HV, The Netherlands
| | - Erik A. Sistermans
- Department of Clinical Genetics, VU University Medical Center, Amsterdam 1007 MB, The Netherlands
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49
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Oksenberg N, Stevison L, Wall JD, Ahituv N. Function and regulation of AUTS2, a gene implicated in autism and human evolution. PLoS Genet 2013; 9:e1003221. [PMID: 23349641 PMCID: PMC3547868 DOI: 10.1371/journal.pgen.1003221] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 11/20/2012] [Indexed: 12/13/2022] Open
Abstract
Nucleotide changes in the AUTS2 locus, some of which affect only noncoding regions, are associated with autism and other neurological disorders, including attention deficit hyperactivity disorder, epilepsy, dyslexia, motor delay, language delay, visual impairment, microcephaly, and alcohol consumption. In addition, AUTS2 contains the most significantly accelerated genomic region differentiating humans from Neanderthals, which is primarily composed of noncoding variants. However, the function and regulation of this gene remain largely unknown. To characterize auts2 function, we knocked it down in zebrafish, leading to a smaller head size, neuronal reduction, and decreased mobility. To characterize AUTS2 regulatory elements, we tested sequences for enhancer activity in zebrafish and mice. We identified 23 functional zebrafish enhancers, 10 of which were active in the brain. Our mouse enhancer assays characterized three mouse brain enhancers that overlap an ASD-associated deletion and four mouse enhancers that reside in regions implicated in human evolution, two of which are active in the brain. Combined, our results show that AUTS2 is important for neurodevelopment and expose candidate enhancer sequences in which nucleotide variation could lead to neurological disease and human-specific traits.
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Affiliation(s)
- Nir Oksenberg
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Laurie Stevison
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
| | - Jeffrey D. Wall
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
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