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Bos-Roubos AG, Wingbermühle E, Giesen M, Kersseboom R, De Graaff LC, Egger JI. Hypertension with hidden causes: the cognitive and behavioral profile of an adult female with chronic stress and 16p11.2 microdeletion. J Hypertens 2024; 42:179-184. [PMID: 37698889 PMCID: PMC10713000 DOI: 10.1097/hjh.0000000000003565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 08/08/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
This case report aims to alert physicians to neuropsychological features and chromosomal variants that may underly resistant hypertension. We present a 35-year-old female patient with hypertensive crisis (BP 260/160 mmHg), initially treated with a combination of calcium antagonists, beta blockers, diuretics and angiotensin-converting enzyme (ACE)-inhibitors, though with little improvement. Cushing's syndrome, Conn's syndrome, and glucocorticoid receptor deficiency were ruled out. Multidisciplinary examination of medical history and (hetero)anamneses including psychosocial factors revealed mild dysmorphic body features, developmental delay, early diagnosis of autism spectrum disorder, a history of being bullied at school, little peer contact, learning disabilities, and special education. Neuropsychological assessment demonstrated below average to low average intelligence quotient, cognitive impairments, and psychopathology. Parallel genetic analyses revealed a rare 16p11.2 microdeletion syndrome. These concurrent examinations explained the patient's life-long high stress levels. After psychological treatment, with additional support at home, her blood pressure lowered to normal levels and antihypertensive drugs were no longer needed.
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Affiliation(s)
- Anja G. Bos-Roubos
- Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray
- Donders Institute for Brain, Cognition and Behaviour, Radboud University
| | - Ellen Wingbermühle
- Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray
- Donders Institute for Brain, Cognition and Behaviour, Radboud University
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen
| | | | - Rogier Kersseboom
- Zuidwester Healthcare Institution for People with Intellectual Disabilities, Middelharnis
- Department of Internal Medicine, Erasmus University Medical Center
| | - Laura C.G. De Graaff
- Department of Internal Medicine, Erasmus University Medical Center
- Center for Adults With Rare Genetic Syndromes, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jos I.M. Egger
- Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray
- Donders Institute for Brain, Cognition and Behaviour, Radboud University
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen
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Woodbury-Smith M, D'Abate L, Stavropoulos DJ, Howe J, Drmic I, Hoang N, Zarrei M, Trost B, Iaboni A, Anagnostou E, Scherer SW. The Phenotypic variability of 16p11.2 distal BP2-BP3 deletion in a transgenerational family and in neurodevelopmentally ascertained samples. J Med Genet 2023; 60:1153-1160. [PMID: 37290907 PMCID: PMC10715508 DOI: 10.1136/jmg-2022-108818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 05/03/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND We present genomic and phenotypic findings of a transgenerational family consisting of three male offspring, each with a maternally inherited distal 220 kb deletion at locus 16p11.2 (BP2-BP3). Genomic analysis of all family members was prompted by a diagnosis of autism spectrum disorder (ASD) in the eldest child, who also presented with a low body mass index. METHODS All male offspring underwent extensive neuropsychiatric evaluation. Both parents were also assessed for social functioning and cognition. The family underwent whole-genome sequencing. Further data curation was undertaken from samples ascertained for neurodevelopmental disorders and congenital abnormalities. RESULTS On medical examination, both the second and third-born male offspring presented with obesity. The second-born male offspring met research diagnostic criteria for ASD at 8 years of age and presented with mild attention deficits. The third-born male offspring was only noted as having motor deficits and received a diagnosis of developmental coordination disorder. Other than the 16p11.2 distal deletion, no additional contributing variants of clinical significance were observed. The mother was clinically evaluated and noted as having a broader autism phenotype. CONCLUSION In this family, the phenotypes observed are most likely caused by the 16p11.2 distal deletion. The lack of other overt pathogenic mutations identified by genomic sequencing reinforces the variable expressivity that should be heeded in a clinical setting. Importantly, distal 16p11.2 deletions can present with a highly variable phenotype even within a single family. Our additional data curation provides further evidence on the variable clinical presentation among those with pathogenetic 16p11.2 (BP2-BP3) mutations.
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Affiliation(s)
- Marc Woodbury-Smith
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Lia D'Abate
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Irene Drmic
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Ron Joyce Children's Health Centre, Autism Spectrum Disorder (ASD) Program and Child and Youth Mental Health Program, McMaster Autism Research Team, McMaster University, Hamilton, Hamilton, Ontario, Canada
| | - Ny Hoang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alana Iaboni
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Centre, Toronto, Ontario, Canada
| | - Evdokia Anagnostou
- Autism Research Centre, Holland Bloorview Kids Rehabilitation Centre, Toronto, Ontario, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
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González-del Angel A, Alcántara-Ortigoza MA, Ramos S, Algara-Ramírez C, Hernández-Hernández MA, Saenger-Rivas L. Unusual Trisomy X Phenotype Associated with a Concurrent Heterozygous 16p11.2 Deletion: Importance of an Integral Approach for Proper Diagnosis. Int J Mol Sci 2023; 24:14643. [PMID: 37834089 PMCID: PMC10572219 DOI: 10.3390/ijms241914643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 10/15/2023] Open
Abstract
Trisomy X is the most frequent sex chromosome anomaly in women, but it is often underdiagnosed postnatally because most patients do not show any clinical manifestation. It is estimated that only 10% of patients with trisomy X are diagnosed by clinical findings. Thus, it has been proposed that the clinical spectrum is not yet fully delimited, and additional uncommon or atypical clinical manifestations could be related to this entity. The present report describes a female carrying trisomy X but presenting atypical manifestations, including severe intellectual disability, short stature, thymus hypoplasia, and congenital hypothyroidism (CH). These clinical findings were initially attributed to trisomy X. However, chromosome microarray analysis (CMA) subsequently revealed that the patient also bears a heterozygous 304-kb deletion at 16p11.2. This pathogenic copy-number variant (CNV) encompasses 13 genes, including TUFM. Some authors recommend that when a phenotype differs from that described for an identified microdeletion, the presence of pathogenic variants in the non-deleted allele should be considered to assess for an autosomal recessive disorder; thus, we used a panel of 697 genes to rule out a pathogenic variant in the non-deleted TUFM allele. We discuss the possible phenotypic modifications that might be related to an additional CNV in individuals with sex chromosome aneuploidy (SCA), as seen in our patient. The presence of karyotype-demonstrated trisomy X and CMA-identified 16p11.2 deletion highlights the importance of always correlating a patient's clinical phenotype with the results of genetic studies. When the phenotype includes unusual manifestations and/or exhibits discrepancies with that described in the literature, as exemplified by our patient, a more extensive analysis should be undertaken to enable a correct diagnosis that will support proper management, genetic counseling, and medical follow-up.
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Affiliation(s)
- Ariadna González-del Angel
- Laboratorio de Biología Molecular, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City CP 04530, Mexico;
- Facultad Mexicana de Medicina, Universidad la Salle, Mexico City CP 14070, Mexico; (C.A.-R.); (M.A.H.-H.); (L.S.-R.)
| | - Miguel Angel Alcántara-Ortigoza
- Laboratorio de Biología Molecular, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City CP 04530, Mexico;
| | - Sandra Ramos
- Laboratorio de Citogenética, Subdirección de Investigación Médica, Instituto Nacional de Pediatría, Secretaría de Salud, Mexico City CP 04530, Mexico;
| | - Carolina Algara-Ramírez
- Facultad Mexicana de Medicina, Universidad la Salle, Mexico City CP 14070, Mexico; (C.A.-R.); (M.A.H.-H.); (L.S.-R.)
| | | | - Lorenza Saenger-Rivas
- Facultad Mexicana de Medicina, Universidad la Salle, Mexico City CP 14070, Mexico; (C.A.-R.); (M.A.H.-H.); (L.S.-R.)
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Jiménez-Romero MS, Fernández-Urquiza M, Benítez-Burraco A. Language and Communication Deficits in Chromosome 16p11.2 Deletion Syndrome. JOURNAL OF SPEECH, LANGUAGE, AND HEARING RESEARCH : JSLHR 2022; 65:4724-4740. [PMID: 36410413 DOI: 10.1044/2022_jslhr-22-00160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
PURPOSE Chromosome 16p11.2 deletion syndrome (OMIM #611913) is a rare genetic condition resulting from the partial deletion of approximately 35 genes located at Chromosome 16. Affected people exhibit a variable clinical profile, featuring mild dysmorphisms, motor problems, developmental delay, mild intellectual disability (ID), socialization deficits and/or autism spectrum disorder (ASD) traits, and problems with language. Specifically, a precise characterization of the speech, language, and communication (dis)abilities of people with this condition is still pending. METHOD We used standardized tests and samples of naturalistic speech to provide a longitudinal profile of the speech, language, and communication problems of a boy with Chromosome 16p11.2 deletion syndrome and without ID or ASD. RESULTS The proband shows impaired expressive abilities as well as problems with receptive language, dysprosody, and ASD-like communication deficits, such as impaired interactive skills, perseverative verbal behavior, overabundance of tangential responses, and lack of metapragmatic awareness and communicative use of gaze, meeting the criteria for social pragmatic communication disorder. CONCLUSIONS Our results support the view that language and communication impairment should be regarded as one core symptom of Chromosome 16p11.2 deletion syndrome, even without a diagnosis of ASD or ID. Clinical implications of our results, with a focus on therapeutic interventions for children with 16p11.2 deletion syndrome and no ASD or ID, are also discussed. SUPPLEMENTAL MATERIAL https://doi.org/10.23641/asha.21561714.
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Affiliation(s)
| | | | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature (Linguistics), Faculty of Philology, University of Seville, Spain
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Giannopoulou EZ, Zorn S, Schirmer M, Herrmann G, Heger S, Reinehr T, Denzer C, Rabenstein H, Hillmer M, Sowada N, Siebert R, von Schnurbein J, Wabitsch M. Genetic Obesity in Children: Overview of Possible Diagnoses with a Focus on SH2B1 Deletion. Horm Res Paediatr 2022; 95:137-148. [PMID: 34689140 DOI: 10.1159/000520402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Genetic obesity is rare and quite challenging for pediatricians in terms of early identification. Src-homology-2 (SH2) B adapter protein 1 (SH2B1) is an important component in the leptin-melanocortin pathway and is found to play an important role in leptin and insulin signaling and therefore in the pathogenesis of obesity and diabetes. Microdeletions in chromosome 16p11.2, encompassing the SH2B1 gene, are known to be associated with obesity, insulin resistance, hyperphagia, and developmental delay. The aim of our study is to report on a case series of young individuals with 16p11.2 microdeletions, including the SH2B1 gene, and provide detailed information on body mass index (BMI) development and obesity-associated comorbidities. In this way, we want to raise awareness of this syndromic form of obesity as a differential diagnosis of genetic obesity. METHODS We describe the phenotype of 7 children (3 male; age range: 2.8-18.0 years) with 16p11.2 microdeletions, encompassing the SH2B1 gene, and present their BMI trajectories from birth onward. Screening for obesity-associated comorbidities was performed at the time of genetic diagnosis. RESULTS All children presented with severe, early-onset obesity already at the age of 5 years combined with variable developmental delay. Five patients presented with elevated fasting insulin levels, 1 patient developed diabetes mellitus type 2, 4 patients had dyslipidemia, and 4 developed nonalcoholic fatty-liver disease. DISCUSSION/CONCLUSION Chromosomal microdeletions in 16p11.2, including the SH2B1 gene, in children are associated with severe, early-onset obesity and comorbidities associated with insulin resistance. Early genetic testing in suspicious patients and early screening for comorbidities are recommended.
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Affiliation(s)
- Eleni Z Giannopoulou
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Stefanie Zorn
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Melanie Schirmer
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Gloria Herrmann
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Sabine Heger
- Department of Pediatric Endocrinology, Children's Hospital Auf der Bult, Hannover, Germany
| | - Thomas Reinehr
- Department of Pediatric Endocrinology, Diabetes and Nutrition Medicine, Vestische Hospital for Children and Adolescents Datteln, University of Witten/Herdecke, Datteln, Germany
| | - Christian Denzer
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Hannah Rabenstein
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Ulm, Germany
| | - Morten Hillmer
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Ulm, Germany
| | - Nadine Sowada
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University & Ulm University Medical Center, Ulm, Germany
| | - Julia von Schnurbein
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Martin Wabitsch
- Division of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
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Yue F, Xi Q, Zhang X, Jiang Y, Zhang H, Liu R. Molecular cytogenetic characterization of 16p11.2 microdeletions with diverse prenatal phenotypes: Four cases report and literature review. Taiwan J Obstet Gynecol 2022; 61:544-550. [PMID: 35595456 DOI: 10.1016/j.tjog.2022.03.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2021] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVE Chromosome 16p11.2 deletions have been recognized as a genetic disorder with well-described postnatal phenotypes. However, the prenatal manifestations are atypical for lacking of enough evidence. CASE REPORT Four pregnant women underwent amniocentesis for cytogenetic analysis and chromosomal microarray analysis (CMA) because of various indications for prenatal diagnosis: prenatal ultrasound abnormalities (cases 1, 2 and 4) and the childbearing history of cerebral palsy child (case 3). No overlapping phenotypes were observed in cases 1, 2 and 4, which might indicate phenotypic diversities in prenatal phenotypes for 16p11.2 microdeletion. All four fetuses showed normal karyotypic results while CMA identified 0.303-0.916 Mb microdeletions of 16p11.2, encompassing BP2-BP3 and BP4-BP5 regions separately. According to the parental CMA verification, case 1 carried a maternal inherited duplication in the region of Xp22.33 and a de novo deletion in the region of Xp21.1. All parents opted for the termination of pregnancies based upon genetic counselling. CONCLUSION Our findings enriched the intrauterine phenotypic features of 16p11.2 microdeletions, which would be beneficial for genetic counselling in clinic. In addition, preimplantation genetic testing was recognized as a first-tier approach for such carriers if they intended to conceive again.
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Affiliation(s)
- Fagui Yue
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Qi Xi
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Xinyue Zhang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Yuting Jiang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Hongguo Zhang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China
| | - Ruizhi Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, 130021, China; Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, 130021, China.
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Kim SS, Hudgins AD, Yang J, Zhu Y, Tu Z, Rosenfeld MG, DiLorenzo TP, Suh Y. A comprehensive integrated post-GWAS analysis of Type 1 diabetes reveals enhancer-based immune dysregulation. PLoS One 2021; 16:e0257265. [PMID: 34529725 PMCID: PMC8445446 DOI: 10.1371/journal.pone.0257265] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 08/31/2021] [Indexed: 01/02/2023] Open
Abstract
Type 1 diabetes (T1D) is an organ-specific autoimmune disease, whereby immune cell-mediated killing leads to loss of the insulin-producing β cells in the pancreas. Genome-wide association studies (GWAS) have identified over 200 genetic variants associated with risk for T1D. The majority of the GWAS risk variants reside in the non-coding regions of the genome, suggesting that gene regulatory changes substantially contribute to T1D. However, identification of causal regulatory variants associated with T1D risk and their affected genes is challenging due to incomplete knowledge of non-coding regulatory elements and the cellular states and processes in which they function. Here, we performed a comprehensive integrated post-GWAS analysis of T1D to identify functional regulatory variants in enhancers and their cognate target genes. Starting with 1,817 candidate T1D SNPs defined from the GWAS catalog and LDlink databases, we conducted functional annotation analysis using genomic data from various public databases. These include 1) Roadmap Epigenomics, ENCODE, and RegulomeDB for epigenome data; 2) GTEx for tissue-specific gene expression and expression quantitative trait loci data; and 3) lncRNASNP2 for long non-coding RNA data. Our results indicated a prevalent enhancer-based immune dysregulation in T1D pathogenesis. We identified 26 high-probability causal enhancer SNPs associated with T1D, and 64 predicted target genes. The majority of the target genes play major roles in antigen presentation and immune response and are regulated through complex transcriptional regulatory circuits, including those in HLA (6p21) and non-HLA (16p11.2) loci. These candidate causal enhancer SNPs are supported by strong evidence and warrant functional follow-up studies.
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Affiliation(s)
- Seung-Soo Kim
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Adam D. Hudgins
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Jiping Yang
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Yizhou Zhu
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Zhidong Tu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Michael G. Rosenfeld
- Howard Hughes Medical Institute, Department of Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Teresa P. DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
- The Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Yousin Suh
- Department of Obstetrics and Gynecology, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
- * E-mail:
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Landolfi A, Barone P, Erro R. The Spectrum of PRRT2-Associated Disorders: Update on Clinical Features and Pathophysiology. Front Neurol 2021; 12:629747. [PMID: 33746883 PMCID: PMC7969989 DOI: 10.3389/fneur.2021.629747] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022] Open
Abstract
Mutations in the PRRT2 (proline-rich transmembrane protein 2) gene have been identified as the main cause of an expanding spectrum of disorders, including paroxysmal kinesigenic dyskinesia and benign familial infantile epilepsy, which places this gene at the border between epilepsy and movement disorders. The clinical spectrum has largely expanded to include episodic ataxia, hemiplegic migraine, and complex neurodevelopmental disorders in cases with biallelic mutations. Prior to the discovery of PRRT2 as the causative gene for this spectrum of disorders, the sensitivity of paroxysmal kinesigenic dyskinesia to anticonvulsant drugs regulating ion channel function as well as the co-occurrence of epilepsy in some patients or families fostered the hypothesis this could represent a channelopathy. However, recent evidence implicates PRRT2 in synapse functioning, which disproves the "channel hypothesis" (although PRRT2 modulates ion channels at the presynaptic level), and justifies the classification of these conditions as synaptopathies, an emerging rubric of brain disorders. This review aims to provide an update of the clinical and pathophysiologic features of PRRT2-associated disorders.
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Affiliation(s)
| | | | - Roberto Erro
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana, ” University of Salerno, Baronissi, Italy
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Lengyel A, Pinti É, Pikó H, Jávorszky E, David D, Tihanyi M, Gönczi É, Kiss E, Tóth Z, Tory K, Fekete G, Haltrich I. Clinical and genetic findings in Hungarian pediatric patients carrying chromosome 16p copy number variants and a review of the literature. Eur J Med Genet 2020; 63:104027. [PMID: 32758661 DOI: 10.1016/j.ejmg.2020.104027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 07/10/2020] [Accepted: 07/25/2020] [Indexed: 11/27/2022]
Abstract
The short arm of chromosome 16 (16p) is enriched for segmental duplications, making it susceptible to recurrent, reciprocal rearrangements implicated in the etiology of several phenotypes, including intellectual disability, speech disorders, developmental coordination disorder, autism spectrum disorders, attention deficit hyperactivity disorders, obesity and congenital skeletal disorders. In our clinical study 73 patients were analyzed by chromosomal microarray, and results were confirmed by fluorescence in situ hybridization or polymerase chain reaction. All patients underwent detailed clinical evaluation, with special emphasis on behavioral symptoms. 16p rearrangements were identified in 10 individuals. We found six pathogenic deletions and duplications of the recurrent regions within 16p11.2: one patient had a deletion of the distal 16p11.2 region associated with obesity, while four individuals had duplications, and one patient a deletion of the proximal 16p11.2 region. The other four patients carried 16p variations as second-site genomic alterations, acting as possible modifying genetic factors. We present the phenotypic and genotypic results of our patients and discuss our findings in relation to the available literature.
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Affiliation(s)
- Anna Lengyel
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary.
| | - Éva Pinti
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Henriett Pikó
- I Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Eszter Jávorszky
- I Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Dezső David
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, Lisbon, Portugal
| | - Mariann Tihanyi
- Department of Genetics, Zala County Hospital, Zalaegerszeg, Hungary
| | - Éva Gönczi
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Eszter Kiss
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Zsuzsa Tóth
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Kálmán Tory
- I Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - György Fekete
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Irén Haltrich
- II Department of Pediatrics, Semmelweis University, Budapest, Hungary
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Ocular Findings in the 16p11.2 Microdeletion Syndrome: A Case Report and Literature Review. Case Rep Pediatr 2020; 2020:2031701. [PMID: 32373379 PMCID: PMC7189309 DOI: 10.1155/2020/2031701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/03/2020] [Accepted: 03/11/2020] [Indexed: 01/22/2023] Open
Abstract
The recurrent 16p11.2 microdeletion is characterized by developmental delays and a wide spectrum of congenital anomalies. It has been well reported that individuals with this ∼593-kb interstitial deletion have an increased susceptibility toward the autism spectrum disorder (ASD). Abnormalities of the eye and ocular adnexa are also commonly associated findings seen in individuals with the 16p11.2 microdeletion syndrome, although these ophthalmic manifestations have not been well characterized. We conducted an extensive literature review to highlight the eye features in patients with the 16p11.2 microdeletion syndrome and describe a 5-year-old boy with the syndrome. The boy initially presented with intellectual disability, speech delay, and defiant behavior; diagnoses of attention deficit hyperactivity disorder (ADHD) and oppositional defiant disorder (ODD) were established. He had a Chiari malformation type 1. His ophthalmic features included strabismus, hyperopia, and ptosis, and a posterior embryotoxon was present bilaterally. From a systematic review of prior reported cases, the most common eye and ocular adnexa findings observed were downslanting palpebral fissures, deep-set eyes, ptosis, and hypertelorism.
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11
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Avramopoulos D. Recent Advances in the Genetics of Schizophrenia. MOLECULAR NEUROPSYCHIATRY 2018; 4:35-51. [PMID: 29998117 PMCID: PMC6032037 DOI: 10.1159/000488679] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/21/2018] [Indexed: 12/27/2022]
Abstract
The last decade brought tremendous progress in the field of schizophrenia genetics. As a result of extensive collaborations and multiple technological advances, we now recognize many types of genetic variants that increase the risk. These include large copy number variants, rare coding inherited and de novο variants, and over 100 loci harboring common risk variants. While the type and contribution to the risk vary among genetic variants, there is concordance in the functions of genes they implicate, such as those whose RNA binds the fragile X-related protein FMRP and members of the activity-regulated cytoskeletal complex involved in learning and memory. Gene expression studies add important information on the biology of the disease and recapitulate the same functional gene groups. Studies of alternative phenotypes help us widen our understanding of the genetic architecture of mental function and dysfunction, how diseases overlap not only with each other but also with non-disease phenotypes. The challenge is to apply this new knowledge to prevention and treatment and help patients. The data generated so far and emerging technologies, including new methods in cell engineering, offer significant promise that in the next decade we will unlock the translational potential of these significant discoveries.
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Affiliation(s)
- Dimitrios Avramopoulos
- Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Department of Psychiatry, Johns Hopkins University, Baltimore, Maryland, USA
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12
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Geets E, Meuwissen MEC, Van Hul W. Clinical, molecular genetics and therapeutic aspects of syndromic obesity. Clin Genet 2018; 95:23-40. [PMID: 29700824 DOI: 10.1111/cge.13367] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 12/13/2022]
Abstract
Obesity has become a major health problem worldwide. To date, more than 25 different syndromic forms of obesity are known in which one (monogenic) or multiple (polygenic) genes are involved. This review gives an overview of these forms and focuses more in detail on 6 syndromes: Prader Willi Syndrome and Prader Willi like phenotype, Bardet Biedl Syndrome, Alström Syndrome, Wilms tumor, Aniridia, Genitourinary malformations and mental Retardation syndrome and 16p11.2 (micro)deletions. Years of research provided plenty of information on the molecular genetics of these disorders and the obesity phenotype leading to a more individualized treatment of the symptoms, however, many questions still remain unanswered. As these obesity syndromes have different signs and symptoms in common, it makes it difficult to accurately diagnose patients which may result in inappropriate treatment of the disease. Therefore, the big challenge for clinicians and scientists is to more clearly differentiate all syndromic forms of obesity to provide conclusive genetic explanations and eventually deliver accurate genetic counseling and treatment. In addition, further delineation of the (functions of the) underlying genes with the use of array- or next-generation sequencing-based technology will be helpful to unravel the mechanisms of energy metabolism in the general population.
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Affiliation(s)
- E Geets
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - M E C Meuwissen
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
| | - W Van Hul
- Department of Medical Genetics, University of Antwerp and Antwerp University Hospital, Antwerp, Belgium
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13
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Loviglio MN, Arbogast T, Jønch AE, Collins SC, Popadin K, Bonnet CS, Giannuzzi G, Maillard AM, Jacquemont S, Yalcin B, Katsanis N, Golzio C, Reymond A. The Immune Signaling Adaptor LAT Contributes to the Neuroanatomical Phenotype of 16p11.2 BP2-BP3 CNVs. Am J Hum Genet 2017; 101:564-577. [PMID: 28965845 PMCID: PMC5630231 DOI: 10.1016/j.ajhg.2017.08.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/21/2017] [Indexed: 02/04/2023] Open
Abstract
Copy-number changes in 16p11.2 contribute significantly to neuropsychiatric traits. Besides the 600 kb BP4-BP5 CNV found in 0.5%-1% of individuals with autism spectrum disorders and schizophrenia and whose rearrangement causes reciprocal defects in head size and body weight, a second distal 220 kb BP2-BP3 CNV is likewise a potent driver of neuropsychiatric, anatomical, and metabolic pathologies. These two CNVs are engaged in complex reciprocal chromatin looping, intimating a functional relationship between genes in these regions that might be relevant to pathomechanism. We assessed the drivers of the distal 16p11.2 duplication by overexpressing each of the nine encompassed genes in zebrafish. Only overexpression of LAT induced a reduction of brain proliferating cells and concomitant microcephaly. Consistently, suppression of the zebrafish ortholog induced an increase of proliferation and macrocephaly. These phenotypes were not unique to zebrafish; Lat knockout mice show brain volumetric changes. Consistent with the hypothesis that LAT dosage is relevant to the CNV pathology, we observed similar effects upon overexpression of CD247 and ZAP70, encoding members of the LAT signalosome. We also evaluated whether LAT was interacting with KCTD13, MVP, and MAPK3, major driver and modifiers of the proximal 16p11.2 600 kb BP4-BP5 syndromes, respectively. Co-injected embryos exhibited an increased microcephaly, suggesting the presence of genetic interaction. Correspondingly, carriers of 1.7 Mb BP1-BP5 rearrangements that encompass both the BP2-BP3 and BP4-BP5 loci showed more severe phenotypes. Taken together, our results suggest that LAT, besides its well-recognized function in T cell development, is a major contributor of the 16p11.2 220 kb BP2-BP3 CNV-associated neurodevelopmental phenotypes.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Adaptor Proteins, Signal Transducing/physiology
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Animals
- Autistic Disorder/genetics
- Autistic Disorder/immunology
- Autistic Disorder/pathology
- Brain/metabolism
- Brain/pathology
- Child
- Child, Preschool
- Chromosome Deletion
- Chromosome Disorders/genetics
- Chromosome Disorders/immunology
- Chromosome Disorders/pathology
- Chromosomes, Human, Pair 16/genetics
- Chromosomes, Human, Pair 16/immunology
- Cohort Studies
- DNA Copy Number Variations
- Embryo, Nonmammalian/metabolism
- Embryo, Nonmammalian/pathology
- Female
- Gene Expression Regulation, Developmental
- Humans
- Infant
- Intellectual Disability/genetics
- Intellectual Disability/immunology
- Intellectual Disability/pathology
- Male
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Membrane Proteins/physiology
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Microcephaly/genetics
- Microcephaly/pathology
- Middle Aged
- Phenotype
- Phosphoproteins/physiology
- Signal Transduction
- Young Adult
- Zebrafish/embryology
- Zebrafish/genetics
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
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Affiliation(s)
- Maria Nicla Loviglio
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Thomas Arbogast
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Aia Elise Jønch
- Service of Medical Genetics, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Stephan C Collins
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics; Centre National de la Recherche Scientifique, UMR7104; Institut National de la Santé et de la Recherche Médicale, U964; Université de Strasbourg, 67400 Illkirch-Graffenstaden, France
| | - Konstantin Popadin
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Immanuel Kant Baltic Federal University, 14 A. Nevskogo ul., Kaliningrad 236041, Russia
| | - Camille S Bonnet
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Anne M Maillard
- Service of Medical Genetics, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Sébastien Jacquemont
- Service of Medical Genetics, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Binnaz Yalcin
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics; Centre National de la Recherche Scientifique, UMR7104; Institut National de la Santé et de la Recherche Médicale, U964; Université de Strasbourg, 67400 Illkirch-Graffenstaden, France
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Christelle Golzio
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland.
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14
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Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Mol Psychiatry 2017; 22:836-849. [PMID: 27240531 PMCID: PMC5508252 DOI: 10.1038/mp.2016.84] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/18/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
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15
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Kaur Y, de Souza RJ, Gibson WT, Meyre D. A systematic review of genetic syndromes with obesity. Obes Rev 2017; 18:603-634. [PMID: 28346723 DOI: 10.1111/obr.12531] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 11/29/2022]
Abstract
Syndromic monogenic obesity typically follows Mendelian patterns of inheritance and involves the co-presentation of other characteristics, such as mental retardation, dysmorphic features and organ-specific abnormalities. Previous reviews on obesity have reported 20 to 30 syndromes but no systematic review has yet been conducted on syndromic obesity. We searched seven databases using terms such as 'obesity', 'syndrome' and 'gene' to conduct a systematic review of literature on syndromic obesity. Our literature search identified 13,719 references. After abstract and full-text review, 119 relevant papers were eligible, and 42 papers were identified through additional searches. Our analysis of these 161 papers found that 79 obesity syndromes have been reported in literature. Of the 79 syndromes, 19 have been fully genetically elucidated, 11 have been partially elucidated, 27 have been mapped to a chromosomal region and for the remaining 22, neither the gene(s) nor the chromosomal location(s) have yet been identified. Interestingly, 54.4% of the syndromes have not been assigned a name, whereas 13.9% have more than one name. We report on organizational inconsistencies (e.g. naming discrepancies and syndrome classification) and provide suggestions for improvements. Overall, this review illustrates the need for increased clinical and genetic research on syndromes with obesity.
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Affiliation(s)
- Y Kaur
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - R J de Souza
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada
| | - W T Gibson
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
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16
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Li L, Huang L, Lin S, Luo Y, Fang Q. Discordant phenotypes in monozygotic twins with 16p11.2 microdeletions including the SH2B1 gene. Am J Med Genet A 2017; 173:2284-2288. [PMID: 28544142 DOI: 10.1002/ajmg.a.38284] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 04/13/2017] [Indexed: 11/07/2022]
Abstract
A 200∼240 kb SH2B1-containing deletion region on 16p11.2 is associated with early-onset obesity and developmental delay. Here, we describe monozygotic twin brothers with discordant clinical presentations. Intrauterine fetal growth restriction was present in both twins. Additionally, twin A exhibited coarctation of aorta, left ventricular noncompaction, atrial septal defect, pericardial effusion, left hydronephrosis, and moderate developmental delay, whereas twin B exhibited single umbilical artery. Chromosome microarray analysis was performed on both twins and their parents. An identical 244 kb microdeletion on 16p11.2 including 9 Refseq genes, including SH2B1, was identified in the twins. The novel findings in monozygotic twins may expand the phenotypic spectrum of 16p11.2 microdeletion. Further studies are needed to strengthen the correlation between genotypes and abnormal clinical features.
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Affiliation(s)
- Lin Li
- Fetal Medicine Centre, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Linhuan Huang
- Fetal Medicine Centre, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shaobin Lin
- Fetal Medicine Centre, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yanmin Luo
- Fetal Medicine Centre, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Qun Fang
- Fetal Medicine Centre, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
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17
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Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. BMC SYSTEMS BIOLOGY 2016. [DOI: 10.1186/s12918-016-0366-0 order by 8029-- awyx] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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18
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Lin M, Pedrosa E, Hrabovsky A, Chen J, Puliafito BR, Gilbert SR, Zheng D, Lachman HM. Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. BMC SYSTEMS BIOLOGY 2016. [DOI: 10.1186/s12918-016-0366-0 and 1880=1880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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19
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Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. BMC SYSTEMS BIOLOGY 2016. [DOI: 10.1186/s12918-016-0366-0 order by 8029-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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20
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Lin M, Pedrosa E, Hrabovsky A, Chen J, Puliafito BR, Gilbert SR, Zheng D, Lachman HM. Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. BMC SYSTEMS BIOLOGY 2016. [DOI: 10.1186/s12918-016-0366-0 order by 8029-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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21
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Lin M, Pedrosa E, Hrabovsky A, Chen J, Puliafito BR, Gilbert SR, Zheng D, Lachman HM. Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. BMC SYSTEMS BIOLOGY 2016. [DOI: 10.1186/s12918-016-0366-0 order by 1-- -] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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22
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Lin M, Pedrosa E, Hrabovsky A, Chen J, Puliafito BR, Gilbert SR, Zheng D, Lachman HM. Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. BMC SYSTEMS BIOLOGY 2016. [DOI: 10.1186/s12918-016-0366-0 order by 1-- gadu] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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23
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Lin M, Pedrosa E, Hrabovsky A, Chen J, Puliafito BR, Gilbert SR, Zheng D, Lachman HM. Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. BMC SYSTEMS BIOLOGY 2016. [DOI: 10.1186/s12918-016-0366-0 order by 1-- #] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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24
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Lin M, Pedrosa E, Hrabovsky A, Chen J, Puliafito BR, Gilbert SR, Zheng D, Lachman HM. Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion. BMC SYSTEMS BIOLOGY 2016; 10:105. [PMID: 27846841 PMCID: PMC5111260 DOI: 10.1186/s12918-016-0366-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 11/06/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Individuals with 22q11.2 Deletion Syndrome (22q11.2 DS) are a specific high-risk group for developing schizophrenia (SZ), schizoaffective disorder (SAD) and autism spectrum disorders (ASD). Several genes in the deleted region have been implicated in the development of SZ, e.g., PRODH and DGCR8. However, the mechanistic connection between these genes and the neuropsychiatric phenotype remains unclear. To elucidate the molecular consequences of 22q11.2 deletion in early neural development, we carried out RNA-seq analysis to investigate gene expression in early differentiating human neurons derived from induced pluripotent stem cells (iPSCs) of 22q11.2 DS SZ and SAD patients. METHODS Eight cases (ten iPSC-neuron samples in total including duplicate clones) and seven controls (nine in total including duplicate clones) were subjected to RNA sequencing. Using a systems level analysis, differentially expressed genes/gene-modules and pathway of interests were identified. Lastly, we related our findings from in vitro neuronal cultures to brain development by mapping differentially expressed genes to BrainSpan transcriptomes. RESULTS We observed ~2-fold reduction in expression of almost all genes in the 22q11.2 region in SZ (37 genes reached p-value < 0.05, 36 of which reached a false discovery rate < 0.05). Outside of the deleted region, 745 genes showed significant differences in expression between SZ and control neurons (p < 0.05). Function enrichment and network analysis of the differentially expressed genes uncovered converging evidence on abnormal expression in key functional pathways, such as apoptosis, cell cycle and survival, and MAPK signaling in the SZ and SAD samples. By leveraging transcriptome profiles of normal human brain tissues across human development into adulthood, we showed that the differentially expressed genes converge on a sub-network mediated by CDC45 and the cell cycle, which would be disrupted by the 22q11.2 deletion during embryonic brain development, and another sub-network modulated by PRODH, which could contribute to disruption of brain function during adolescence. CONCLUSIONS This study has provided evidence for disruption of potential molecular events in SZ patient with 22q11.2 deletion and related our findings from in vitro neuronal cultures to functional perturbations that can occur during brain development in SZ.
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Affiliation(s)
- Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Anastasia Hrabovsky
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Jian Chen
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Benjamin R. Puliafito
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Stephanie R. Gilbert
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
| | - Herbert M. Lachman
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
- Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY USA
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25
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Schuh AM, Taylor JD, Font-Montgomery EE, Tosh AK. Obesity and facial dysmorphism in an adolescent patient with a 16p11.2 microdeletion. Int J Adolesc Med Health 2016; 30:/j/ijamh.ahead-of-print/ijamh-2016-0041/ijamh-2016-0041.xml. [PMID: 27394043 DOI: 10.1515/ijamh-2016-0041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 06/03/2016] [Indexed: 11/15/2022]
Abstract
A 17-year-old mixed race male has been followed in our adolescent clinic for severe obesity, dysmorphic features, and behavioral issues. Among other interventions, he has received symptomatic treatment for hypertension, insulin resistance, and attention deficit hyperactivity disorder. Genetic investigation identified a 16p11.2 microdeletion, commonly associated with severe obesity and developmental delay. We present the clinical history, treatment, and implications for this patient.
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Affiliation(s)
- Aaron M Schuh
- University of Missouri School of Medicine, MA215 Medical Sciences Building, Columbia, Missouri 65212, MO,USA
| | - Jacob D Taylor
- University of Missouri School of Medicine, Columbia, MO, USA
| | | | - Aneesh K Tosh
- University of Missouri School of Medicine, Department of Child Health: Adolescent Division, 1 Hospital Dr., Columbia, MO, USA
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26
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Chatzimichali EA, Brent S, Hutton B, Perrett D, Wright CF, Bevan AP, Hurles ME, Firth HV, Swaminathan GJ. Facilitating collaboration in rare genetic disorders through effective matchmaking in DECIPHER. Hum Mutat 2015. [PMID: 26220709 PMCID: PMC4832335 DOI: 10.1002/humu.22842] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
DECIPHER (https://decipher.sanger.ac.uk) is a web‐based platform for secure deposition, analysis, and sharing of plausibly pathogenic genomic variants from well‐phenotyped patients suffering from genetic disorders. DECIPHER aids clinical interpretation of these rare sequence and copy‐number variants by providing tools for variant analysis and identification of other patients exhibiting similar genotype–phenotype characteristics. DECIPHER also provides mechanisms to encourage collaboration among a global community of clinical centers and researchers, as well as exchange of information between clinicians and researchers within a consortium, to accelerate discovery and diagnosis. DECIPHER has contributed to matchmaking efforts by enabling the global clinical genetics community to identify many previously undiagnosed syndromes and new disease genes, and has facilitated the publication of over 700 peer‐reviewed scientific publications since 2004. At the time of writing, DECIPHER contains anonymized data from ∼250 registered centers on more than 51,500 patients (∼18000 patients with consent for data sharing and ∼25000 anonymized records shared privately). In this paper, we describe salient features of the platform, with special emphasis on the tools and processes that aid interpretation, sharing, and effective matchmaking with other data held in the database and that make DECIPHER an invaluable clinical and research resource.
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Affiliation(s)
- Eleni A Chatzimichali
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Simon Brent
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Benjamin Hutton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Daniel Perrett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Caroline F Wright
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Andrew P Bevan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Helen V Firth
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom.,Cambridge University Department of Medical Genetics, Addenbrooke's Hospital, Cambridge, CB2 2QQ, United Kingdom
| | - Ganesh J Swaminathan
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom
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Brunner D, Kabitzke P, He D, Cox K, Thiede L, Hanania T, Sabath E, Alexandrov V, Saxe M, Peles E, Mills A, Spooren W, Ghosh A, Feliciano P, Benedetti M, Luo Clayton A, Biemans B. Comprehensive Analysis of the 16p11.2 Deletion and Null Cntnap2 Mouse Models of Autism Spectrum Disorder. PLoS One 2015; 10:e0134572. [PMID: 26273832 PMCID: PMC4537259 DOI: 10.1371/journal.pone.0134572] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 07/10/2015] [Indexed: 01/12/2023] Open
Abstract
Autism spectrum disorder comprises several neurodevelopmental conditions presenting symptoms in social communication and restricted, repetitive behaviors. A major roadblock for drug development for autism is the lack of robust behavioral signatures predictive of clinical efficacy. To address this issue, we further characterized, in a uniform and rigorous way, mouse models of autism that are of interest because of their construct validity and wide availability to the scientific community. We implemented a broad behavioral battery that included but was not restricted to core autism domains, with the goal of identifying robust, reliable phenotypes amenable for further testing. Here we describe comprehensive findings from two known mouse models of autism, obtained at different developmental stages, using a systematic behavioral test battery combining standard tests as well as novel, quantitative, computer-vision based systems. The first mouse model recapitulates a deletion in human chromosome 16p11.2, found in 1% of individuals with autism. The second mouse model harbors homozygous null mutations in Cntnap2, associated with autism and Pitt-Hopkins-like syndrome. Consistent with previous results, 16p11.2 heterozygous null mice, also known as Del(7Slx1b-Sept1)4Aam weighed less than wild type littermates displayed hyperactivity and no social deficits. Cntnap2 homozygous null mice were also hyperactive, froze less during testing, showed a mild gait phenotype and deficits in the three-chamber social preference test, although less robust than previously published. In the open field test with exposure to urine of an estrous female, however, the Cntnap2 null mice showed reduced vocalizations. In addition, Cntnap2 null mice performed slightly better in a cognitive procedural learning test. Although finding and replicating robust behavioral phenotypes in animal models is a challenging task, such functional readouts remain important in the development of therapeutics and we anticipate both our positive and negative findings will be utilized as a resource for the broader scientific community.
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Affiliation(s)
- Daniela Brunner
- PsychoGenics, Inc., Tarrytown, NY, United States of America
- Department of Psychiatry, Columbia University, New York, NY, United States of America
- * E-mail:
| | - Patricia Kabitzke
- PsychoGenics, Inc., Tarrytown, NY, United States of America
- Department of Psychiatry, Columbia University, New York, NY, United States of America
| | - Dansha He
- PsychoGenics, Inc., Tarrytown, NY, United States of America
| | - Kimberly Cox
- PsychoGenics, Inc., Tarrytown, NY, United States of America
| | - Lucinda Thiede
- PsychoGenics, Inc., Tarrytown, NY, United States of America
| | - Taleen Hanania
- PsychoGenics, Inc., Tarrytown, NY, United States of America
| | - Emily Sabath
- PsychoGenics, Inc., Tarrytown, NY, United States of America
| | | | | | - Elior Peles
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alea Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | | | | | - Pamela Feliciano
- Simons Foundation Autism Research Initiative, New York, NY, United States of America
| | - Marta Benedetti
- Simons Foundation Autism Research Initiative, New York, NY, United States of America
| | - Alice Luo Clayton
- Simons Foundation Autism Research Initiative, New York, NY, United States of America
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Aerts E, Beckers S, Zegers D, Van Camp JK, Van Hoorenbeeck K, Massa G, Verrijken A, Mertens IL, Verhulst SL, Rooman RR, Van Gaal LF, Van Hul W. Genetic and structural variation in the SH2B1 gene in the Belgian population. Mol Genet Metab 2015; 115:193-8. [PMID: 26031769 DOI: 10.1016/j.ymgme.2015.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/21/2015] [Accepted: 05/21/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVE Animal studies, genome-wide association and genomic structural variation studies have identified the SH2B1 gene as a candidate gene for obesity. Therefore, we have designed an extensive mutation and copy number variation (CNV) analysis investigating the prevalence of genetic and structural variations in SH2B1 in the Belgian population. DESIGN AND METHODS In the first part of this study, we performed a mutation screen for variants in the SH2B1 coding region in 581 obese children and adolescents and 433 healthy, lean individuals with high-resolution melting curve analysis followed by direct sequencing. In the second part of this study, Multiplex Amplicon Quantification (MAQ) analysis was used to identify CNVs in the distal SH2B1-containing chr.16p11.2 region in 421 obese children and adolescents with no developmental delay or behavioral phenotype. RESULTS Mutation analysis resulted in the identification of fifteen rare non-synonymous heterozygous variants. Several of these were found both in lean and obese subjects, suggesting that these are neutral polymorphisms. However, six private, heterozygous, non-synonymous variations were present in obese children only. Furthermore, we also identified six missense variants solely in lean individuals. CNV analysis could not identify carriers of the distal 16p11.2 deletion in our population. CONCLUSION Our mutation analysis has demonstrated that variation in the SH2B1 gene is frequent in both lean and obese groups, with distinctive variations being present on either side of the weight spectrum. Although the equal variation frequency does not immediately support disease causality, it cannot be excluded that some variations are weight-increasing or -decreasing. Further functional testing of the variants will be necessary to fully understand the impact of these variants on SH2B1. We were not able to detect carriers of the distal 16p11.2 deletion in our study population. As we excluded patients with developmental or behavioral problems, we suggest that in addition to obesity, the distal deletion might predispose for these traits. Further characterization of the phenotype is therefore necessary to clearly identify the phenotype of the distal 16p11.2 microdeletion syndrome.
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Affiliation(s)
- Evi Aerts
- Centre of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Sigri Beckers
- Centre of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Doreen Zegers
- Centre of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | | | - Guy Massa
- Department of Pediatrics, Jessa Hospital, Hasselt, Belgium
| | - An Verrijken
- Department of Endocrinology, Diabetology and Metabolic Diseases, Antwerp University Hospital, Antwerp, Belgium
| | - Ilse L Mertens
- Department of Endocrinology, Diabetology and Metabolic Diseases, Antwerp University Hospital, Antwerp, Belgium
| | - Stijn L Verhulst
- Department of Pediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Raoul R Rooman
- Department of Pediatrics, Antwerp University Hospital, Antwerp, Belgium
| | - Luc F Van Gaal
- Department of Endocrinology, Diabetology and Metabolic Diseases, Antwerp University Hospital, Antwerp, Belgium
| | - Wim Van Hul
- Centre of Medical Genetics, University of Antwerp, Antwerp, Belgium.
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Gerundino F, Marseglia G, Pescucci C, Pelo E, Benelli M, Giachini C, Federighi B, Antonelli C, Torricelli F. 16p11.2 de novo microdeletion encompassing SRCAP gene in a patient with speech impairment, global developmental delay and behavioural problems. Eur J Med Genet 2015; 57:649-53. [PMID: 25451714 DOI: 10.1016/j.ejmg.2014.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 09/21/2014] [Indexed: 11/28/2022]
Abstract
We describe a patient with speech impairment, global developmental delay, behavioural problems and a 186 kb de novo microdeletion on 16p11.2. There are four OMIM Phenotypes entries partially overlapping with the deleted region and related to recurrent microdeletions/microduplications in 16p11.2. A detailed review of published data shows that microdeletions/microduplications' boundaries do not include genes that are deleted in the case here reported. The deletion encompasses 9 RefSeq genes and includes SRCAP (Snf2-related CREBBP activator protein, OMIM*611421), a disease causing gene. Recently, truncating mutations in the SRCAP gene have been shown to cause Floating-Harbor syndrome (FHS, OMIM#136140), a rare disorder characterized by peculiar facial features, short stature with delayed osseous maturation and speech impairment. The patient reported here shows few subtle phenotypic features resembling that of FHS, but she does not have sufficient signs and symptoms for the clinical diagnosis and a clinical classification based on facial gestalt is not possible. This is the first report of a 16p11.2 deletion completely removing one copy of SRCAP, suggesting that haploinsufficiency of this gene could be associated to speech impairment, global developmental delay, behavioural problems and few subtle phenotypic features resembling FHS. However, further evidence for the putative causative role of SRCAP isolated deletion is needed.
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Abstract
The discovery of leptin has provided a robust framework upon which our current understanding of the mechanisms involved in energy homeostasis has been built. In this review, we describe how the identification of humans with mutations in the genes encoding leptin and the leptin receptor and the characterisation of the associated clinical phenotypes have provided insights into the role of leptin-responsive pathways in the regulation of eating behaviour, intermediary metabolism and the onset of puberty. Importantly, administration of recombinant human leptin in leptin deficiency represents the first mechanistically based targeted therapy for obesity and has provided immense clinical benefits for the patients concerned. In subsequent years, we and others have shown that human obesity can result from a multiplicity of defects in the pathways downstream of leptin signalling within the brain.
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Affiliation(s)
- I Sadaf Farooqi
- MRC Metabolic Diseases UnitMetabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Stephen O'Rahilly
- MRC Metabolic Diseases UnitMetabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, NIHR Cambridge Biomedical Research Centre, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
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Genetic strategies to understand physiological pathways regulating body weight. Mamm Genome 2014; 25:377-83. [PMID: 25154910 PMCID: PMC4164839 DOI: 10.1007/s00335-014-9541-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 08/11/2014] [Indexed: 11/29/2022]
Abstract
Body weight is a highly heritable trait across species. In humans, genetic variation plays a major role in determining the inter-individual differences in susceptibility or resistance to environmental factors which influence energy intake and expenditure. In this review, I discuss how genetic studies have contributed to our understanding of the central pathways that govern energy homeostasis. The study of individuals harboring highly penetrant genetic variants that disrupt the leptin–melanocortin pathway has informed our understanding of the physiological pathways involved in mammalian energy homeostasis.
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Blumenthal I, Ragavendran A, Erdin S, Klei L, Sugathan A, Guide J, Manavalan P, Zhou J, Wheeler V, Levin J, Ernst C, Roeder K, Devlin B, Gusella J, Talkowski M. Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families. Am J Hum Genet 2014; 94:870-83. [PMID: 24906019 DOI: 10.1016/j.ajhg.2014.05.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/12/2014] [Indexed: 12/18/2022] Open
Abstract
Reciprocal copy-number variation (CNV) of a 593 kb region of 16p11.2 is a common genetic cause of autism spectrum disorder (ASD), yet it is not completely penetrant and can manifest in a wide array of phenotypes. To explore its molecular consequences, we performed RNA sequencing of cerebral cortex from mouse models with CNV of the syntenic 7qF3 region and lymphoblast lines from 34 members of 7 multiplex ASD-affected families harboring the 16p11.2 CNV. Expression of all genes in the CNV region correlated well with their DNA copy number, with no evidence of dosage compensation. We observed effects on gene expression outside the CNV region, including apparent positional effects in cis and in trans at genomic segments with evidence of physical interaction in Hi-C chromosome conformation data. One of the most significant positional effects was telomeric to the 16p11.2 CNV and includes the previously described "distal" 16p11.2 microdeletion. Overall, 16p11.2 CNV was associated with altered expression of genes and networks that converge on multiple hypotheses of ASD pathogenesis, including synaptic function (e.g., NRXN1, NRXN3), chromatin modification (e.g., CHD8, EHMT1, MECP2), transcriptional regulation (e.g., TCF4, SATB2), and intellectual disability (e.g., FMR1, CEP290). However, there were differences between tissues and species, with the strongest effects being consistently within the CNV region itself. Our analyses suggest that through a combination of indirect regulatory effects and direct effects on nuclear architecture, alteration of 16p11.2 genes disrupts expression networks that involve other genes and pathways known to contribute to ASD, suggesting an overlap in mechanisms of pathogenesis.
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González JR, Cáceres A, Esko T, Cuscó I, Puig M, Esnaola M, Reina J, Siroux V, Bouzigon E, Nadif R, Reinmaa E, Milani L, Bustamante M, Jarvis D, Antó JM, Sunyer J, Demenais F, Kogevinas M, Metspalu A, Cáceres M, Pérez-Jurado LA. A common 16p11.2 inversion underlies the joint susceptibility to asthma and obesity. Am J Hum Genet 2014; 94:361-72. [PMID: 24560518 PMCID: PMC3951940 DOI: 10.1016/j.ajhg.2014.01.015] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 01/28/2014] [Indexed: 12/21/2022] Open
Abstract
The prevalence of asthma and obesity is increasing worldwide, and obesity is a well-documented risk factor for asthma. The mechanisms underlying this association and parallel time trends remain largely unknown but genetic factors may be involved. Here, we report on a common ~0.45 Mb genomic inversion at 16p11.2 that can be accurately genotyped via SNP array data. We show that the inversion allele protects against the joint occurrence of asthma and obesity in five large independent studies (combined sample size of 317 cases and 543 controls drawn from a total of 5,809 samples; combined OR = 0.48, p = 5.5 × 10(-6)). Allele frequencies show remarkable worldwide population stratification, ranging from 10% in East Africa to 49% in Northern Europe, consistent with discordant and extreme genetic drifts or adaptive selections after human migration out of Africa. Inversion alleles strongly correlate with expression levels of neighboring genes, especially TUFM (p = 3.0 × 10(-40)) that encodes a mitochondrial protein regulator of energy balance and inhibitor of type 1 interferon, and other candidates for asthma (IL27) and obesity (APOB48R and SH2B1). Therefore, by affecting gene expression, the ~0.45 Mb 16p11.2 inversion provides a genetic basis for the joint susceptibility to asthma and obesity, with a population attributable risk of 39.7%. Differential mitochondrial function and basal energy balance of inversion alleles might also underlie the potential selection signature that led to their uneven distribution in world populations.
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Affiliation(s)
- Juan R González
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain.
| | - Alejandro Cáceres
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu 50090, Estonia
| | - Ivon Cuscó
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain
| | - Mikel Esnaola
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain
| | - Judith Reina
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain
| | - Valerie Siroux
- INSERM-UJF, U823, Institut Albert Bonniot, 38042 Grenoble, France; Université Joseph Fourier - BP 53, 38041 Grenoble, France
| | - Emmanuelle Bouzigon
- INSERM, UMRS-946, Genetic Variation of Human Diseases Unit, 75010 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, 75010 Paris, France
| | - Rachel Nadif
- INSERM, U1018, CESP Centre for Research in Epidemiology and Population Health, Respiratory and Environmental Epidemiology Team, 94807 Villejuif, France; Université Paris-Sud 11, UMRS 1018, 94807 Villejuif, France
| | - Eva Reinmaa
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia
| | - Mariona Bustamante
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; Genes and Disease Group, Centre for Genomic Regulation (CRG), Barcelona 08003, Spain
| | - Deborah Jarvis
- National Heart and Lung Institute, Imperial College, London SW7 2AZ, UK
| | - Josep M Antó
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Jordi Sunyer
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Florence Demenais
- INSERM, UMRS-946, Genetic Variation of Human Diseases Unit, 75010 Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, 75010 Paris, France
| | - Manolis Kogevinas
- Center for Research in Environmental Epidemiology (CREAL), Barcelona 08003, Spain; Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona 08003, Spain; National School of Public Health, Athens 115 21, Greece
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 50090, Estonia; Institute of Molecular and Cell Biology, University of Tartu, Tartu 50090, Estonia
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra (Barcelona) 08193, Spain; Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona 08010, Spain
| | - Luis A Pérez-Jurado
- Hospital del Mar Research Institute (IMIM), Barcelona 08003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona 08003, Spain.
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Huguet G, Nava C, Lemière N, Patin E, Laval G, Ey E, Brice A, Leboyer M, Szepetowski P, Gillberg C, Depienne C, Delorme R, Bourgeron T. Heterogeneous pattern of selective pressure for PRRT2 in human populations, but no association with autism spectrum disorders. PLoS One 2014; 9:e88600. [PMID: 24594579 PMCID: PMC3940422 DOI: 10.1371/journal.pone.0088600] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/11/2014] [Indexed: 11/22/2022] Open
Abstract
Inherited and de novo genomic imbalances at chromosome 16p11.2 are associated with autism spectrum disorders (ASD), but the causative genes remain unknown. Among the genes located in this region, PRRT2 codes for a member of the synaptic SNARE complex that allows the release of synaptic vesicles. PRRT2 is a candidate gene for ASD since homozygote mutations are associated with intellectual disability and heterozygote mutations cause benign infantile seizures, paroxysmal dyskinesia, or hemiplegic migraine. Here, we explored the contribution of PRRT2 mutations in ASD by screening its coding part in a large sample of 1578 individuals including 431 individuals with ASD, 186 controls and 961 individuals from the human genome Diversity Panel. We detected 24 nonsynonymous variants, 1 frameshift (A217PfsX8) and 1 in-frame deletion of 6 bp (p.A361_P362del). The frameshift mutation was observed in a control with no history of neurological or psychiatric disorders. The p.A361_P362del was observed in two individuals with autism from sub-Saharan African origin. Overall, the frequency of PRRT2 deleterious variants was not different between individuals with ASD and controls. Remarkably, PRRT2 displays a highly significant excess of nonsynonymous (pN) vs synonymous (pS) mutations in Asia (pN/pS = 4.85) and Europe (pN/pS = 1.62) compared with Africa (pN/pS = 0.26; Asia vs Africa: P = 0.000087; Europe vs Africa P = 0.00035; Europe vs Asia P = P = 0.084). We also showed that whole genome amplification performed through rolling cycle amplification could artificially introduce the A217PfsX8 mutation indicating that this technology should not be performed prior to PRRT2 mutation screening. In summary, our results do not support a role for PRRT2 coding sequence variants in ASD, but provide an ascertainment of its genetic variability in worldwide populations that should help researchers and clinicians to better investigate the role of PRRT2 in human diseases.
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Affiliation(s)
- Guillaume Huguet
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 ‘Genes, synapses and cognition’, Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Caroline Nava
- INSERM, U975—CRICM, Institut du cerveau et de la moelle épinière (ICM), Hôpital Pitié-Salpêtrière, Paris, France
- CNRS 7225—CRICM, Hôpital Pitié-Salpêtrière, Paris, France
- Université Pierre et Marie Curie-Paris-6 (UPMC), UMR_S 975, Paris, France
- Département de Génétique et de Cytogénétique, Unité fonctionnelle de génétique clinique, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Nathalie Lemière
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 ‘Genes, synapses and cognition’, Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Etienne Patin
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Guillaume Laval
- Unit of Human Evolutionary Genetics, Institut Pasteur, Paris, France
| | - Elodie Ey
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 ‘Genes, synapses and cognition’, Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
| | - Alexis Brice
- INSERM, U975—CRICM, Institut du cerveau et de la moelle épinière (ICM), Hôpital Pitié-Salpêtrière, Paris, France
- CNRS 7225—CRICM, Hôpital Pitié-Salpêtrière, Paris, France
- Université Pierre et Marie Curie-Paris-6 (UPMC), UMR_S 975, Paris, France
- Département de Génétique et de Cytogénétique, Unité fonctionnelle de neurogénétique moléculaire et cellulaire, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Marion Leboyer
- INSERM, U955, Psychiatry Genetic team, Creteil, France
- Fondation FondaMental, Créteil, France
| | - Pierre Szepetowski
- INSERM, UMR_S901, Marseille, France
- Aix-Marseille University, Marseille, France
- Mediterranean Institute of Neurobiology (INMED), Marseille, France
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, University of Gothenburg, Göteborg, Sweden
- Institute of Neuroscience and Physiology, Department of Pharmacology, Gothenburg University, Gothenburg, Sweden
- Institute of Child Health, University College London, London, United Kingdom
| | - Christel Depienne
- INSERM, U975—CRICM, Institut du cerveau et de la moelle épinière (ICM), Hôpital Pitié-Salpêtrière, Paris, France
- CNRS 7225—CRICM, Hôpital Pitié-Salpêtrière, Paris, France
- Université Pierre et Marie Curie-Paris-6 (UPMC), UMR_S 975, Paris, France
- Département de Génétique et de Cytogénétique, Unité fonctionnelle de neurogénétique moléculaire et cellulaire, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France
| | - Richard Delorme
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 ‘Genes, synapses and cognition’, Institut Pasteur, Paris, France
- Fondation FondaMental, Créteil, France
- Assistance Publique-Hôpitaux de Paris, Robert Debré Hospital, Department of Child and Adolescent Psychiatry, Paris, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, Paris, France
- CNRS URA 2182 ‘Genes, synapses and cognition’, Institut Pasteur, Paris, France
- University Denis Diderot Paris 7, Paris, France
- Fondation FondaMental, Créteil, France
- * E-mail:
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Bragin E, Chatzimichali EA, Wright CF, Hurles ME, Firth HV, Bevan AP, Swaminathan GJ. DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res 2013; 42:D993-D1000. [PMID: 24150940 PMCID: PMC3965078 DOI: 10.1093/nar/gkt937] [Citation(s) in RCA: 160] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The DECIPHER database (https://decipher.sanger.ac.uk/) is an accessible online repository of genetic variation with associated phenotypes that facilitates the identification and interpretation of pathogenic genetic variation in patients with rare disorders. Contributing to DECIPHER is an international consortium of >200 academic clinical centres of genetic medicine and ≥1600 clinical geneticists and diagnostic laboratory scientists. Information integrated from a variety of bioinformatics resources, coupled with visualization tools, provides a comprehensive set of tools to identify other patients with similar genotype–phenotype characteristics and highlights potentially pathogenic genes. In a significant development, we have extended DECIPHER from a database of just copy-number variants to allow upload, annotation and analysis of sequence variants such as single nucleotide variants (SNVs) and InDels. Other notable developments in DECIPHER include a purpose-built, customizable and interactive genome browser to aid combined visualization and interpretation of sequence and copy-number variation against informative datasets of pathogenic and population variation. We have also introduced several new features to our deposition and analysis interface. This article provides an update to the DECIPHER database, an earlier instance of which has been described elsewhere [Swaminathan et al. (2012) DECIPHER: web-based, community resource for clinical interpretation of rare variants in developmental disorders. Hum. Mol. Genet., 21, R37–R44].
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Affiliation(s)
- Eugene Bragin
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Cambridge University Department of Medical Genetics, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
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Frank GR, Fox J, Candela N, Jovanovic Z, Bochukova E, Levine J, Papenhausen PR, O'Rahilly S, Farooqi IS. Severe obesity and diabetes insipidus in a patient with PCSK1 deficiency. Mol Genet Metab 2013; 110:191-4. [PMID: 23800642 PMCID: PMC3759845 DOI: 10.1016/j.ymgme.2013.04.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/03/2013] [Accepted: 04/03/2013] [Indexed: 12/16/2022]
Abstract
Non-synonymous mutations affecting both alleles of PCSK1 (proprotein convertase 1/3) are associated with obesity and impaired prohormone processing. We report a proband who was compound heterozygous for a maternally inherited frameshift mutation and a paternally inherited 474kb deletion that encompasses PCSK1, representing a novel genetic mechanism underlying this phenotype. Although pro-vasopressin is not a known physiological substrate of PCSK1, the development of central diabetes insipidus in this proband suggests that PCSK1 deficiency can be associated with impaired osmoregulation.
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Affiliation(s)
- Graeme R Frank
- Cohen Children's Medical Center, Division of Pediatric Endocrinology, New Hyde Park, NY 11042, USA
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An unusual clinical severity of 16p11.2 deletion syndrome caused by unmasked recessive mutation of CLN3. Eur J Hum Genet 2013; 22:369-73. [PMID: 23860047 DOI: 10.1038/ejhg.2013.141] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 05/29/2013] [Accepted: 06/03/2013] [Indexed: 01/09/2023] Open
Abstract
With the introduction of array comparative genomic hybridization (aCGH) techniques in the diagnostic setting of patients with developmental delay and congenital malformations, many new microdeletion syndromes have been recognized. One of these recently recognized microdeletion syndromes is the 16p11.2 deletion syndrome, associated with variable clinical outcomes including developmental delay, autism spectrum disorder, epilepsy, and obesity, but also apparently normal phenotype. We report on a 16-year-old patient with developmental delay, exhibiting retinis pigmentosa with progressive visual failure from the age of 9 years, ataxia, and peripheral neuropathy. Chromosomal microarray analysis identified a 1.7-Mb 16p11.2 deletion encompassing the 593-kb common deletion (∼29.5 to ∼30.1 Mb; Hg18) and the 220-kb distal deletion (∼28.74 to ∼28.95 Mb; Hg18) that partially included the CLN3 gene. As the patient's clinical findings were different from usual 16p11.2 microdeletion phenotypes and showed some features reminiscent of juvenile neuronal ceroid-lipofuscinosis (JNCL, Batten disease, OMIM 204200), we suspected and confirmed a mutation of the remaining CLN3 allele. This case further illustrates that unmasking of hemizygous recessive mutations by chromosomal deletion represents one explanation for the phenotypic variability observed in chromosomal deletion disorders.
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Zafeiriou DI, Ververi A, Dafoulis V, Kalyva E, Vargiami E. Autism spectrum disorders: the quest for genetic syndromes. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:327-66. [PMID: 23650212 DOI: 10.1002/ajmg.b.32152] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 03/01/2013] [Indexed: 11/10/2022]
Abstract
Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disabilities with various etiologies, but with a heritability estimate of more than 90%. Although the strong correlation between autism and genetic factors has been long established, the exact genetic background of ASD remains unclear. A number of genetic syndromes manifest ASD at higher than expected frequencies compared to the general population. These syndromes account for more than 10% of all ASD cases and include tuberous sclerosis, fragile X, Down, neurofibromatosis, Angelman, Prader-Willi, Williams, Duchenne, etc. Clinicians are increasingly required to recognize genetic disorders in individuals with ASD, in terms of providing proper care and prognosis to the patient, as well as genetic counseling to the family. Vice versa, it is equally essential to identify ASD in patients with genetic syndromes, in order to ensure correct management and appropriate educational placement. During investigation of genetic syndromes, a number of issues emerge: impact of intellectual disability in ASD diagnoses, identification of autistic subphenotypes and differences from idiopathic autism, validity of assessment tools designed for idiopathic autism, possible mechanisms for the association with ASD, etc. Findings from the study of genetic syndromes are incorporated into the ongoing research on autism etiology and pathogenesis; different syndromes converge upon common biological backgrounds (such as disrupted molecular pathways and brain circuitries), which probably account for their comorbidity with autism. This review paper critically examines the prevalence and characteristics of the main genetic syndromes, as well as the possible mechanisms for their association with ASD.
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Houten SM, Te Brinke H, Denis S, Ruiter JP, Knegt AC, de Klerk JB, Augoustides-Savvopoulou P, Häberle J, Baumgartner MR, Coşkun T, Zschocke J, Sass JO, Poll-The BT, Wanders RJ, Duran M. Genetic basis of hyperlysinemia. Orphanet J Rare Dis 2013; 8:57. [PMID: 23570448 PMCID: PMC3626681 DOI: 10.1186/1750-1172-8-57] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 03/29/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Hyperlysinemia is an autosomal recessive inborn error of L-lysine degradation. To date only one causal mutation in the AASS gene encoding α-aminoadipic semialdehyde synthase has been reported. We aimed to better define the genetic basis of hyperlysinemia. METHODS We collected the clinical, biochemical and molecular data in a cohort of 8 hyperlysinemia patients with distinct neurological features. RESULTS We found novel causal mutations in AASS in all affected individuals, including 4 missense mutations, 2 deletions and 1 duplication. In two patients originating from one family, the hyperlysinemia was caused by a contiguous gene deletion syndrome affecting AASS and PTPRZ1. CONCLUSIONS Hyperlysinemia is caused by mutations in AASS. As hyperlysinemia is generally considered a benign metabolic variant, the more severe neurological disease course in two patients with a contiguous deletion syndrome may be explained by the additional loss of PTPRZ1. Our findings illustrate the importance of detailed biochemical and genetic studies in any hyperlysinemia patient.
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Affiliation(s)
- Sander M Houten
- Department of Clinical Chemistry, Laboratory Genetic Metabolic Diseases, Academic Medical Center, University of Amsterdam, Meibergdreef 9, Amsterdam, AZ 1105, The Netherlands.
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40
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Guha S, Rees E, Darvasi A, Ivanov D, Ikeda M, Bergen SE, Magnusson PK, Cormican P, Morris D, Gill M, Cichon S, Rosenfeld JA, Lee A, Gregersen PK, Kane JM, Malhotra AK, Rietschel M, Nöthen MM, Degenhardt F, Priebe L, Breuer R, Strohmaier J, Ruderfer DM, Moran JL, Chambert KD, Sanders AR, Shi J, Kendler K, Riley B, O’Neill T, Walsh D, Malhotra D, Corvin A, Purcell S, Sklar P, Iwata N, Hultman CM, Sullivan PF, Sebat J, McCarthy S, Gejman PV, Levinson DF, Owen MJ, O’Donovan MC, Lencz T, Kirov G. Implication of a rare deletion at distal 16p11.2 in schizophrenia. JAMA Psychiatry 2013; 70:253-60. [PMID: 23325106 PMCID: PMC3750982 DOI: 10.1001/2013.jamapsychiatry.71] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
CONTEXT Large genomic copy number variations have been implicated as strong risk factors for schizophrenia. However, the rarity of these events has created challenges for the identification of further pathogenic loci, and extremely large samples are required to provide convincing replication. OBJECTIVE To detect novel copy number variations that increase the susceptibility to schizophrenia by using 2 ethnically homogeneous discovery cohorts and replication in large samples. DESIGN Genetic association study of microarray data. SETTING Samples of DNA were collected at 9 sites from different countries. PARTICIPANTS Two discovery cohorts consisted of 790 cases with schizophrenia and schizoaffective disorder and 1347 controls of Ashkenazi Jewish descent and 662 parent-offspring trios from Bulgaria, of which the offspring had schizophrenia or schizoaffective disorder. Replication data sets consisted of 12,398 cases and 17,945 controls. MAIN OUTCOME MEASURES Statistically increased rate of specific copy number variations in cases vs controls. RESULTS One novel locus was implicated: a deletion at distal 16p11.2, which does not overlap the proximal 16p11.2 locus previously reported in schizophrenia and autism. Deletions at this locus were found in 13 of 13,850 cases (0.094%) and 3 of 19,954 controls (0.015%) (odds ratio, 6.25 [95% CI, 1.78-21.93]; P = .001, Fisher exact test). CONCLUSIONS Deletions at distal 16p11.2 have been previously implicated in developmental delay and obesity. The region contains 9 genes, several of which are implicated in neurological diseases, regulation of body weight, and glucose homeostasis. A telomeric extension of the deletion, observed in about half the cases but no controls, potentially implicates an additional 8 genes. Our findings add a new locus to the list of copy number variations that increase the risk for development of schizophrenia.
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Affiliation(s)
- Saurav Guha
- The Zucker Hillside Hospital, Psychiatry Research, 75–59 263rd Street, Glen Oaks, NY 11004, USA
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - Dobril Ivanov
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Masashi Ikeda
- Fujita Healt University School of Medicine, 1–98 Kutsukake-cho Dengakugakubo, Toyoake, Aichi, 470–1192, Japan
| | - Sarah E. Bergen
- Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute, 7 Cambridge Center, Cambridge, MA, USA
| | - Patrik K Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden
| | - Paul Cormican
- Trinity College Dublin, Dept Psychiatry, College Green, Dublin, Ireland
| | - Derek Morris
- Trinity College Dublin, Dept Psychiatry, College Green, Dublin, Ireland
| | - Michael Gill
- Trinity College Dublin, Dept Psychiatry, College Green, Dublin, Ireland
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn
- Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany
| | - Jeffrey A. Rosenfeld
- The Zucker Hillside Hospital, Psychiatry Research, 75–59 263rd Street, Glen Oaks, NY 11004, USA
| | - Annette Lee
- Robert S. Boas Center for Human Genetics and Genomics, The Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - Peter K. Gregersen
- Robert S. Boas Center for Human Genetics and Genomics, The Feinstein Institute for Medical Research, Manhasset, NY, USA
| | - John M. Kane
- The Zucker Hillside Hospital, Psychiatry Research, 75–59 263rd Street, Glen Oaks, NY 11004, USA
| | - Anil K. Malhotra
- The Zucker Hillside Hospital, Psychiatry Research, 75–59 263rd Street, Glen Oaks, NY 11004, USA
| | - Marcella Rietschel
- Dept. of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn
- German Center for Neurodegenerative Diseases (DZNE), Mount Siani school of Medicine, NY
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn
| | - Lutz Priebe
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn
| | - René Breuer
- Dept. of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim
| | - Jana Strohmaier
- Dept. of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Mannheim
| | - Douglas M Ruderfer
- Division of Psychiatric Genomics, Department Psychiatric, Mount Siani school of Medicine, NY
| | - Jennifer L Moran
- Stanley Center for Psychiatric Research, Broad Institute, 7 Cambridge Center, Cambridge, MA, USA
| | - Kimberly D Chambert
- Stanley Center for Psychiatric Research, Broad Institute, 7 Cambridge Center, Cambridge, MA, USA
| | - Alan R. Sanders
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem Research Institute, Evanston, IL & Department of Psychiatry and Behavioral Sciences, University of Chicago, Chicago, Illinois, USA
| | | | | | | | - Kenneth Kendler
- Virginia Institute for Psychatry and Behavioral Genetics, School of Medicine, Virginia Commonwealth University, Virginia, USA
| | - Brien Riley
- Department of Psychiatry, School of Medicine, Virginia Commonwealth University, Virginia, USA
| | - Tony O’Neill
- Department of Psychiatry, Queens University Belfast, Ireland
| | | | - Dheeraj Malhotra
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aiden Corvin
- Trinity College Dublin, Dept Psychiatry, College Green, Dublin, Ireland
| | - Shaun Purcell
- Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Human Genetics Research, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute, 7 Cambridge Center, Cambridge, MA, USA
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department Psychiatric, Mount Siani school of Medicine, NY
| | - Nakao Iwata
- Fujita Healt University School of Medicine, 1–98 Kutsukake-cho Dengakugakubo, Toyoake, Aichi, 470–1192, Japan
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Sweden
| | - Patrick F. Sullivan
- Departments of Genetics, Psychiatry, and Epidemiology, University of North Carolina at Chapel Hill, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shane McCarthy
- Stanley Institute for Cognitive Genomics. Woodbury Genome Center. Cold Spring Harbor Laboratory. Cold Spring Harbor, NY, USA
| | - Pablo V. Gejman
- Department of Psychiatry and Behavioral Sciences, NorthShore University HealthSystem Research Institute, Evanston, IL & Department of Psychiatry and Behavioral Sciences, University of Chicago, Chicago, Illinois, USA
| | - Douglas F. Levinson
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Michael C O’Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
| | - Todd Lencz
- The Zucker Hillside Hospital, Psychiatry Research, 75–59 263rd Street, Glen Oaks, NY 11004, USA
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, and Neuroscience and Mental Health Research Institute, Cardiff University, Heath Park, Cardiff CF4 4XN, UK
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Barber JCK, Hall V, Maloney VK, Huang S, Roberts AM, Brady AF, Foulds N, Bewes B, Volleth M, Liehr T, Mehnert K, Bateman M, White H. 16p11.2-p12.2 duplication syndrome; a genomic condition differentiated from euchromatic variation of 16p11.2. Eur J Hum Genet 2013; 21:182-9. [PMID: 22828807 PMCID: PMC3548261 DOI: 10.1038/ejhg.2012.144] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 05/02/2012] [Accepted: 05/04/2012] [Indexed: 11/08/2022] Open
Abstract
Chromosome 16 contains multiple copy number variations (CNVs) that predispose to genomic disorders. Here, we differentiate pathogenic duplications of 16p11.2-p12.2 from microscopically similar euchromatic variants of 16p11.2. Patient 1 was a girl of 18 with autism, moderate intellectual disability, behavioural difficulties, dysmorphic features and a 7.71-Mb (megabase pair) duplication (16:21 521 005-29 233 146). Patient 2 had a 7.81-Mb duplication (16:21 382 561-29 191 527), speech delay and obsessional behaviour as a boy and, as an adult, short stature, macrocephaly and mild dysmorphism. The duplications contain 65 coding genes of which Polo-like kinase 1 (PLK1) has the highest likelihood of being haploinsufficient and, by implication, a triplosensitive gene. An additional 1.11-Mb CNV of 10q11.21 in Patient 1 was a possible modifier containing the G-protein-regulated inducer of neurite growth 2 (GPRIN2) gene. In contrast, the euchromatic variants in Patients 3 and 4 were amplifications from a 945-kb region containing non-functional immunoglobulin heavy chain (IGHV), hect domain pseudogene (HERC2P4) and TP53-inducible target gene 3 (TP53TG3) loci in proximal 16p11.2 (16:31 953 353-32 898 635). Paralogous pyrosequencing gave a total copy number of 3-8 in controls and 8 to >10 in Patients 3 and 4. The 16p11.2-p12.2 duplication syndrome is a recurrent genomic disorder with a variable phenotype including developmental delay, dysmorphic features, mild to severe intellectual disability, autism, obsessive or stereotyped behaviour, short stature and anomalies of the hands and fingers. It is important to differentiate pathogenic 16p11.2-p12.2 duplications from harmless, microscopically similar euchromatic variants of proximal 16p11.2, especially at prenatal diagnosis.
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Affiliation(s)
- John C K Barber
- Department of Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, Hampshire, UK.
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Abdelmalik N, van Haelst M, Mancini G, Schrander-Stumpel C, Marcus-Soekarman D, Hennekam R, Cobben JM. Diagnostic outcomes of 27 children referred by pediatricians to a genetics clinic in the Netherlands with suspicion of fetal alcohol spectrum disorders. Am J Med Genet A 2013; 161A:254-60. [PMID: 23303648 DOI: 10.1002/ajmg.a.35672] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Accepted: 08/23/2012] [Indexed: 11/10/2022]
Abstract
The characteristics of fetal alcohol spectrum disorders (FASD) constitute a specific facial phenotype, growth failure and neurodevelopmental defects. Reported FASD prevalences vary widely from 0.08 per 1,000 up to 68.0-89.2 per 1,000. We aimed to evaluate to which extent children referred with a suspicion of FASD, indeed have FASD. We included all 27 children referred to our genetic department with a suspicion of FASD between 2005 and 2010. Nineteen children (70.3%) were of non-Dutch ancestry, and 24 (88.9%) had been adopted. We used both the 4-Digit Code and the Revised Institute of Medicine criteria. More than half of the children did not meet either criteria for the diagnosis of FASD. Of note, after evaluation 8/27 children appeared not to have confirmed prenatal alcohol exposure. Two children referred for suspicion of FASD (neither of which were exposed to alcohol or met the criteria for FASD) had a pathogenic microstructural chromosomal rearrangement (del16p11.2 of 542 KB and dup1q44 of 915 KB). In 22/24 children (91.7%) there were other factors that may have affected their intellectual abilities, such as familial intellectual disability and social deprivation. We recommend a critical approach towards the diagnosis FASD, and to investigate all patients suspected to have FASD for other causative factors including genetic abnormalities.
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Affiliation(s)
- Nadia Abdelmalik
- Department of Pediatric Genetics, Emma Children's Hospital, Academic Medical Center, Amsterdam, The Netherlands
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43
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Newbury DF, Mari F, Sadighi Akha E, Macdermot KD, Canitano R, Monaco AP, Taylor JC, Renieri A, Fisher SE, Knight SJL. Dual copy number variants involving 16p11 and 6q22 in a case of childhood apraxia of speech and pervasive developmental disorder. Eur J Hum Genet 2012; 21:361-5. [PMID: 22909776 PMCID: PMC3598310 DOI: 10.1038/ejhg.2012.166] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant. Nature 2012; 485:363-7. [PMID: 22596160 PMCID: PMC3366115 DOI: 10.1038/nature11091] [Citation(s) in RCA: 283] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Accepted: 03/27/2012] [Indexed: 12/15/2022]
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Cotman SL, Staropoli JF. The juvenile Batten disease protein, CLN3, and its role in regulating anterograde and retrograde post-Golgi trafficking. ACTA ACUST UNITED AC 2012; 7:79-91. [PMID: 22545070 DOI: 10.2217/clp.11.70] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Loss-of-function mutations in CLN3 are responsible for juvenile-onset neuronal ceroid lipofuscinosis (JNCL), or Batten disease, which is an incurable lysosomal disease that manifests with vision loss, followed by seizures and progressive neurodegeneration, robbing children of motor skills, speech and cognition, and eventually leading to death in the second or third decade of life. Emerging clinical evidence points to JNCL pathology outside of the CNS, including the cardiovascular system. The CLN3 gene encodes an unusual transmembrane protein, CLN3 or battenin, whose elusive function has been the subject of intense study for more than 10 years. Owing to the detailed characterization of a large number of disease models, our knowledge of CLN3 protein function is finally coming into focus. This review will describe the most current understanding of CLN3 structure, function and dysfunction in JNCL.
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Affiliation(s)
- Susan L Cotman
- Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
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46
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Tabet AC, Pilorge M, Delorme R, Amsellem F, Pinard JM, Leboyer M, Verloes A, Benzacken B, Betancur C. Autism multiplex family with 16p11.2p12.2 microduplication syndrome in monozygotic twins and distal 16p11.2 deletion in their brother. Eur J Hum Genet 2012; 20:540-6. [PMID: 22234155 DOI: 10.1038/ejhg.2011.244] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The pericentromeric region of chromosome 16p is rich in segmental duplications that predispose to rearrangements through non-allelic homologous recombination. Several recurrent copy number variations have been described recently in chromosome 16p. 16p11.2 rearrangements (29.5-30.1 Mb) are associated with autism, intellectual disability (ID) and other neurodevelopmental disorders. Another recognizable but less common microdeletion syndrome in 16p11.2p12.2 (21.4 to 28.5-30.1 Mb) has been described in six individuals with ID, whereas apparently reciprocal duplications, studied by standard cytogenetic and fluorescence in situ hybridization techniques, have been reported in three patients with autism spectrum disorders. Here, we report a multiplex family with three boys affected with autism, including two monozygotic twins carrying a de novo 16p11.2p12.2 duplication of 8.95 Mb (21.28-30.23 Mb) characterized by single-nucleotide polymorphism array, encompassing both the 16p11.2 and 16p11.2p12.2 regions. The twins exhibited autism, severe ID, and dysmorphic features, including a triangular face, deep-set eyes, large and prominent nasal bridge, and tall, slender build. The eldest brother presented with autism, mild ID, early-onset obesity and normal craniofacial features, and carried a smaller, overlapping 16p11.2 microdeletion of 847 kb (28.40-29.25 Mb), inherited from his apparently healthy father. Recurrent deletions in this region encompassing the SH2B1 gene were recently reported in early-onset obesity and in individuals with neurodevelopmental disorders associated with phenotypic variability. We discuss the clinical and genetic implications of two different 16p chromosomal rearrangements in this family, and suggest that the 16p11.2 deletion in the father predisposed to the formation of the duplication in his twin children.
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Affiliation(s)
- Anne-Claude Tabet
- AP-HP, Robert Debré Hospital, Department of Genetics, Cytogenetics Unit, Paris, France
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Deak KL, Horn SR, Rehder CW. The evolving picture of microdeletion/microduplication syndromes in the age of microarray analysis: variable expressivity and genomic complexity. Clin Lab Med 2011; 31:543-64, viii. [PMID: 22118736 DOI: 10.1016/j.cll.2011.08.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several new microdeletion and microduplication syndromes have been discovered in a genotype-first approach. Many of these disorders are caused by nonallelic homologous recombination between blocks of segmental duplication. The authors describe 9 regions for which copy number alteration is proposed to cause an abnormal phenotype. Some of these disorders have been observed in affected individuals and individuals lacking a clearly abnormal phenotype. These deletions and duplications are thought to be contributory, but not always sufficient, to elicit an abnormal outcome. Additional studies are necessary to further evaluate the penetrance and delineate the clinical spectrum associated with many of these newly described disorders.
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Affiliation(s)
- Kristen L Deak
- Department of Pathology, Duke University, Durham, NC, USA
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