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Seigfried FA, Britsch S. The Role of Bcl11 Transcription Factors in Neurodevelopmental Disorders. BIOLOGY 2024; 13:126. [PMID: 38392344 PMCID: PMC10886639 DOI: 10.3390/biology13020126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024]
Abstract
Neurodevelopmental disorders (NDDs) comprise a diverse group of diseases, including developmental delay, autism spectrum disorder (ASD), intellectual disability (ID), and attention-deficit/hyperactivity disorder (ADHD). NDDs are caused by aberrant brain development due to genetic and environmental factors. To establish specific and curative therapeutic approaches, it is indispensable to gain precise mechanistic insight into the cellular and molecular pathogenesis of NDDs. Mutations of BCL11A and BCL11B, two closely related, ultra-conserved zinc-finger transcription factors, were recently reported to be associated with NDDs, including developmental delay, ASD, and ID, as well as morphogenic defects such as cerebellar hypoplasia. In mice, Bcl11 transcription factors are well known to orchestrate various cellular processes during brain development, for example, neural progenitor cell proliferation, neuronal migration, and the differentiation as well as integration of neurons into functional circuits. Developmental defects observed in both, mice and humans display striking similarities, suggesting Bcl11 knockout mice provide excellent models for analyzing human disease. This review offers a comprehensive overview of the cellular and molecular functions of Bcl11a and b and links experimental research to the corresponding NDDs observed in humans. Moreover, it outlines trajectories for future translational research that may help to better understand the molecular basis of Bcl11-dependent NDDs as well as to conceive disease-specific therapeutic approaches.
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Affiliation(s)
- Franziska Anna Seigfried
- Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Stefan Britsch
- Institute of Molecular and Cellular Anatomy, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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2
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Miceli M, Failla P, Saccuzzo L, Galesi O, Amata S, Romano C, Bonaglia MC, Fichera M. Trait - driven analysis of the 2p15p16.1 microdeletion syndrome suggests a complex pattern of interactions between candidate genes. Genes Genomics 2023; 45:491-505. [PMID: 36807877 PMCID: PMC10027778 DOI: 10.1007/s13258-023-01369-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023]
Abstract
BACKGROUND Individuals with the 2p15p16.1 microdeletion syndrome share a complex phenotype including neurodevelopmental delay, brain malformations, microcephaly, and autistic behavior. The analysis of the shortest region of overlap (SRO) between deletions in ~ 40 patients has led to the identification of two critical regions and four strongly candidate genes (BCL11A, REL, USP34 and XPO1). However, the delineation of their role in the occurrence of specific traits is hampered by their incomplete penetrance. OBJECTIVE To better delineate the role of hemizygosity of specific regions in selected traits by leveraging information both from penetrant and non - penetrant deletions. METHODS Deletions in patients that do not present a specific trait cannot contribute to delineate the SROs. We recently developed a probabilistic model that, by considering also the non - penetrant deletions, allows a more reliable assignment of peculiar traits to specific genomic segments. We apply this method adding two new patients to the published cases. RESULTS Our results delineate an intricate pattern of genotype - phenotype correlation where BCL11A emerges as the main gene for autistic behavior while USP34 and/or XPO1 haploinsufficiency are mainly associated with microcephaly, hearing loss and IUGR. BCL11A, USP34 and XPO1 genes are broadly related with brain malformations albeit with distinct patterns of brain damage. CONCLUSIONS The observed penetrance of deletions encompassing different SROs and that predicted when considering each single SRO as acting independently, may reflect a more complex model than the additive one. Our approach may improve the genotype/phenotype correlation and may help to identify specific pathogenic mechanisms in contiguous gene syndromes.
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Affiliation(s)
- Martina Miceli
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
| | | | - Lucia Saccuzzo
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
| | | | | | - Corrado Romano
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
| | - Maria Clara Bonaglia
- Cytogenetics Laboratory, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Marco Fichera
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, Catania, Italy.
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy.
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3
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Bruce L, Peter B. Three children with different de novo BCL11A variants and diverse developmental phenotypes, but shared global motor discoordination and apraxic speech: Evidence for a functional gene network influencing the developing cerebellum and motor and auditory cortices. Am J Med Genet A 2022; 188:3401-3415. [PMID: 35856171 DOI: 10.1002/ajmg.a.62904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 06/28/2022] [Accepted: 07/04/2022] [Indexed: 01/31/2023]
Abstract
BCL11A is implicated in BCL11A-Related Intellectual Development Disorder (BCL11A-IDD). Previously reported cases had various types of BCL11A variants (copy-number variations [CNVs], singlenucleotide variants [SNVs]). Phenotypes included global, cognitive, and motor delays, autism spectrum disorder (ASD), craniofacial dysmorphology, and speech and language delays described generally, with only two reports specifying childhood apraxia of speech (CAS). Here, we present three additional children with CAS and de novo BCL11A variants, a p.Ala182Thr nonconservative missense and a p.GLu611.Ter nonsense variant, both in exon 4, and a 106 kb deletion harboring exons 1 and 2. All three children have fine and gross motor discoordination, feeding difficulties, and visual motor disorders. Intellectual and learning disabilities and disordered language skills were seen only in the child with the missense variant and the child with the deletion. These findings align with, and expand, previous findings in that BCL11A variants have significant and highly penetrant apraxic effects across motor systems, consistent with cerebellar involvement. The deletion of exons 1 and 2 is the smallest BCL11A CNV with the full phenotypic expression reported to date. The present results support previous findings in that BCL11A-IDD can result from BCL11A variants regardless of type (deletion, SNVs). A gene expression study shows that BCL11 is expressed highly in the early developing cerebellum and primary motor and auditory cortices. Significant co-expression rates in these regions with genes previously implicated in disorders of spoken language and in ASD support the phenotypic overlaps in children with BCL11A-IDD, CAS, and ASD.
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Affiliation(s)
- Laurel Bruce
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
| | - Beate Peter
- College of Health Solutions, Arizona State University, Tempe, Arizona, USA
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4
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Du H, Wang Z, Guo R, Yang L, Liu G, Zhang Z, Xu Z, Tian Y, Yang Z, Li X, Chen B. Transcription factors Bcl11a and Bcl11b are required for the production and differentiation of cortical projection neurons. Cereb Cortex 2022; 32:3611-3632. [PMID: 34963132 PMCID: PMC9433425 DOI: 10.1093/cercor/bhab437] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/02/2021] [Indexed: 12/31/2022] Open
Abstract
The generation and differentiation of cortical projection neurons are extensively regulated by interactive programs of transcriptional factors. Here, we report the cooperative functions of transcription factors Bcl11a and Bcl11b in regulating the development of cortical projection neurons. Among the cells derived from the cortical neural stem cells, Bcl11a is expressed in the progenitors and the projection neurons, while Bcl11b expression is restricted to the projection neurons. Using conditional knockout mice, we show that deficiency of Bcl11a leads to reduced proliferation and precocious differentiation of cortical progenitor cells, which is exacerbated when Bcl11b is simultaneously deleted. Besides defective neuronal production, the differentiation of cortical projection neurons is blocked in the absence of both Bcl11a and Bcl11b: Expression of both pan-cortical and subtype-specific genes is reduced or absent; axonal projections to the thalamus, hindbrain, spinal cord, and contralateral cortical hemisphere are reduced or absent. Furthermore, neurogenesis-to-gliogenesis switch is accelerated in the Bcl11a-CKO and Bcl11a/b-DCKO mice. Bcl11a likely regulates neurogenesis through repressing the Nr2f1 expression. These results demonstrate that Bcl11a and Bcl11b jointly play critical roles in the generation and differentiation of cortical projection neurons and in controlling the timing of neurogenesis-to-gliogenesis switch.
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Affiliation(s)
- Heng Du
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Ziwu Wang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Rongliang Guo
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Lin Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Guoping Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhuangzhi Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhejun Xu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Yu Tian
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Zhengang Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Xiaosu Li
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute of Pediatrics, Children’s Hospital of Fudan University, Institutes of Brain Science, Fudan University, Shanghai 200032, China
| | - Bin Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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5
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Wessels MW, Cnossen MH, van Dijk TB, Gillemans N, Schmidt KLJ, van Lom K, Vinjamur DS, Coyne S, Kurita R, Nakamura Y, de Man SA, Pfundt R, Azmani Z, Brouwer RWW, Bauer DE, van den Hout MCGN, van IJcken WFJ, Philipsen S. Molecular analysis of the erythroid phenotype of a patient with BCL11A haploinsufficiency. Blood Adv 2021; 5:2339-2349. [PMID: 33938942 PMCID: PMC8114548 DOI: 10.1182/bloodadvances.2020003753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/12/2021] [Indexed: 12/29/2022] Open
Abstract
The BCL11A gene encodes a transcriptional repressor with essential functions in multiple tissues during human development. Haploinsufficiency for BCL11A causes Dias-Logan syndrome (OMIM 617101), an intellectual developmental disorder with hereditary persistence of fetal hemoglobin (HPFH). Due to the severe phenotype, disease-causing variants in BCL11A occur de novo. We describe a patient with a de novo heterozygous variant, c.1453G>T, in the BCL11A gene, resulting in truncation of the BCL11A-XL protein (p.Glu485X). The truncated protein lacks the 3 C-terminal DNA-binding zinc fingers and the nuclear localization signal, rendering it inactive. The patient displayed high fetal hemoglobin (HbF) levels (12.1-18.7% of total hemoglobin), in contrast to the parents who had HbF levels of 0.3%. We used cultures of patient-derived erythroid progenitors to determine changes in gene expression and chromatin accessibility. In addition, we investigated DNA methylation of the promoters of the γ-globin genes HBG1 and HBG2. HUDEP1 and HUDEP2 cells were used as models for fetal and adult human erythropoiesis, respectively. Similar to HUDEP1 cells, the patient's cells displayed Assay for Transposase-Accessible Chromatin (ATAC) peaks at the HBG1/2 promoters and significant expression of HBG1/2 genes. In contrast, HBG1/2 promoter methylation and genome-wide gene expression profiling were consistent with normal adult erythropoiesis. We conclude that HPFH is the major erythroid phenotype of constitutive BCL11A haploinsufficiency. Given the essential functions of BCL11A in other hematopoietic lineages and the neuronal system, erythroid-specific targeting of the BCL11A gene has been proposed for reactivation of γ-globin expression in β-hemoglobinopathy patients. Our data strongly support this approach.
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Affiliation(s)
| | - Marjon H Cnossen
- Department of Pediatric Hematology
- Academic Center for Hemoglobinopathies and Rare Anemias
| | - Thamar B van Dijk
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Nynke Gillemans
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - K L Juliëtte Schmidt
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Kirsten van Lom
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Divya S Vinjamur
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Steven Coyne
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN, BioResource Center, Tsukuba, Japan
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; and
| | - Zakia Azmani
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Daniel E Bauer
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | | | - Wilfred F J van IJcken
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Sjaak Philipsen
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
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6
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Prasad M, Balci TB, Prasad C, Andrews JD, Lee R, Jurkiewicz MT, Napier MP, Colaiacovo S, Guillen Sacoto MJ, Karp N. BCL11B-related disorder in two canadian children: Expanding the clinical phenotype. Eur J Med Genet 2020; 63:104007. [PMID: 32659295 DOI: 10.1016/j.ejmg.2020.104007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/06/2020] [Accepted: 07/07/2020] [Indexed: 12/29/2022]
Abstract
The product of the BCL11B (B-Cell Leukemia 11) gene is a bi-functional transcriptional regulator that can act as either a repressor or an activator. It plays an important role in the development of the nervous, immune, and cutaneous systems, and is also involved in dental and craniofacial development. BCL11B-Related Disorder (BCL11BRD) is a novel rare neurodevelopmental disorder associated with mutations in BCL11B. A total of 17 patients have been described in the literature thus far. The main symptoms of BCL11BRD include global developmental delay, speech impairment, dental anomalies, feeding difficulties, refractive errors, dysmorphic features, and immunological abnormalities. In this report, we describe two Canadian girls, with pathogenic de novo BCL11B variants, both diagnosed via exome sequencing. One of the patients had global developmental delay, dental anomalies, dysmorphic features, dyskinesia and hypotonia; the latter two symptoms have not been previously reported in patients with BCL11BRD. She also had dysgenesis of corpus callosum and dilatation of the frontal horns of lateral ventricles, a brain anomaly that has been previously reported in only one other patient. The second patient had developmental delay, dysmorphic features, spasticity in lower limbs and dental anomalies. Our report contributes to the knowledge of the BCL11BRD, expands the clinical phenotype, and can also aid with genetic counseling of newly identified patients.
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Affiliation(s)
- M Prasad
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - T B Balci
- Schulich School of Medicine and Dentistry, Western University, Department of Pediatrics, Division of Medical Genetics, London Health Sciences Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | - C Prasad
- Schulich School of Medicine and Dentistry, Western University, Department of Pediatrics, Division of Medical Genetics, London Health Sciences Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada
| | - J D Andrews
- Lawson Health Research Institute, London Health Sciences Centre, London, Ontario, Canada
| | - R Lee
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Dentistry, London Health Sciences Centre, London, Ontario, Canada
| | - M T Jurkiewicz
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada; Department of Medical Imaging, London Health Sciences Centre, London, Ontario, Canada
| | - M P Napier
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | - S Colaiacovo
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, Ontario, Canada
| | | | - N Karp
- Schulich School of Medicine and Dentistry, Western University, Department of Pediatrics, Division of Medical Genetics, London Health Sciences Centre, London, Ontario, Canada; Children's Health Research Institute, London, Ontario, Canada.
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Simon R, Wiegreffe C, Britsch S. Bcl11 Transcription Factors Regulate Cortical Development and Function. Front Mol Neurosci 2020; 13:51. [PMID: 32322190 PMCID: PMC7158892 DOI: 10.3389/fnmol.2020.00051] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/11/2020] [Indexed: 12/21/2022] Open
Abstract
Transcription factors regulate multiple processes during brain development and in the adult brain, from brain patterning to differentiation and maturation of highly specialized neurons as well as establishing and maintaining the functional neuronal connectivity. The members of the zinc-finger transcription factor family Bcl11 are mainly expressed in the hematopoietic and central nervous systems regulating the expression of numerous genes involved in a wide range of pathways. In the brain Bcl11 proteins are required to regulate progenitor cell proliferation as well as differentiation, migration, and functional integration of neural cells. Mutations of the human Bcl11 genes lead to anomalies in multiple systems including neurodevelopmental impairments like intellectual disabilities and autism spectrum disorders.
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Affiliation(s)
- Ruth Simon
- Institute of Molecular and Cellular Anatomy, Ulm University, Germany
| | | | - Stefan Britsch
- Institute of Molecular and Cellular Anatomy, Ulm University, Germany
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Amrom D, Poduri A, Goldman JS, Dan B, Deconinck N, Pichon B, Nadaf J, Andermann F, Andermann E, Walsh CA, Dobyns WB. Duplication 2p16 is associated with perisylvian polymicrogyria. Am J Med Genet A 2019; 179:2343-2356. [PMID: 31660690 DOI: 10.1002/ajmg.a.61342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 07/01/2019] [Accepted: 08/12/2019] [Indexed: 11/07/2022]
Abstract
Polymicrogyria (PMG) is a heterogeneous brain malformation that may result from prenatal vascular disruption or infection, or from numerous genetic causes that still remain difficult to identify. We identified three unrelated patients with polymicrogyria and duplications of chromosome 2p, defined the smallest region of overlap, and performed gene pathway analysis using Cytoscape. The smallest region of overlap in all three children involved 2p16.1-p16.3. All three children have bilateral perisylvian polymicrogyria (BPP), intrauterine and postnatal growth deficiency, similar dysmorphic features, and poor feeding. Two of the three children had documented intellectual disability. Gene pathway analysis suggested a number of developmentally relevant genes and gene clusters that were over-represented in the critical region. We narrowed a rare locus for polymicrogyria to a region of 2p16.1-p16.3 that contains 33-34 genes, 23 of which are expressed in cerebral cortex during human fetal development. Using pathway analysis, we showed that several of the duplicated genes contribute to neurodevelopmental pathways including morphogen, cytokine, hormonal and growth factor signaling, regulation of cell cycle progression, cell morphogenesis, axonal guidance, and neuronal migration. These findings strengthen the evidence for a novel locus associated with polymicrogyria on 2p16.1-p16.3, and comprise the first step in defining the underlying genetic etiology.
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Affiliation(s)
- Dina Amrom
- Neurogenetics Unit, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada.,Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada.,Department of Neurology, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Annapurna Poduri
- Division of Epilepsy & Clinical Neurophysiology, Children's Hospital, Boston, Massachusetts.,Department of Neurology, Children's Hospital, Boston, Massachusetts
| | - Jennifer S Goldman
- Ludmer Centre for Neuroinformatics and Mental Health and the Department of Biomedical Engineering, McGill Centre for Integrative Neuroscience, McGill University, Montreal, Quebec, Canada
| | | | | | - Bruno Pichon
- Department of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Genome Quebec Innovation Center, McGill University, Montreal, Quebec, Canada
| | - Frederick Andermann
- Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada.,Epilepsy Research Group, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada.,Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Eva Andermann
- Neurogenetics Unit, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada.,Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Epilepsy Research Group, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada
| | - Christopher A Walsh
- Department of Neurology, Children's Hospital, Boston, Massachusetts.,Division of Genetics and Manton Center for Orphan Disease Research, Children's Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts
| | - William B Dobyns
- Department of Pediatrics (Genetics) and Neurology, University of Washington, and Seattle Children's Research Institute, Seattle, Washington
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Guzeva VI, Okhrim IV, Guzeva OV, Guzeva VV. Phenotypic and neuroimaging differentiation of polymicrogiry in children. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:14-20. [DOI: 10.17116/jnevro201911904114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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10
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Chromosome 2p15-p16.1 microduplication in a boy with congenital anomalies: Is it a distinctive syndrome? Eur J Med Genet 2019; 62:47-54. [PMID: 29864511 DOI: 10.1016/j.ejmg.2018.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 04/30/2018] [Accepted: 05/03/2018] [Indexed: 11/17/2022]
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11
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Chen CP, Chern SR, Wu PS, Chen SW, Lai ST, Chuang TY, Chen WL, Yang CW, Wang W. Prenatal diagnosis of a 3.2-Mb 2p16.1-p15 duplication associated with familial intellectual disability. Taiwan J Obstet Gynecol 2018; 57:578-582. [PMID: 30122582 DOI: 10.1016/j.tjog.2018.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2018] [Indexed: 02/07/2023] Open
Abstract
OBJECTIVE We present prenatal diagnosis of a 2p16.1-p15 duplication associated with familial intellectual disability, and we discuss the genotype-phenotype correlation. CASE REPORT A 22-year-old, primigravid woman underwent amniocentesis at 22 weeks of gestation because of a family history of intellectual disability. The woman and her two sisters had intellectual disability but no behavioral disorders. The intellectual disability was noted in at least one paternal aunt and six paternal cousins of the woman. Cytogenetic analysis revealed the karyotype of 46,XX in the fetus and the two women. Array comparative genomic hybridization (aCGH) analysis on the DNAs extracted from cultured amniocytes and the bloods of the woman and the her sister revealed a 3.244-Mb duplication of 2p16.1-p15 or arr 2p16.1p15 (58,288,588-61,532,538) × 3.0 [GRCh37 (hg19)] encompassing eight Online Mendelian Inheritance in Man (OMIM) genes of VRK2, FANCL, BCL11A, PAPOLG, REL, PUS10, PEX13 and USP34 in the fetus and the two women. Prenatal ultrasound findings were unremarkable. The woman elected to continue the pregnancy. A 3244-g female baby was delivered at term with neither craniofacial dysmorphism nor structural abnormalities. CONCLUSION aCGH is useful in prenatal diagnosis of inherited subtle chromosome imbalance in pregnancy with familial intellectual disability. Chromosome 2p16.1-p15 duplication can be associated with intellectual disability.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shih-Ting Lai
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Tzu-Yun Chuang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wen-Lin Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chien-Wen Yang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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Wirthlin M, Lima NCB, Guedes RLM, Soares AER, Almeida LGP, Cavaleiro NP, Loss de Morais G, Chaves AV, Howard JT, Teixeira MDM, Schneider PN, Santos FR, Schatz MC, Felipe MS, Miyaki CY, Aleixo A, Schneider MPC, Jarvis ED, Vasconcelos ATR, Prosdocimi F, Mello CV. Parrot Genomes and the Evolution of Heightened Longevity and Cognition. Curr Biol 2018; 28:4001-4008.e7. [PMID: 30528582 DOI: 10.1016/j.cub.2018.10.050] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 08/14/2018] [Accepted: 10/23/2018] [Indexed: 10/27/2022]
Abstract
Parrots are one of the most distinct and intriguing groups of birds, with highly expanded brains [1], highly developed cognitive [2] and vocal communication [3] skills, and a long lifespan compared to other similar-sized birds [4]. Yet the genetic basis of these traits remains largely unidentified. To address this question, we have generated a high-coverage, annotated assembly of the genome of the blue-fronted Amazon (Amazona aestiva) and carried out extensive comparative analyses with 30 other avian species, including 4 additional parrots. We identified several genomic features unique to parrots, including parrot-specific novel genes and parrot-specific modifications to coding and regulatory sequences of existing genes. We also discovered genomic features under strong selection in parrots and other long-lived birds, including genes previously associated with lifespan determination as well as several hundred new candidate genes. These genes support a range of cellular functions, including telomerase activity; DNA damage repair; control of cell proliferation, cancer, and immunity; and anti-oxidative mechanisms. We also identified brain-expressed, parrot-specific paralogs with known functions in neural development or vocal-learning brain circuits. Intriguingly, parrot-specific changes in conserved regulatory sequences were overwhelmingly associated with genes that are linked to cognitive abilities and have undergone similar selection in the human lineage, suggesting convergent evolution. These findings bring novel insights into the genetics and evolution of longevity and cognition, as well as provide novel targets for exploring the mechanistic basis of these traits.
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Affiliation(s)
- Morgan Wirthlin
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Nicholas C B Lima
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Rafael Lucas Muniz Guedes
- Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Quitandinha, Petrópolis, RJ 25651-070, Brazil
| | - André E R Soares
- Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Quitandinha, Petrópolis, RJ 25651-070, Brazil
| | - Luiz Gonzaga P Almeida
- Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Quitandinha, Petrópolis, RJ 25651-070, Brazil
| | - Nathalia P Cavaleiro
- Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Quitandinha, Petrópolis, RJ 25651-070, Brazil
| | - Guilherme Loss de Morais
- Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Quitandinha, Petrópolis, RJ 25651-070, Brazil
| | - Anderson V Chaves
- Programa de Pós-graduação em Manejo e Conservação de Ecossistemas Naturais e Agrários, Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Florestal, Minas Gerais, Brazil
| | - Jason T Howard
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Marcus de Melo Teixeira
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília, DF 70910-900, Brazil
| | - Patricia N Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Fabrício R Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Michael C Schatz
- Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Maria Sueli Felipe
- Programa de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília e Depto. de Biologia Celular, Universidade de Brasilia, Brasilia, DF, Brazil
| | - Cristina Y Miyaki
- Instituto de Biociências, Universidade de São Paulo, R. do Matão, 277, São Paulo, SP 05508-090, Brazil
| | - Alexandre Aleixo
- Coordenação de Zoologia, Museu Paraense Emilio Goeldi, Belém, PA 66040-170, Brazil
| | - Maria P C Schneider
- Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brazil
| | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Ana Tereza R Vasconcelos
- Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Quitandinha, Petrópolis, RJ 25651-070, Brazil
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Claudio V Mello
- Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA.
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13
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Identification of the Gene Expression Rules That Define the Subtypes in Glioma. J Clin Med 2018; 7:jcm7100350. [PMID: 30322114 PMCID: PMC6210469 DOI: 10.3390/jcm7100350] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/09/2018] [Accepted: 10/11/2018] [Indexed: 11/16/2022] Open
Abstract
As a common brain cancer derived from glial cells, gliomas have three subtypes: glioblastoma, diffuse astrocytoma, and anaplastic astrocytoma. The subtypes have distinctive clinical features but are closely related to each other. A glioblastoma can be derived from the early stage of diffuse astrocytoma, which can be transformed into anaplastic astrocytoma. Due to the complexity of these dynamic processes, single-cell gene expression profiles are extremely helpful to understand what defines these subtypes. We analyzed the single-cell gene expression profiles of 5057 cells of anaplastic astrocytoma tissues, 261 cells of diffuse astrocytoma tissues, and 1023 cells of glioblastoma tissues with advanced machine learning methods. In detail, a powerful feature selection method, Monte Carlo feature selection (MCFS) method, was adopted to analyze the gene expression profiles of cells, resulting in a feature list. Then, the incremental feature selection (IFS) method was applied to the obtained feature list, with the help of support vector machine (SVM), to extract key features (genes) and construct an optimal SVM classifier. Several key biomarker genes, such as IGFBP2, IGF2BP3, PRDX1, NOV, NEFL, HOXA10, GNG12, SPRY4, and BCL11A, were identified. In addition, the underlying rules of classifying the three subtypes were produced by Johnson reducer algorithm. We found that in diffuse astrocytoma, PRDX1 is highly expressed, and in glioblastoma, the expression level of PRDX1 is low. These rules revealed the difference among the three subtypes, and how they are formed and transformed. These genes are not only biomarkers for glioma subtypes, but also drug targets that may switch the clinical features or even reverse the tumor progression.
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14
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Identification of novel genomic imbalances in Saudi patients with congenital heart disease. Mol Cytogenet 2018; 11:9. [PMID: 29416564 PMCID: PMC5784682 DOI: 10.1186/s13039-018-0356-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/03/2018] [Indexed: 11/10/2022] Open
Abstract
Background Quick genetic diagnosis of a patient with congenital heart disease (CHD) is quite important for proper health care and management. Copy number variations (CNV), chromosomal imbalances and rearrangements have been frequently associated with CHD. Previously, due to limitations of microscope based standard karyotyping techniques copious CNVs and submicroscopic imbalances could not be detected in numerous CHD patients. The aim of our study is to identify cytogenetic abnormalities among the selected CHD cases (n = 17) of the cohort using high density oligo arrays. Results Our screening study indicated that six patients (~35%) have various cytogenetic abnormalities. Among the patients, only patient 2 had a duplication whereas the rest carried various deletions. The patients 1, 4 and 6 have only single large deletions throughout their genome; a 3.2 Mb deletion on chromosome 7, a 3.35 Mb deletion on chromosome 3, and a 2.78 Mb a deletion on chromosome 2, respectively. Patients 3 and 5 have two deletions on different chromosomes. Patient 3 has deletions on chromosome 2 (2q24.1; 249 kb) and 16 (16q22.2; 1.8 Mb). Patient 4 has a 3.35 Mb an interstitial deletion on chromosome 3 (3q13.2q13.31).Based on our search on the latest available literature, our study is the first inclusive array CGH evaluation on Saudi cohort of CHD patients. Conclusions This study emphasizes the importance of the arrays in genetic diagnosis of CHD. Based on our results the high resolution arrays should be utilized as first-tier diagnostic tool in clinical care as suggested before by others. Moreover, previously evaluated negative CHD cases (based on standard karyotyping methods) should be re-examined by microarray based cytogenetic methods.
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15
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Borlot F, Regan BM, Bassett AS, Stavropoulos DJ, Andrade DM. Prevalence of Pathogenic Copy Number Variation in Adults With Pediatric-Onset Epilepsy and Intellectual Disability. JAMA Neurol 2017; 74:1301-1311. [PMID: 28846756 DOI: 10.1001/jamaneurol.2017.1775] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Importance Copy number variation (CNV) is an important cause of neuropsychiatric disorders. Little is known about the role of CNV in adults with epilepsy and intellectual disability. Objectives To evaluate the prevalence of pathogenic CNVs and identify possible candidate CNVs and genes in patients with epilepsy and intellectual disability. Design, Setting, and Participants In this cross-sectional study, genome-wide microarray was used to evaluate a cohort of 143 adults with unexplained childhood-onset epilepsy and intellectual disability who were recruited from the Toronto Western Hospital epilepsy outpatient clinic from January 1, 2012, through December 31, 2014. The inclusion criteria were (1) pediatric seizure onset with ongoing seizure activity in adulthood, (2) intellectual disability of any degree, and (3) no structural brain abnormalities or metabolic conditions that could explain the seizures. Main Outcomes and Measures DNA screening was performed using genome-wide microarray platforms. Pathogenicity of CNVs was assessed based on the American College of Medical Genetics guidelines. The Residual Variation Intolerance Score was used to evaluate genes within the identified CNVs that could play a role in each patient's phenotype. Results Of the 2335 patients, 143 probands were investigated (mean [SD] age, 24.6 [10.8] years; 69 male and 74 female). Twenty-three probands (16.1%) and 4 affected relatives (2.8%) (mean [SD] age, 24.1 [6.1] years; 11 male and 16 female) presented with pathogenic or likely pathogenic CNVs (0.08-18.9 Mb). Five of the 23 probands with positive results (21.7%) had more than 1 CNV reported. Parental testing revealed de novo CNVs in 11 (47.8%), with CNVs inherited from a parent in 4 probands (17.4%). Sixteen of 23 probands (69.6%) presented with previously cataloged human genetic disorders and/or defined CNV hot spots in epilepsy. Eight nonrecurrent rare CNVs that overlapped 1 or more genes associated with intellectual disability, autism, and/or epilepsy were identified: 2p16.1-p15 duplication, 6p25.3-p25.1 duplication, 8p23.3p23.1 deletion, 9p24.3-p23 deletion, 10q11.22-q11.23 duplication, 12p13.33-13.2 duplication, 13q34 deletion, and 16p13.2 duplication. Five genes are of particular interest given their potential pathogenicity in the corresponding phenotypes and least tolerability to variation: ABAT, KIAA2022, COL4A1, CACNA1C, and SMARCA2. ABAT duplication was associated with Lennox-Gastaut syndrome and KIAA2022 deletion with Jeavons syndrome. Conclusions and Relevance The high prevalence of pathogenic CNVs in this study highlights the importance of microarray analysis in adults with unexplained childhood-onset epilepsy and intellectual disability. Additional studies and comparison with similar cases are required to evaluate the effects of deletions and duplications that overlap specific genes.
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Affiliation(s)
- Felippe Borlot
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada.,Clinical Neurosciences Center, Department of Neurology, University of Utah, Salt Lake City
| | - Brigid M Regan
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - D James Stavropoulos
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Danielle M Andrade
- Epilepsy Genetics Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, Ontario, Canada.,Division of Neurology, Krembil Neuroscience Centre, Toronto Western Hospital, University of Toronto, Toronto, Ontario, Canada
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16
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Soblet J, Dimov I, Graf von Kalckreuth C, Cano-Chervel J, Baijot S, Pelc K, Sottiaux M, Vilain C, Smits G, Deconinck N. BCL11A frameshift mutation associated with dyspraxia and hypotonia affecting the fine, gross, oral, and speech motor systems. Am J Med Genet A 2017; 176:201-208. [PMID: 28960836 PMCID: PMC5765401 DOI: 10.1002/ajmg.a.38479] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 12/08/2017] [Accepted: 08/21/2017] [Indexed: 12/14/2022]
Abstract
We report the case of a 7‐year‐old male of Western European origin presenting with moderate intellectual disability, severe childhood apraxia of speech in the presence of oral and manual dyspraxia, and hypotonia across motor systems including the oral and speech motor systems. Exome sequencing revealed a de novo frameshift protein truncating mutation in the fourth exon of BCL11A, a gene recently demonstrated as being involved in cognition and language development. Making parallels with a previously described patient with a 200 kb 2p15p16.1 deletion encompassing the entire BCL11A gene and displaying a similar phenotype, we characterize in depth how BCL11A is involved in clinical aspects of language development and oral praxis.
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Affiliation(s)
- Julie Soblet
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Ivan Dimov
- Faculté de Médecine ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Clemens Graf von Kalckreuth
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Julie Cano-Chervel
- Department of Child and Adolescent Psychiatry, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Simon Baijot
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium.,Department of Child and Adolescent Psychiatry, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Karin Pelc
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Martine Sottiaux
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Catheline Vilain
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicolas Deconinck
- Department of Pediatric Neurology, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, Brussels, Belgium
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17
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Lévy J, Coussement A, Dupont C, Guimiot F, Baumann C, Viot G, Passemard S, Capri Y, Drunat S, Verloes A, Pipiras E, Benzacken B, Dupont JM, Tabet AC. Molecular and clinical delineation of 2p15p16.1 microdeletion syndrome. Am J Med Genet A 2017; 173:2081-2087. [PMID: 28573701 DOI: 10.1002/ajmg.a.38302] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/21/2017] [Accepted: 05/06/2017] [Indexed: 11/05/2022]
Abstract
Interstitial 2p15p16.1 microdeletion is a rare chromosomal syndrome previously reported in 33 patients. It is characterized by intellectual disability, developmental delay, autism spectrum disorders, microcephaly, short stature, dysmorphic features, and multiple congenital organ defects. It is defined as a contiguous gene syndrome and two critical regions have been proposed at 2p15 and 2p16.1 loci. Nevertheless, patients with deletion of both critical regions shared similar features of the phenotype and the correlation genotype-phenotype is still unclear. We review all published cases and describe three additional patients, to define the phenotype-genotype correlation more precisely. We reported on two patients including the first prenatal case described so far, carrying a 2p15 deletion affecting two genes: XPO1 and part of USP34. Both patients shared similar features including facial dysmorphism and cerebral abnormalities. We considered the genes involved in the deleted segment to further understand the abnormal phenotype. The third case we described here was a 4-year-old boy with a heterozygous de novo 427 kb deletion encompassing BCL11A and PAPOLG at 2p16.1. He displayed speech delay, autistic traits, and motor stereotypies associated with brain structure abnormalities. We discuss the contribution of the genes included in the deletion to the abnormal phenotype. Our three new patients compared to previous cases, highlighted that despite two critical regions, both distal deletion at 2p16.1 and proximal deletion at 2p15 are associated with phenotypes that are very close to each other. Finally, we also discuss the genetic counseling of this microdeletion syndrome particularly in the course of prenatal diagnosis.
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Affiliation(s)
- Jonathan Lévy
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
- INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France
| | - Aurélie Coussement
- Cytogenetics Laboratory, APHP, Cochin Hospital, Paris Descartes University, Paris, France
| | - Céline Dupont
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Fabien Guimiot
- INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France
- Department of Developmental Biology, APHP Robert-Debré hospital, Paris Diderot University, Sorbonne Paris Cité, Paris, France
| | - Clarisse Baumann
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Géraldine Viot
- Cytogenetics Laboratory, APHP, Cochin Hospital, Paris Descartes University, Paris, France
| | - Sandrine Passemard
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
- INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France
| | - Yline Capri
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Séverine Drunat
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Alain Verloes
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
| | - Eva Pipiras
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
- INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France
- University Hospital Jean-Verdier, Department of Cytogenetic, Embryology and Histology, Bondy, France
| | - Brigitte Benzacken
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
- INSERM UMR1141, Paris Diderot University, AP-HP, Robert-Debré Hospital, Paris, France
- University Hospital Jean-Verdier, Department of Cytogenetic, Embryology and Histology, Bondy, France
| | - Jean-Michel Dupont
- Cytogenetics Laboratory, APHP, Cochin Hospital, Paris Descartes University, Paris, France
| | - Anne-Claude Tabet
- Genetics Department, AP-HP, Robert-Debré University Hospital, Paris, France
- Neuroscience Department, Génétique Humaine et Fonction Cognitive Unit, Pasteur Institute, Paris, France
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18
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Shimbo H, Yokoi T, Aida N, Mizuno S, Suzumura H, Nagai J, Ida K, Enomoto Y, Hatano C, Kurosawa K. Haploinsufficiency of BCL11A associated with cerebellar abnormalities in 2p15p16.1 deletion syndrome. Mol Genet Genomic Med 2017; 5:429-437. [PMID: 28717667 PMCID: PMC5511803 DOI: 10.1002/mgg3.289] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Chromosome 2p15p16.1 deletion syndrome is a rare genetic disorder characterized by intellectual disability (ID), neurodevelopmental delay, language delay, growth retardation, microcephaly, structural brain abnormalities, and dysmorphic features. More than 30 patients with 2p15p16.1 microdeletion syndrome have been reported in the literature. METHODS Molecular analysis was performed using microarray-based comparative genomic hybridization (array CGH). Clinical characteristics and brain magnetic resonance imaging features of these patients were also reviewed. RESULTS We identified four patients with ID, neurodevelopmental delay, brain malformations, and dysmorphic features; two patients with 2p15p16.1 deletions (3.24 Mb, 5.04 Mb), one patient with 2p16.1 deletion (1.12 Mb), and one patient with 2p14p16.1 deletion (5.12 Mb). Three patients with 2p15p16.1 deletions or 2p16.1 deletions encompassing BCL11A,PAPOLG, and REL showed hypoplasia of the pons and cerebellum. The patient with 2p14p16.1 deletion, which did not include three genes showed normal size and shape of the cerebellar hemispheres and pons. CONCLUSION The zinc finger transcription factor BCL11A associated with the BAF chromatin remodeling complex has been identified to be critical for neural development and BCL11A haploinsufficiency is closely related to cerebellar abnormalities.
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Affiliation(s)
- Hiroko Shimbo
- Clinical Research InstituteKanagawa Children's Medical CenterYokohamaJapan
| | - Takayuki Yokoi
- Division of Medical GeneticsKanagawa Children's Medical CenterYokohamaJapan
| | - Noriko Aida
- Division of RadiologyKanagawa Children's Medical CenterYokohamaJapan
| | - Seiji Mizuno
- Department of PediatricsAichi Human Service CenterCentral HospitalKasugaiJapan
| | - Hiroshi Suzumura
- Department of PediatricsDokkyo Medical University School of MedicineTochigiJapan
| | - Junichi Nagai
- Laboratory MedicineKanagawa Children's Medical CenterYokohamaJapan
| | - Kazumi Ida
- Division of Medical GeneticsKanagawa Children's Medical CenterYokohamaJapan
| | - Yumi Enomoto
- Clinical Research InstituteKanagawa Children's Medical CenterYokohamaJapan
| | - Chihiro Hatano
- Division of Medical GeneticsKanagawa Children's Medical CenterYokohamaJapan
| | - Kenji Kurosawa
- Division of Medical GeneticsKanagawa Children's Medical CenterYokohamaJapan
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19
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Codipilly DC, Gavrilova RH, Tangalos EG. De novo 2p16.1 microdeletion with metastatic esophageal adenocarcinoma. BMJ Case Rep 2017; 2017:bcr-2016-218016. [PMID: 28108439 DOI: 10.1136/bcr-2016-218016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Microdeletions involving chromosome 2p15-16.1 are a rare genetic abnormality and have been reported in 18 separate patients, mainly children, since 2007. This microdeletion syndrome is characterised by a heterogeneous expression of intellectual impairment, dysmorphic facies, musculoskeletal abnormalities and potential neurodevelopmental anomalies. We report the first case of natural progression in an adult patient who died at a young age of metastatic esophageal adenocarcinoma. Important learning points include the variable phenotypic expression of this microdeletion syndrome and the fact that clinicians must be thorough in investigating objective discrepancies in patients who cannot endorse classical symptoms.
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Affiliation(s)
- Don Chamil Codipilly
- Department of Internal Medicine, Mayo Clinic Minnesota, Rochester, Minnesota, USA
| | - Ralitza H Gavrilova
- Department of Clinical Genomics and Neurology, Mayo Clinic Minnesota, Rochester, Minnesota, USA
| | - Eric G Tangalos
- Department of Primary Care Internal Medicine, Mayo Clinic Minnesota, Rochester, Minnesota, USA
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20
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BCL11A Haploinsufficiency Causes an Intellectual Disability Syndrome and Dysregulates Transcription. Am J Hum Genet 2016; 99:253-74. [PMID: 27453576 PMCID: PMC4974071 DOI: 10.1016/j.ajhg.2016.05.030] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/30/2016] [Indexed: 02/06/2023] Open
Abstract
Intellectual disability (ID) is a common condition with considerable genetic heterogeneity. Next-generation sequencing of large cohorts has identified an increasing number of genes implicated in ID, but their roles in neurodevelopment remain largely unexplored. Here we report an ID syndrome caused by de novo heterozygous missense, nonsense, and frameshift mutations in BCL11A, encoding a transcription factor that is a putative member of the BAF swi/snf chromatin-remodeling complex. Using a comprehensive integrated approach to ID disease modeling, involving human cellular analyses coupled to mouse behavioral, neuroanatomical, and molecular phenotyping, we provide multiple lines of functional evidence for phenotypic effects. The etiological missense variants cluster in the amino-terminal region of human BCL11A, and we demonstrate that they all disrupt its localization, dimerization, and transcriptional regulatory activity, consistent with a loss of function. We show that Bcl11a haploinsufficiency in mice causes impaired cognition, abnormal social behavior, and microcephaly in accordance with the human phenotype. Furthermore, we identify shared aberrant transcriptional profiles in the cortex and hippocampus of these mouse models. Thus, our work implicates BCL11A haploinsufficiency in neurodevelopmental disorders and defines additional targets regulated by this gene, with broad relevance for our understanding of ID and related syndromes.
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21
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Bagheri H, Badduke C, Qiao Y, Colnaghi R, Abramowicz I, Alcantara D, Dunham C, Wen J, Wildin RS, Nowaczyk MJ, Eichmeyer J, Lehman A, Maranda B, Martell S, Shan X, Lewis SM, O’Driscoll M, Gregory-Evans CY, Rajcan-Separovic E. Identifying candidate genes for 2p15p16.1 microdeletion syndrome using clinical, genomic, and functional analysis. JCI Insight 2016; 1:e85461. [PMID: 27699255 PMCID: PMC5033885 DOI: 10.1172/jci.insight.85461] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/09/2016] [Indexed: 01/14/2023] Open
Abstract
The 2p15p16.1 microdeletion syndrome has a core phenotype consisting of intellectual disability, microcephaly, hypotonia, delayed growth, common craniofacial features, and digital anomalies. So far, more than 20 cases of 2p15p16.1 microdeletion syndrome have been reported in the literature; however, the size of the deletions and their breakpoints vary, making it difficult to identify the candidate genes. Recent reports pointed to 4 genes (XPO1, USP34, BCL11A, and REL) that were included, alone or in combination, in the smallest deletions causing the syndrome. Here, we describe 8 new patients with the 2p15p16.1 deletion and review all published cases to date. We demonstrate functional deficits for the above 4 candidate genes using patients' lymphoblast cell lines (LCLs) and knockdown of their orthologs in zebrafish. All genes were dosage sensitive on the basis of reduced protein expression in LCLs. In addition, deletion of XPO1, a nuclear exporter, cosegregated with nuclear accumulation of one of its cargo molecules (rpS5) in patients' LCLs. Other pathways associated with these genes (e.g., NF-κB and Wnt signaling as well as the DNA damage response) were not impaired in patients' LCLs. Knockdown of xpo1a, rel, bcl11aa, and bcl11ab resulted in abnormal zebrafish embryonic development including microcephaly, dysmorphic body, hindered growth, and small fins as well as structural brain abnormalities. Our multifaceted analysis strongly implicates XPO1, REL, and BCL11A as candidate genes for 2p15p16.1 microdeletion syndrome.
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Affiliation(s)
- Hani Bagheri
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Chansonette Badduke
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Ying Qiao
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Rita Colnaghi
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Iga Abramowicz
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Diana Alcantara
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Christopher Dunham
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
| | - Jiadi Wen
- University of Texas at Dallas, Dallas, Texas, USA
| | | | - Malgorzata J.M. Nowaczyk
- Department of Pathology and Molecular Medicine, McMaster University Medical Centre, Hamilton, Ontario, Canada
| | | | - Anna Lehman
- Department of Medical Genetics, UBC, Vancouver, British Columbia, Canada
| | - Bruno Maranda
- Medical Genetics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Sally Martell
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
| | - Xianghong Shan
- Department of Ophthalmology, UBC, Vancouver, British Columbia, Canada
| | - Suzanne M.E. Lewis
- Department of Medical Genetics, UBC, Vancouver, British Columbia, Canada
| | - Mark O’Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | | | - Evica Rajcan-Separovic
- Department of Pathology and Laboratory Medicine, University of British Columbia (UBC), Vancouver, British Columbia, Canada
- Child and Family Research Institute, Vancouver, British Columbia, Canada
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Pule GD, Ngo Bitoungui VJ, Chetcha Chemegni B, Kengne AP, Antonarakis S, Wonkam A. Association between Variants at BCL11A Erythroid-Specific Enhancer and Fetal Hemoglobin Levels among Sickle Cell Disease Patients in Cameroon: Implications for Future Therapeutic Interventions. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:627-31. [PMID: 26393293 DOI: 10.1089/omi.2015.0124] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Variants in BCL11A were previously associated with fetal hemoglobin (HbF) levels among Cameroonian sickle cell disease (SCD) patients, however explaining only ∼2% of the variance. In the same patients, we have investigated the relationship between HbF and two SNPs in a BCL11A erythroid-specific enhancer (N=626). Minor allele frequencies in rs7606173 and rs1427407 were 0.42 and 0.24, respectively. Both variants were significantly associated with HbF levels (p=3.11e-08 and p=6.04e-06, respectively) and explained 8% and 6.2% variations, respectively. These data have confirmed a stronger effect on HbF of genomic variations at the BCL11A erythroid-specific enhancer among patients with SCD in Cameroon, the first report on a West African population. The relevance of these findings is of prime importance because the disruption of this enhancer would alter BCL11A expression in erythroid precursors and thus HbF expression, while sparing the induced functional challenges of any alterations on the expression of this transcription factor in non-erythroid lineages, thus providing an attractive approach for new treatment strategies of SCD.
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Affiliation(s)
- Gift Dineo Pule
- 1 Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | | | | | - Andre Pascal Kengne
- 3 Non-Communicable Diseases Research Unit, South African Medical Research Council , Cape Town, South Africa
| | - Stylianos Antonarakis
- 4 Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva , Switzerland
| | - Ambroise Wonkam
- 1 Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
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