101
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Alural B, Genc S, Haggarty SJ. Diagnostic and therapeutic potential of microRNAs in neuropsychiatric disorders: Past, present, and future. Prog Neuropsychopharmacol Biol Psychiatry 2017; 73:87-103. [PMID: 27072377 PMCID: PMC5292013 DOI: 10.1016/j.pnpbp.2016.03.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 12/12/2022]
Abstract
Neuropsychiatric disorders are common health problems affecting approximately 1% of the population. Twin, adoption, and family studies have displayed a strong genetic component for many of these disorders; however, the underlying pathophysiological mechanisms and neural substrates remain largely unknown. Given the critical need for new diagnostic markers and disease-modifying treatments, expanding the focus of genomic studies of neuropsychiatric disorders to include the role of non-coding RNAs (ncRNAs) is of growing interest. Of known types of ncRNAs, microRNAs (miRNAs) are 20-25-nucleotide, single-stranded, molecules that regulate gene expression through post-transcriptional mechanisms and have the potential to coordinately regulate complex regulatory networks. In this review, we summarize the current knowledge on miRNA alteration/dysregulation in neuropsychiatric disorders, with a special emphasis on schizophrenia (SCZ), bipolar disorder (BD), and major depressive disorder (MDD). With an eye toward the future, we also discuss the diagnostic and prognostic potential of miRNAs for neuropsychiatric disorders in the context of personalized treatments and network medicine.
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Affiliation(s)
- Begum Alural
- Department of Neuroscience, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylul University, Izmir, Turkey
| | - Sermin Genc
- Department of Neuroscience, Faculty of Medicine, Dokuz Eylul University, Izmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylul University, Izmir, Turkey
| | - Stephen J Haggarty
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Chemical Neurobiology Laboratory, Departments of Neurology and Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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102
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Aquino A, Perini M, Cosmai S, Zanon S, Pisa V, Castagna C, Uberti S. Osteopathic Manipulative Treatment Limits Chronic Constipation in a Child with Pitt-Hopkins Syndrome. Case Rep Pediatr 2017; 2017:5437830. [PMID: 28251008 PMCID: PMC5306969 DOI: 10.1155/2017/5437830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/15/2017] [Indexed: 11/19/2022] Open
Abstract
Pitt-Hopkins Syndrome (PTHS) is a rare genetic disorder caused by insufficient expression of the TCF4 gene. Children with PTHS typically present with gastrointestinal disorders and early severe chronic constipation is frequently found (75%). Here we describe the case of a PTHS male 10-year-old patient with chronic constipation in whom Osteopathic Manipulative Treatment (OMT) resulted in improved bowel functions, as assessed by the diary, the QPGS-Form A Section C questionnaire, and the Paediatric Bristol Stool Form Scale. The authors suggested that OMT may be a valid tool to improve the defecation frequency and reduce enema administration in PTHS patients.
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Affiliation(s)
- Alessandro Aquino
- Research Department, Istituto Superiore di Osteopatia, 20126 Milan, Italy
- Department of Clinical Paediatrics & Obstetrics-Gynaecology, Istituto Superiore di Osteopatia, 20126 Milan, Italy
| | - Mattia Perini
- Department of Clinical Paediatrics & Obstetrics-Gynaecology, Istituto Superiore di Osteopatia, 20126 Milan, Italy
| | - Silvia Cosmai
- Department of Clinical Paediatrics & Obstetrics-Gynaecology, Istituto Superiore di Osteopatia, 20126 Milan, Italy
| | - Silvia Zanon
- Department of Clinical Paediatrics & Obstetrics-Gynaecology, Istituto Superiore di Osteopatia, 20126 Milan, Italy
| | - Viviana Pisa
- Research Department, Istituto Superiore di Osteopatia, 20126 Milan, Italy
| | - Carmine Castagna
- Research Department, Istituto Superiore di Osteopatia, 20126 Milan, Italy
| | - Stefano Uberti
- Research Department, Istituto Superiore di Osteopatia, 20126 Milan, Italy
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103
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Chen T, Wu Q, Zhang Y, Lu T, Yue W, Zhang D. Tcf4 Controls Neuronal Migration of the Cerebral Cortex through Regulation of Bmp7. Front Mol Neurosci 2016; 9:94. [PMID: 27752241 PMCID: PMC5046712 DOI: 10.3389/fnmol.2016.00094] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/20/2016] [Indexed: 11/14/2022] Open
Abstract
Background: Transcription factor 4 (TCF4) is found to be associated with schizophrenia. TCF4 mutations also cause Pitt-Hopkins Syndrome, a neurodevelopmental disorder associated with severe mental retardation. However, the function of TCF4 during brain development remains unclear. Results: Here, we report that Tcf4 is expressed in the developing cerebral cortex. In utero suppression of Tcf4 arrested neuronal migration, leading to accumulation of ectopic neurons in the intermediate zone. Knockdown of Tcf4 impaired leading process formation. Furthermore, Bone Morphogenetic Protein 7 (Bmp7) is upregulated in Tcf4-deficient neurons. In vivo gain of function and rescue experiments demonstrated that Bmp7 is the major downstream effector of Tcf4 required for neuronal migration. Conclusion: Thus, we have uncovered a new Tcf4/Bmp7-dependent mechanism underlying neuronal migration, and provide insights into the pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Tianda Chen
- Institute of Mental Health, Peking University Sixth Hospital, BeijingChina; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders, Peking University, BeijingChina
| | - Qinwei Wu
- Institute of Mental Health, Peking University Sixth Hospital, BeijingChina; Academy for Advanced Interdisciplinary Studies, Peking UniversityBeijing, China; Peking-Tsinghua Center for Life Sciences, Peking UniversityBeijing, China
| | - Yang Zhang
- Institute of Mental Health, Peking University Sixth Hospital, BeijingChina; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders, Peking University, BeijingChina
| | - Tianlan Lu
- Institute of Mental Health, Peking University Sixth Hospital, BeijingChina; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders, Peking University, BeijingChina
| | - Weihua Yue
- Institute of Mental Health, Peking University Sixth Hospital, BeijingChina; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders, Peking University, BeijingChina
| | - Dai Zhang
- Institute of Mental Health, Peking University Sixth Hospital, BeijingChina; Key Laboratory of Mental Health, Ministry of Health & National Clinical Research Center for Mental Disorders, Peking University, BeijingChina; Peking-Tsinghua Center for Life Sciences, Peking UniversityBeijing, China; PKU-IDG/McGovern Institute for Brain Research, Peking UniversityBeijing, China
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104
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Ozel MD, Onder ME, Sazci A. Transcription factor 4 gene rs9960767 polymorphism in bipolar disorder. Biomed Rep 2016; 5:506-510. [PMID: 27699022 DOI: 10.3892/br.2016.742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/08/2016] [Indexed: 12/18/2022] Open
Abstract
The transcription factor 4 (TCF4) gene encodes a helix-loop-helix transcription factor protein, which initiates neuronal differentiation and is primarily expressed during nervous system development. The aim of the present study is to investigate the association of the TCF4 rs9960767 polymorphism and bipolar disorder, which is highly heritable. DNA isolation was performed on 95 patients with bipolar disorder and 108 healthy control subjects to examine the TCF4 rs9960767 polymorphism. Genotypic and allelic frequencies were determined using the polymerase chain reaction-restriction fragment length polymorphism method designed in our laboratory. Statistical analysis was performed using χ2 test within the 95% confidence interval. Odds ratios were calculated and Hardy-Weinberg equilibrium (HWE) was verified for all control subjects and patients. The A allele frequency was 95.8% in the patients and 94.4% in the control subjects, and 4.2% in the patients and 5.6% in the control subjects for the C allele. The genotype frequencies of the TCF4 gene rs9960767 variant were as follows: AA, 91.6% and AC, 8.4% in patients with bipolar (CC genotype was not observed in cases); AA, 89.8%; AC, 9.3% and CC, 0.9% in the control subjects. No statistically significant difference was identified between the patients and control subjects (χ2=0.937; P=0.626). In addition, gender specific analysis was performed, although no significant association was found according to the gender distrubition. All patients and control subjects were in HWE (P>0.05). Statistical analysis of the data indicates that the TCF4 gene rs9960767 polymorphism is not an independent risk factor for bipolar disorder in the overall population or in terms of gender; however, an increased population size would improve the statistical power. Furthermore, additional gene variants that are specifically involved in neuronal development may be analyzed for revealing the complex genetic architecture of bipolar disorder. An improved approach would be better to evaluate the TCF4 gene in a pathway specific manner due to its role as a transcription factor.
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Affiliation(s)
- Mavi Deniz Ozel
- Department of Medical Biology, International School of Medicine, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Mehmet Emin Onder
- Department of Psychiatry, Faculty of Medicine, University of Kocaeli, Kocaeli 41380, Turkey
| | - Ali Sazci
- Department of Medical Biology and Genetics, Faculty of Medicine, University of Kocaeli, Kocaeli 41380, Turkey
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105
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Tcf4 transgenic female mice display delayed adaptation in an auditory latent inhibition paradigm. Eur Arch Psychiatry Clin Neurosci 2016; 266:505-12. [PMID: 26404636 DOI: 10.1007/s00406-015-0643-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/07/2015] [Indexed: 12/18/2022]
Abstract
Schizophrenia (SZ) is a severe mental disorder affecting about 1 % of the human population. Patients show severe deficits in cognitive processing often characterized by an improper filtering of environmental stimuli. Independent genome-wide association studies confirmed a number of risk variants for SZ including several associated with the gene encoding the transcription factor 4 (TCF4). TCF4 is widely expressed in the central nervous system of mice and humans and seems to be important for brain development. Transgenic mice overexpressing murine Tcf4 (Tcf4tg) in the adult brain display cognitive impairments and sensorimotor gating disturbances. To address the question of whether increased Tcf4 gene dosage may affect cognitive flexibility in an auditory associative task, we tested latent inhibition (LI) in female Tcf4tg mice. LI is a widely accepted translational endophenotype of SZ and results from a maladaptive delay in switching a response to a previously unconditioned stimulus when this becomes conditioned. Using an Audiobox, we pre-exposed Tcf4tg mice and their wild-type littermates to either a 3- or a 12-kHz tone before conditioning them to a 12-kHz tone. Tcf4tg animals pre-exposed to a 12-kHz tone showed significantly delayed conditioning when the previously unconditioned tone became associated with an air puff. These results support findings that associate TCF4 dysfunction with cognitive inflexibility and improper filtering of sensory stimuli observed in SZ patients.
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106
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Rannals MD, Page SC, Campbell MN, Gallo RA, Mayfield B, Maher BJ. Neurodevelopmental models of transcription factor 4 deficiency converge on a common ion channel as a potential therapeutic target for Pitt Hopkins syndrome. Rare Dis 2016; 4:e1220468. [PMID: 28032012 PMCID: PMC5154382 DOI: 10.1080/21675511.2016.1220468] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/11/2016] [Accepted: 07/28/2016] [Indexed: 01/31/2023] Open
Abstract
The clinically pleiotropic gene, Transcription Factor 4 (TCF4), is a broadly expressed basic helix-loop-helix (bHLH) transcription factor linked to multiple neurodevelopmental disorders, including schizophrenia, 18q deletion syndrome, and Pitt Hopkins syndrome (PTHS). In vivo suppression of Tcf4 by shRNA or mutation by CRISPR/Cas9 in the developing rat prefrontal cortex resulted in attenuated action potential output. To explain this intrinsic excitability deficit, we demonstrated that haploinsufficiency of TCF4 lead to the ectopic expression of two ion channels, Scn10a and Kcnq1. These targets of TCF4 regulation were identified through molecular profiling experiments that used translating ribosome affinity purification to enrich mRNA from genetically manipulated neurons. Using a mouse model of PTHS (Tcf4+/tr), we observed a similar intrinsic excitability deficit, however the underlying mechanism appeared slightly different than our rat model - as Scn10a expression was similarly increased but Kcnq1 expression was decreased. Here, we show that the truncated TCF4 protein expressed in our PTHS mouse model binds to wild-type TCF4 protein, and we suggest the difference in Kcnq1 expression levels between these two rodent models appears to be explained by a dominant-negative function of the truncated TCF4 protein. Despite the differences in the underlying molecular mechanisms, we observed common underlying intrinsic excitability deficits that are consistent with ectopic expression of Scn10a. The converging molecular function of TCF4 across two independent rodent models indicates SCN10a is a potential therapeutic target for Pitt-Hopkins syndrome.
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Affiliation(s)
- Matthew D. Rannals
- Department of Neurobiology, School of
Medicine, University of Pittsburgh, Pittsburgh, PA,
USA
| | - Stephanie Cerceo Page
- Lieber Institute for Brain Development, Johns
Hopkins Medical Campus, Baltimore, MD, USA
| | - Morganne N. Campbell
- Lieber Institute for Brain Development, Johns
Hopkins Medical Campus, Baltimore, MD, USA
| | - Ryan A. Gallo
- Lieber Institute for Brain Development, Johns
Hopkins Medical Campus, Baltimore, MD, USA
| | - Brent Mayfield
- Lieber Institute for Brain Development, Johns
Hopkins Medical Campus, Baltimore, MD, USA
| | - Brady J. Maher
- Lieber Institute for Brain Development, Johns
Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral
Sciences, Johns Hopkins School of Medicine, Baltimore, MD,
USA
- Department of Neuroscience, Johns Hopkins
School of Medicine, Baltimore, MD, USA
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107
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Maduro V, Pusey BN, Cherukuri PF, Atkins P, du Souich C, Rupps R, Limbos M, Adams DR, Bhatt SS, Eydoux P, Links AE, Lehman A, Malicdan MC, Mason CE, Morimoto M, Mullikin JC, Sear A, Van Karnebeek C, Stankiewicz P, Gahl WA, Toro C, Boerkoel CF. Complex translocation disrupting TCF4 and altering TCF4 isoform expression segregates as mild autosomal dominant intellectual disability. Orphanet J Rare Dis 2016; 11:62. [PMID: 27179618 PMCID: PMC4868023 DOI: 10.1186/s13023-016-0439-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/25/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Mutations of TCF4, which encodes a basic helix-loop-helix transcription factor, cause Pitt-Hopkins syndrome (PTHS) via multiple genetic mechanisms. TCF4 is a complex locus expressing multiple transcripts by alternative splicing and use of multiple promoters. To address the relationship between mutation of these transcripts and phenotype, we report a three-generation family segregating mild intellectual disability with a chromosomal translocation disrupting TCF4. RESULTS Using whole genome sequencing, we detected a complex unbalanced karyotype disrupting TCF4 (46,XY,del(14)(q23.3q23.3)del(18)(q21.2q21.2)del(18)(q21.2q21.2)inv(18)(q21.2q21.2)t(14;18)(q23.3;q21.2)(14pter®14q23.3::18q21.2®18q21.2::18q21.1®18qter;18pter®18q21.2::14q23.3®14qter). Subsequent transcriptome sequencing, qRT-PCR and nCounter analyses revealed that cultured skin fibroblasts and peripheral blood had normal expression of genes along chromosomes 14 or 18 and no marked changes in expression of genes other than TCF4. Affected individuals had 12-33 fold higher mRNA levels of TCF4 than did unaffected controls or individuals with PTHS. Although the derivative chromosome generated a PLEKHG3-TCF4 fusion transcript, the increased levels of TCF4 mRNA arose from transcript variants originating distal to the translocation breakpoint, not from the fusion transcript. CONCLUSIONS Although validation in additional patients is required, our findings suggest that the dysmorphic features and severe intellectual disability characteristic of PTHS are partially rescued by overexpression of those short TCF4 transcripts encoding a nuclear localization signal, a transcription activation domain, and the basic helix-loop-helix domain.
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Affiliation(s)
- Valerie Maduro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Barbara N Pusey
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Praveen F Cherukuri
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Paul Atkins
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Christèle du Souich
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Rosemarie Rupps
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | | | - David R Adams
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Samarth S Bhatt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Patrice Eydoux
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Amanda E Links
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Anna Lehman
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - May C Malicdan
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute (BMRI), New York, NY, USA
| | - Marie Morimoto
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - James C Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Sear
- Department of General Practice, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Clara Van Karnebeek
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
- NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD, USA.
- Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, BC, Canada.
- Child and Family Research Institute, University of British Columbia, Vancouver, BC, Canada.
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108
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Kharbanda M, Kannike K, Lampe A, Berg J, Timmusk T, Sepp M. Partial deletion of TCF4 in three generation family with non-syndromic intellectual disability, without features of Pitt-Hopkins syndrome. Eur J Med Genet 2016; 59:310-4. [PMID: 27132474 DOI: 10.1016/j.ejmg.2016.04.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
Abstract
Mutations in TCF4 (basic helix-loop-helix transcription factor 4), a gene with complex organization and multiple transcription initiation sites, are usually associated with Pitt-Hopkins syndrome (PTHS). However, a translocation encompassing the 5' end of TCF4 and several point mutations have been linked to non-syndromic intellectual disability (NSID). Here we describe a family with autosomal dominantly inherited NSID in seven relatives with a partial deletion of TCF4, disrupting the 5' end of the gene, predicted to result in the reduction of the number of mRNAs that can be produced by alternative transcription initiation. Functional studies indicate that it leads to reduced levels of transcripts coding for TCF4 protein isoforms with a nuclear localization signal, which may be relevant to the phenotype. The findings in our family support the notion that the position of the mutation in TCF4 is relevant to the phenotype, with those mutations in the 5' region, cassette exons and regions not affecting the important functional domains being linked to NSID rather than PTHS. We suggest that screening for mutations in TCF4 could be considered in the investigation of NSID.
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Affiliation(s)
- Mira Kharbanda
- West of Scotland Clinical Genetics Service, Level 2A Laboratory Medicine Building, Queen Elizabeth University Hospital, 1345 Govan Road, Glasgow, G51 4TF, UK.
| | - Kaja Kannike
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, Tallinn, 12618, Estonia
| | - Anne Lampe
- South East of Scotland Department of Clinical Genetics, Molecular Medicine Centre, Western General Hospital, Edinburgh, UK
| | - Jonathan Berg
- Department of Clinical Genetics, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Tõnis Timmusk
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, Tallinn, 12618, Estonia
| | - Mari Sepp
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, Tallinn, 12618, Estonia
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109
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de Winter CF, Baas M, Bijlsma EK, van Heukelingen J, Routledge S, Hennekam RCM. Phenotype and natural history in 101 individuals with Pitt-Hopkins syndrome through an internet questionnaire system. Orphanet J Rare Dis 2016; 11:37. [PMID: 27072915 PMCID: PMC4830011 DOI: 10.1186/s13023-016-0422-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/07/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Pitt-Hopkins syndrome (PTHS; MIM# 610954) is a genetically determined entity mainly caused by mutations in TransCription Factor 4 (TCF4). We have developed a new way to collect information on (ultra-)rare disorders through a web-based database which we call 'waihonapedia' (waihona [meaning treasure in Hawaiian] encyclopaedia). METHODS We have built a waihonapedia system in a collaboration between physicians, social scientists, and parent support groups. The system consists of an initial extensive questionnaire for background cross-sectional data, and subsequent follow-up using small questionnaires, with a particular focus on behavioural aspects. The system was built to be used through the internet, ensuring a secure environment, respecting privacy for participants, and acting automated to allow for low costs and limiting human mistakes in data handling. Recruitment of participants is through the patient support groups. In addition, as a sub-study, we used the data from the waihonapedia system to compare the two proposed diagnostic classification systems for PTHS. RESULTS We present here the results of the initial, cross-sectional questionnaire in which early development, physical health, cognition and behaviour are interrogated, and to which modules specific for PTHS were added on epilepsy and breathing patterns. We describe 101 individuals with a molecularly confirmed diagnosis of PTHS. Comparison of the two classification systems aimed at helping the clinical diagnosis was performed in 47 of the present PTHS individuals, with disappointing results for both. Internationally accepted clinical diagnostic criteria are needed. CONCLUSION The present cross-sectional data on the natural history of PTHS have yielded useful information which will further increase when follow-up data will be added. No doubt this will improve both care and research.
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Affiliation(s)
- Channa F de Winter
- Reinaerde, Organisation for people with intellectual disabilities, Utrecht, The Netherlands
| | - Melanie Baas
- Department of Paediatrics and Translational Genetics, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | | | | | - Raoul C M Hennekam
- Department of Paediatrics and Translational Genetics, Academic Medical Centre, University of Amsterdam, Meibergdreef 9, 1105AZ, Amsterdam, The Netherlands.
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110
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Rannals MD, Hamersky GR, Page SC, Campbell MN, Briley A, Gallo RA, Phan BN, Hyde TM, Kleinman JE, Shin JH, Jaffe AE, Weinberger DR, Maher BJ. Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1. Neuron 2016; 90:43-55. [PMID: 26971948 PMCID: PMC4824652 DOI: 10.1016/j.neuron.2016.02.021] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 10/09/2015] [Accepted: 02/12/2016] [Indexed: 01/28/2023]
Abstract
Transcription Factor 4 (TCF4) is a clinically pleiotropic gene associated with schizophrenia and Pitt-Hopkins syndrome (PTHS). To gain insight about the neurobiology of TCF4, we created an in vivo model of PTHS by suppressing Tcf4 expression in rat prefrontal neurons immediately prior to neurogenesis. This cell-autonomous genetic insult attenuated neuronal spiking by increasing the afterhyperpolarization. At the molecular level, using a novel technique called iTRAP that combined in utero electroporation and translating ribosome affinity purification, we identified increased translation of two ion channel genes, Kcnq1 and Scn10a. These ion channel candidates were validated by pharmacological rescue and molecular phenocopy. Remarkably, similar excitability deficits were observed in prefrontal neurons from a Tcf4(+/tr) mouse model of PTHS. Thus, we identify TCF4 as a regulator of neuronal intrinsic excitability in part by repression of Kcnq1 and Scn10a and suggest that this molecular function may underlie pathophysiology associated with neuropsychiatric disorders.
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Affiliation(s)
- Matthew D Rannals
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Gregory R Hamersky
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Stephanie Cerceo Page
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Morganne N Campbell
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Aaron Briley
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Ryan A Gallo
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - BaDoi N Phan
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; Department of Neurology and the McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; Department of Neurology and the McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Neurology and the McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Brady J Maher
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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D'Rozario M, Zhang T, Waddell EA, Zhang Y, Sahin C, Sharoni M, Hu T, Nayal M, Kutty K, Liebl F, Hu W, Marenda DR. Type I bHLH Proteins Daughterless and Tcf4 Restrict Neurite Branching and Synapse Formation by Repressing Neurexin in Postmitotic Neurons. Cell Rep 2016; 15:386-97. [PMID: 27050508 DOI: 10.1016/j.celrep.2016.03.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 01/22/2016] [Accepted: 03/09/2016] [Indexed: 11/17/2022] Open
Abstract
Proneural proteins of the class I/II basic-helix-loop-helix (bHLH) family are highly conserved transcription factors. Class I bHLH proteins are expressed in a broad number of tissues during development, whereas class II bHLH protein expression is more tissue restricted. Our understanding of the function of class I/II bHLH transcription factors in both invertebrate and vertebrate neurobiology is largely focused on their function as regulators of neurogenesis. Here, we show that the class I bHLH proteins Daughterless and Tcf4 are expressed in postmitotic neurons in Drosophila melanogaster and mice, respectively, where they function to restrict neurite branching and synapse formation. Our data indicate that Daughterless performs this function in part by restricting the expression of the cell adhesion molecule Neurexin. This suggests a role for these proteins outside of their established roles in neurogenesis.
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Affiliation(s)
| | - Ting Zhang
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Edward A Waddell
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Yonggang Zhang
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Cem Sahin
- Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA 19104, USA
| | - Michal Sharoni
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Tina Hu
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Mohammad Nayal
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Kaveesh Kutty
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA
| | - Faith Liebl
- Department of Biological Sciences, Southern Illinois University Edwardsville, Edwardsville, IL 62026, USA
| | - Wenhui Hu
- Department of Neuroscience, Temple University School of Medicine, Philadelphia, PA 19140, USA.
| | - Daniel R Marenda
- Department of Biology, Drexel University, Philadelphia, PA 19104, USA; Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, PA 19104, USA.
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Wang LH, Baker NE. E Proteins and ID Proteins: Helix-Loop-Helix Partners in Development and Disease. Dev Cell 2016; 35:269-80. [PMID: 26555048 DOI: 10.1016/j.devcel.2015.10.019] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 10/18/2015] [Accepted: 10/23/2015] [Indexed: 01/12/2023]
Abstract
The basic Helix-Loop-Helix (bHLH) proteins represent a well-known class of transcriptional regulators. Many bHLH proteins act as heterodimers with members of a class of ubiquitous partners, the E proteins. A widely expressed class of inhibitory heterodimer partners-the Inhibitor of DNA-binding (ID) proteins-also exists. Genetic and molecular analyses in humans and in knockout mice implicate E proteins and ID proteins in a wide variety of diseases, belying the notion that they are non-specific partner proteins. Here, we explore relationships of E proteins and ID proteins to a variety of disease processes and highlight gaps in knowledge of disease mechanisms.
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Affiliation(s)
- Lan-Hsin Wang
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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Dixit A, Suri M. When the face says it all: dysmorphology in identifying syndromic causes of epilepsy. Pract Neurol 2016; 16:111-21. [PMID: 26864574 DOI: 10.1136/practneurol-2015-001247] [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] [Accepted: 11/12/2015] [Indexed: 11/04/2022]
Abstract
Identifying the underlying cause of epilepsy often helps in choosing the appropriate management, suggests the long-term prognosis and clarifies the risk of the same condition in relatives. Epilepsy has many causes and a small but significant proportion of affected people have an identifiable genetic cause. Here, we discuss the role of genetic testing in adults with epilepsy, focusing on dysmorphic features noticeable on physical examination that might provide a strong clue to a specific genetic syndrome. We give illustrative examples of recognisable facial 'gestalt'. An astute clinician can recognise such clues and significantly shorten the process of making the underlying diagnosis in their patient.
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Affiliation(s)
- Abhijit Dixit
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Mohnish Suri
- Department of Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
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Lim ECP, Brett M, Lai AHM, Lee SP, Tan ES, Jamuar SS, Ng ISL, Tan EC. Next-generation sequencing using a pre-designed gene panel for the molecular diagnosis of congenital disorders in pediatric patients. Hum Genomics 2015; 9:33. [PMID: 26666243 PMCID: PMC4678573 DOI: 10.1186/s40246-015-0055-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/22/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) has revolutionized genetic research and offers enormous potential for clinical application. Sequencing the exome has the advantage of casting the net wide for all known coding regions while targeted gene panel sequencing provides enhanced sequencing depths and can be designed to avoid incidental findings in adult-onset conditions. A HaloPlex panel consisting of 180 genes within commonly altered chromosomal regions is available for use on both the Ion Personal Genome Machine (PGM) and MiSeq platforms to screen for causative mutations in these genes. METHODS We used this Haloplex ICCG panel for targeted sequencing of 15 patients with clinical presentations indicative of an abnormality in one of the 180 genes. Sequencing runs were done using the Ion 318 Chips on the Ion Torrent PGM. Variants were filtered for known polymorphisms and analysis was done to identify possible disease-causing variants before validation by Sanger sequencing. When possible, segregation of variants with phenotype in family members was performed to ascertain the pathogenicity of the variant. RESULTS More than 97% of the target bases were covered at >20×. There was an average of 9.6 novel variants per patient. Pathogenic mutations were identified in five genes for six patients, with two novel variants. There were another five likely pathogenic variants, some of which were unreported novel variants. CONCLUSIONS In a cohort of 15 patients, we were able to identify a likely genetic etiology in six patients (40%). Another five patients had candidate variants for which further evaluation and segregation analysis are ongoing. Our results indicate that the HaloPlex ICCG panel is useful as a rapid, high-throughput and cost-effective screening tool for 170 of the 180 genes. There is low coverage for some regions in several genes which might have to be supplemented by Sanger sequencing. However, comparing the cost, ease of analysis, and shorter turnaround time, it is a good alternative to exome sequencing for patients whose features are suggestive of a genetic etiology involving one of the genes in the panel.
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Affiliation(s)
- Eileen C P Lim
- KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore.
| | - Maggie Brett
- KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore.
| | - Angeline H M Lai
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
| | - Siew-Peng Lee
- KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore.
| | - Ee-Shien Tan
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
| | - Saumya S Jamuar
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
| | - Ivy S L Ng
- Genetics Service, Department of Paediatrics, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
| | - Ene-Choo Tan
- KK Research Centre, KK Women's and Children's Hospital, 100 Bukit Timah Road, Singapore, 229899, Singapore. .,Paediatrics Academic Clinical Programme, SingHealth Duke-NUS Graduate Medical School, Singapore, 169857, Singapore.
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Tamberg L, Sepp M, Timmusk T, Palgi M. Introducing Pitt-Hopkins syndrome-associated mutations of TCF4 to Drosophila daughterless. Biol Open 2015; 4:1762-71. [PMID: 26621827 PMCID: PMC4736037 DOI: 10.1242/bio.014696] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Pitt-Hopkins syndrome (PTHS) is caused by haploinsufficiency of Transcription factor 4 (TCF4), one of the three human class I basic helix-loop-helix transcription factors called E-proteins. Drosophila has a single E-protein, Daughterless (Da), homologous to all three mammalian counterparts. Here we show that human TCF4 can rescue Da deficiency during fruit fly nervous system development. Overexpression of Da or TCF4 specifically in adult flies significantly decreases their survival rates, indicating that these factors are crucial even after development has been completed. We generated da transgenic fruit fly strains with corresponding missense mutations R578H, R580W, R582P and A614V found in TCF4 of PTHS patients and studied the impact of these mutations in vivo. Overexpression of wild type Da as well as human TCF4 in progenitor tissues induced ectopic sensory bristles and the rough eye phenotype. By contrast, overexpression of DaR580W and DaR582P that disrupt DNA binding reduced the number of bristles and induced the rough eye phenotype with partial lack of pigmentation, indicating that these act dominant negatively. Compared to the wild type, DaR578H and DaA614V were less potent in induction of ectopic bristles and the rough eye phenotype, respectively, suggesting that these are hypomorphic. All studied PTHS-associated mutations that we introduced into Da led to similar effects in vivo as the same mutations in TCF4 in vitro. Consequently, our Drosophila models of PTHS are applicable for further studies aiming to unravel the molecular mechanisms of this disorder. Summary: Introducing mutations of the TCF4 gene found in human patients into its fly orthologue daughterless allows the generation of Drosophila models for research into Pitt-Hopkins syndrome.
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Affiliation(s)
- Laura Tamberg
- Laboratory of Molecular Neurobiology, Department of Gene Technology, Tallinn University of Technology, Akadeemia Rd.15, Tallinn 12618, Estonia
| | - Mari Sepp
- Laboratory of Molecular Neurobiology, Department of Gene Technology, Tallinn University of Technology, Akadeemia Rd.15, Tallinn 12618, Estonia
| | - Tõnis Timmusk
- Laboratory of Molecular Neurobiology, Department of Gene Technology, Tallinn University of Technology, Akadeemia Rd.15, Tallinn 12618, Estonia
| | - Mari Palgi
- Laboratory of Molecular Neurobiology, Department of Gene Technology, Tallinn University of Technology, Akadeemia Rd.15, Tallinn 12618, Estonia
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Wang P, Lin M, Pedrosa E, Hrabovsky A, Zhang Z, Guo W, Lachman HM, Zheng D. CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment. Mol Autism 2015; 6:55. [PMID: 26491539 PMCID: PMC4612430 DOI: 10.1186/s13229-015-0048-6] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/10/2015] [Indexed: 01/24/2023] Open
Abstract
Background Disruptive mutation in the CHD8 gene is one of the top genetic risk factors in autism spectrum disorders (ASDs). Previous analyses of genome-wide CHD8 occupancy and reduced expression of CHD8 by shRNA knockdown in committed neural cells showed that CHD8 regulates multiple cell processes critical for neural functions, and its targets are enriched with ASD-associated genes. Methods To further understand the molecular links between CHD8 functions and ASD, we have applied the CRISPR/Cas9 technology to knockout one copy of CHD8 in induced pluripotent stem cells (iPSCs) to better mimic the loss-of-function status that would exist in the developing human embryo prior to neuronal differentiation. We then carried out transcriptomic and bioinformatic analyses of neural progenitors and neurons derived from the CHD8 mutant iPSCs. Results Transcriptome profiling revealed that CHD8 hemizygosity (CHD8+/−) affected the expression of several thousands of genes in neural progenitors and early differentiating neurons. The differentially expressed genes were enriched for functions of neural development, β-catenin/Wnt signaling, extracellular matrix, and skeletal system development. They also exhibited significant overlap with genes previously associated with autism and schizophrenia, as well as the downstream transcriptional targets of multiple genes implicated in autism. Providing important insight into how CHD8 mutations might give rise to macrocephaly, we found that seven of the twelve genes associated with human brain volume or head size by genome-wide association studies (e.g., HGMA2) were dysregulated in CHD8+/− neural progenitors or neurons. Conclusions We have established a renewable source of CHD8+/− iPSC lines that would be valuable for investigating the molecular and cellular functions of CHD8. Transcriptomic profiling showed that CHD8 regulates multiple genes implicated in ASD pathogenesis and genes associated with brain volume. Electronic supplementary material The online version of this article (doi:10.1186/s13229-015-0048-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ping Wang
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA
| | - Mingyan Lin
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA
| | - Erika Pedrosa
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA
| | - Anastasia Hrabovsky
- Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA
| | - Zheng Zhang
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA ; Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA
| | - Wenjun Guo
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA ; Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA
| | - Herbert M Lachman
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA ; Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA ; Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA ; Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, New York USA
| | - Deyou Zheng
- Department of Neurology, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA ; Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA ; Department of Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave, Bronx, NY 10461 USA
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Gonsales MC, Montenegro MA, Soler CV, Coan AC, Guerreiro MM, Lopes-Cendes I. Recent developments in the genetics of childhood epileptic encephalopathies: impact in clinical practice. ARQUIVOS DE NEURO-PSIQUIATRIA 2015; 73:946-58. [PMID: 26517219 DOI: 10.1590/0004-282x20150122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/20/2015] [Indexed: 01/03/2023]
Abstract
Recent advances in molecular genetics led to the discovery of several genes for childhood epileptic encephalopathies (CEEs). As the knowledge about the genes associated with this group of disorders develops, it becomes evident that CEEs present a number of specific genetic characteristics, which will influence the use of molecular testing for clinical purposes. Among these, there are the presence of marked genetic heterogeneity and the high frequency of de novo mutations. Therefore, the main objectives of this review paper are to present and discuss current knowledge regarding i) new genetic findings in CEEs, ii) phenotype-genotype correlations in different forms of CEEs; and, most importantly, iii) the impact of these new findings in clinical practice. Accompanying this text we have included a comprehensive table, containing the list of genes currently known to be involved in the etiology of CEEs.
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Affiliation(s)
- Marina C Gonsales
- Instituto Brasileiro de Neurociências e Neurotecnologia, Faculdade de Ciências Médicas, Universidade de Campinas, Campinas, SP, Brazil
| | - Maria Augusta Montenegro
- Instituto Brasileiro de Neurociências e Neurotecnologia, Faculdade de Ciências Médicas, Universidade de Campinas, Campinas, SP, Brazil
| | - Camila V Soler
- Instituto Brasileiro de Neurociências e Neurotecnologia, Faculdade de Ciências Médicas, Universidade de Campinas, Campinas, SP, Brazil
| | - Ana Carolina Coan
- Instituto Brasileiro de Neurociências e Neurotecnologia, Faculdade de Ciências Médicas, Universidade de Campinas, Campinas, SP, Brazil
| | - Marilisa M Guerreiro
- Instituto Brasileiro de Neurociências e Neurotecnologia, Faculdade de Ciências Médicas, Universidade de Campinas, Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Instituto Brasileiro de Neurociências e Neurotecnologia, Faculdade de Ciências Médicas, Universidade de Campinas, Campinas, SP, Brazil
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Grubišić V, Kennedy AJ, Sweatt JD, Parpura V. Pitt-Hopkins Mouse Model has Altered Particular Gastrointestinal Transits In Vivo. Autism Res 2015; 8:629-33. [PMID: 25728630 PMCID: PMC5724775 DOI: 10.1002/aur.1467] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 02/04/2015] [Indexed: 12/31/2022]
Abstract
Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder, classified as an autism spectrum disorder that is caused by the haploinsufficiency of Transcription Factor 4 (TCF4). The most common non-neurological symptoms in PTHS patients are gastrointestinal (GI) disturbances, mainly gastroesophageal reflux and severe constipation (in about 30 and 75% of PTHS patients, respectively). We hypothesized that the recently recognized mouse model of PTHS will exhibit problems with their gut function. We conducted series of in vivo tests on 15- to 19- week old male mice, heterozygous for the TCF4 functional deletion, mimicking the TCF4 haploinsufficiency in PTHS patients, and their wild type littermates. Data collection and initial analysis were performed blindly, that is, the genotyping key was received after the mean values were calculated for each individual animal, and then mean/median of each group was subsequently calculated. Body weight, fecal pellet output, and fluid content were similar between the groups, indicating normal gross growth of PTHS mice and their overall physiological GI motility and intestinal secretion/absorption. There were no significant differences in gut length and gross appearance pointing out that PTHS mice have normal gut in gross anatomical terms. However, the assessment of gut transit indicates that, while whole-gut transit velocity was similar between the groups, the upper GI and distal colon transit velocities were significantly reduced in the PTHS mice. This is the first evidence of specific gut related problems in the PTHS mice. Our study also validates the TCF4 functional knockout mice as an animal model to study PTHS-associated GI disturbances.
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Affiliation(s)
- Vladimir Grubišić
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Andrew J Kennedy
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - J David Sweatt
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Vladimir Parpura
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
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Marangi G, Zollino M. Pitt-Hopkins Syndrome and Differential Diagnosis: A Molecular and Clinical Challenge. J Pediatr Genet 2015; 4:168-76. [PMID: 27617128 DOI: 10.1055/s-0035-1564570] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 12/30/2022]
Abstract
Pitt-Hopkins syndrome is an emerging neurodevelopmental disorder caused by haploinsufficiency of the TCF4 gene on chromosome 18q21. It is characterized by severe intellectual disability, seizures, microcephaly, constipation and a distinctive facial gestalt. Although the overlapping phenotype of microcephaly, epilepsy, absent speech and constipation represents a challenge for the differential diagnosis with Angelman syndrome, Rett syndrome and Mowat-Wilson syndrome, distinctive of Pitt-Hopkins syndrome are breathing abnormalities, that can occur as either hyperventilation episodes or apnea crises, and a typical facial dysmorphism, including bitemporal narrowing, squared forehead, deep-set eyes, peculiar nose conformation, with broad nasal bridge, down-turned nasal tip and flaring nostrils, typical shape of the mouth, with a tented and M shaped upper lip, and widely spaced teeth. The occurrence of these signs in variable association of uncoordinated movements, microcephaly of postnatal onset, eye abnormalities, constipation, epilepsy and subtle brain abnormalities is highly predictive of a TCF4 mutation, making it possible to plan a genetic test of choice among severe encephalopathies. Angelman syndrome represents the nosological condition closest to Pitt-Hopkins syndrome.
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Affiliation(s)
- Giuseppe Marangi
- Department of Laboratory Medicine, Institute of Medical Genetics, Catholic University, Rome, Italy
| | - Marcella Zollino
- Department of Laboratory Medicine, Institute of Medical Genetics, Catholic University, Rome, Italy
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Cody JD, Sebold C, Heard P, Carter E, Soileau B, Hasi-Zogaj M, Hill A, Rupert D, Perry B, O'Donnell L, Gelfond J, Lancaster J, Fox PT, Hale DE. Consequences of chromsome18q deletions. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2015; 169:265-80. [PMID: 26235940 DOI: 10.1002/ajmg.c.31446] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 06/28/2015] [Indexed: 11/11/2022]
Abstract
Providing clinically relevant prognoses and treatment information for people with a chromsome18q deletion is particularly challenging because every unrelated person has a unique region of hemizygosity. The hemizygous region can involve almost any region of 18q including between 1 and 101 genes (30 Mb of DNA). Most individuals have terminal deletions, but in our cohort of over 350 individuals 23% have interstitial deletions. Because of this heterogeneity, we take a gene by gene approach to understanding the clinical consequences. There are 196 genes on 18q. We classified 133 of them as dosage insensitive, 15 (8%) as dosage sensitive leading to haploinsufficiency while another 10 (5%) have effects that are conditionally haploinsufficient and are dependent on another factor, genetic or environmental in order to cause an abnormal phenotype. Thirty-seven genes (19%) have insufficient information to classify their dosage effect. Phenotypes attributed to single genes include: congenital heart disease, minor bone morphology changes, central nervous system dysmyelination, expressive speech delay, vesicouretreral reflux, polyposis, Pitt-Hopkins syndrome, intellectual disability, executive function impairment, male infertility, aural atresia, and high frequency sensorineural hearing loss. Additionally, identified critical regions for other phenotypes include: adolescent idiopathic scoliosis and pectus excavatum, Virchow-Robin perivascular spaces, small corpus callosum, strabismus, atopic disorders, mood disorder, IgA deficiency, nystagmus, congenital heart disease, kidney malformation, vertical talus, CNS dysmyelination growth hormone deficiency and cleft palate. Together these findings make it increasingly feasible to compile an individualized syndrome description based on each person's individuated genotype. Future work will focus on understanding molecular mechanisms leading to treatment.
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Grubišić V, Parpura V. The second brain in autism spectrum disorder: could connexin 43 expressed in enteric glial cells play a role? Front Cell Neurosci 2015; 9:242. [PMID: 26190971 PMCID: PMC4490256 DOI: 10.3389/fncel.2015.00242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 06/15/2015] [Indexed: 12/28/2022] Open
Affiliation(s)
- Vladimir Grubišić
- Department of Neurobiology, University of Alabama at Birmingham Birmingham, AL, USA ; Neuroscience Program, Department of Physiology, Michigan State University East Lansing, MI, USA
| | - Vladimir Parpura
- Department of Neurobiology, University of Alabama at Birmingham Birmingham, AL, USA
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Abstract
Background In recent years, high-throughput protein interaction identification methods have generated a large amount of data. When combined with the results from other in vivo and in vitro experiments, a complex set of relationships between biological molecules emerges. The growing popularity of network analysis and data mining has allowed researchers to recognize indirect connections between these molecules. Due to the interdependent nature of network entities, evaluating proteins in this context can reveal relationships that may not otherwise be evident. Methods We examined the human protein interaction network as it relates to human illness using the Disease Ontology. After calculating several topological metrics, we trained an alternating decision tree (ADTree) classifier to identify disease-associated proteins. Using a bootstrapping method, we created a tree to highlight conserved characteristics shared by many of these proteins. Subsequently, we reviewed a set of non-disease-associated proteins that were misclassified by the algorithm with high confidence and searched for evidence of a disease relationship. Results Our classifier was able to predict disease-related genes with 79% area under the receiver operating characteristic (ROC) curve (AUC), which indicates the tradeoff between sensitivity and specificity and is a good predictor of how a classifier will perform on future data sets. We found that a combination of several network characteristics including degree centrality, disease neighbor ratio, eccentricity, and neighborhood connectivity help to distinguish between disease- and non-disease-related proteins. Furthermore, the ADTree allowed us to understand which combinations of strongly predictive attributes contributed most to protein-disease classification. In our post-processing evaluation, we found several examples of potential novel disease-related proteins and corresponding literature evidence. In addition, we showed that first- and second-order neighbors in the PPI network could be used to identify likely disease associations. Conclusions We analyzed the human protein interaction network and its relationship to disease and found that both the number of interactions with other proteins and the disease relationship of neighboring proteins helped to determine whether a protein had a relationship to disease. Our classifier predicted many proteins with no annotated disease association to be disease-related, which indicated that these proteins have network characteristics that are similar to disease-related proteins and may therefore have disease associations not previously identified. By performing a post-processing step after the prediction, we were able to identify evidence in literature supporting this possibility. This method could provide a useful filter for experimentalists searching for new candidate protein targets for drug repositioning and could also be extended to include other network and data types in order to refine these predictions.
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Gaffney C, McNally P. Successful use of acetazolamide for central apnea in a child with Pitt-Hopkins syndrome. Am J Med Genet A 2015; 167:1423. [PMID: 25900839 DOI: 10.1002/ajmg.a.37034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 02/07/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Claire Gaffney
- Department of Respiratory Medicine, Our Lady's Children's Hospital Crumlin (OLCHC), Dublin, Ireland
| | - Paul McNally
- Department of Respiratory Medicine, Our Lady's Children's Hospital Crumlin (OLCHC), Dublin, Ireland
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MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers. Neuron 2015; 86:247-63. [PMID: 25801704 DOI: 10.1016/j.neuron.2015.02.038] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/30/2015] [Accepted: 02/20/2015] [Indexed: 11/20/2022]
Abstract
Organismal development requires the precise coordination of genetic programs to regulate cell fate and function. MEF2 transcription factors (TFs) play essential roles in this process but how these broadly expressed factors contribute to the generation of specific cell types during development is poorly understood. Here we show that despite being expressed in virtually all mammalian tissues, in the retina MEF2D binds to retina-specific enhancers and controls photoreceptor cell development. MEF2D achieves specificity by cooperating with a retina-specific factor CRX, which recruits MEF2D away from canonical MEF2 binding sites and redirects it to retina-specific enhancers that lack the consensus MEF2-binding sequence. Once bound to retina-specific enhancers, MEF2D and CRX co-activate the expression of photoreceptor-specific genes that are critical for retinal function. These findings demonstrate that broadly expressed TFs acquire specific functions through competitive recruitment to enhancers by tissue-specific TFs and through selective activation of these enhancers to regulate tissue-specific genes.
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Poot M. Connecting the CNTNAP2 Networks with Neurodevelopmental Disorders. Mol Syndromol 2015; 6:7-22. [PMID: 25852443 DOI: 10.1159/000371594] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2014] [Indexed: 12/23/2022] Open
Abstract
Based on genomic rearrangements and copy number variations, the contactin-associated protein-like 2 gene (CNTNAP2) has been implicated in neurodevelopmental disorders such as Gilles de la Tourette syndrome, intellectual disability, obsessive compulsive disorder, cortical dysplasia-focal epilepsy syndrome, autism, schizophrenia, Pitt-Hopkins syndrome, and attention deficit hyperactivity disorder. To explain the phenotypic pleiotropy of CNTNAP2 alterations, several hypotheses have been put forward. Those include gene disruption, loss of a gene copy by a heterozygous deletion, altered regulation of gene expression due to loss of transcription factor binding and DNA methylation sites, and mutations in the amino acid sequence of the encoded protein which may provoke altered interactions of the CNTNAP2-encoded protein, Caspr2, with other proteins. Also exome sequencing, which covers <0.2% of the CNTNAP2 genomic DNA, has revealed numerous single nucleotide variants in healthy individuals and in patients with neurodevelopmental disorders. In some of these disorders, disruption of CNTNAP2 may be interpreted as a susceptibility factor rather than a directly causative mutation. In addition to being associated with impaired development of language, CNTNAP2 may turn out to be a central node in the molecular networks controlling neurodevelopment. This review discusses the impact of CNTNAP2 mutations on its functioning at multiple levels of the combinatorial genetic networks that govern brain development. In addition, recommendations for genomic testing in the context of clinical genetic management of patients with neurodevelopmental disorders and their families are put forward.
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Affiliation(s)
- Martin Poot
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
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Tan WH, Bird LM, Thibert RL, Williams CA. If not Angelman, what is it? A review of Angelman-like syndromes. Am J Med Genet A 2014; 164A:975-92. [PMID: 24779060 DOI: 10.1002/ajmg.a.36416] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Angelman syndrome (AS) is caused by a lack of expression of the maternally inherited UBE3A gene in the brain. However, about 10% of individuals with a clinical diagnosis of AS do not have an identifiable molecular defect. It is likely that most of those individuals have an AS-like syndrome that is clinically and molecularly distinct from AS. These AS-like syndromes can be broadly classified into chromosomal microdeletion and microduplication syndromes, and single-gene disorders. The microdeletion/microduplication syndromes are now easily identified by chromosomal microarray analysis and include Phelan–McDermid syndrome (chromosome 22q13.3 deletion), MBD5 haploinsufficiency syndrome (chromosome 2q23.1 deletion), and KANSL1 haploinsufficiency syndrome (chromosome 17q21.31 deletion). The single-gene disorders include Pitt–Hopkins syndrome (TCF4), Christianson syndrome (SLC9A6), Mowat–Wilson syndrome (ZEB2), Kleefstra syndrome (EHMT1), and Rett (MECP2) syndrome. They also include disorders due to mutations in HERC2, adenylosuccinase lyase (ADSL), CDKL5, FOXG1, MECP2 (duplications), MEF2C, and ATRX. Although many of these single-gene disorders can be caused by chromosomal microdeletions resulting in haploinsufficiency of the critical gene, the individual disorders are often caused by intragenic mutations that cannot be detected by chromosomal microarray analysis. We provide an overview of the clinical features of these syndromes, comparing and contrasting them with AS, in the hope that it will help guide clinicians in the diagnostic work-up of individuals with AS-like syndromes.
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Malik S, Percin FE, Bornholdt D, Albrecht B, Percesepe A, Koch MC, Landi A, Fritz B, Khan R, Mumtaz S, Akarsu NA, Grzeschik KH. Mutations affecting the BHLHA9 DNA-binding domain cause MSSD, mesoaxial synostotic syndactyly with phalangeal reduction, Malik-Percin type. Am J Hum Genet 2014; 95:649-59. [PMID: 25466284 DOI: 10.1016/j.ajhg.2014.10.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 10/27/2014] [Indexed: 12/25/2022] Open
Abstract
Mesoaxial synostotic syndactyly, Malik-Percin type (MSSD) (syndactyly type IX) is a rare autosomal-recessive nonsyndromic digit anomaly with only two affected families reported so far. We previously showed that the trait is genetically distinct from other syndactyly types, and through autozygosity mapping we had identified a locus on chromosome 17p13.3 for this unique limb malformation. Here, we extend the number of independent pedigrees from various geographic regions segregating MSSD to a total of six. We demonstrate that three neighboring missense mutations affecting the highly conserved DNA-binding region of the basic helix-loop-helix A9 transcription factor (BHLHA9) are associated with this phenotype. Recombinant BHLHA9 generated by transient gene expression is shown to be located in the cytoplasm and the cell nucleus. Transcription factors 3, 4, and 12, members of the E protein (class I) family of helix-loop-helix transcription factors, are highlighted in yeast two-hybrid analysis as potential dimerization partners for BHLHA9. In the presence of BHLHA9, the potential of these three proteins to activate expression of an E-box-regulated target gene is reduced considerably. BHLHA9 harboring one of the three substitutions detected in MSSD-affected individuals eliminates entirely the transcription activation by these class I bHLH proteins. We conclude that by dimerizing with other bHLH protein monomers, BHLHA9 could fine tune the expression of regulatory factors governing determination of central limb mesenchyme cells, a function made impossible by altering critical amino acids in the DNA binding domain. These findings identify BHLHA9 as an essential player in the regulatory network governing limb morphogenesis in humans.
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Affiliation(s)
- Sajid Malik
- Zentrum fuer Humangenetik, Philipps-Universitaet Marburg, 35033 Marburg, Germany; Department of Animal Sciences, Human Genetics Program, Faculty of Biological Sciences, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Ferda E Percin
- Department of Medical Genetics, Faculty of Medicine, Gazi University, Besevler, 06500 Ankara, Turkey
| | - Dorothea Bornholdt
- Zentrum fuer Humangenetik, Philipps-Universitaet Marburg, 35033 Marburg, Germany
| | - Beate Albrecht
- Institut fuer Humangenetik, Universitaetsklinikum Essen, Universitaet Duisburg-Essen, 45147 Essen, Germany
| | - Antonio Percesepe
- Department of Mother and Child, Medical Genetics Unit, University Hospital of Modena, 41124 Modena, Italy
| | - Manuela C Koch
- Zentrum fuer Humangenetik, Philipps-Universitaet Marburg, 35033 Marburg, Germany
| | - Antonio Landi
- Department of Hand Surgery and Microsurgery, University Hospital of Modena, 41100 Modena, Italy
| | - Barbara Fritz
- Zentrum fuer Humangenetik, Philipps-Universitaet Marburg, 35033 Marburg, Germany
| | - Rizwan Khan
- Department of Animal Sciences, Human Genetics Program, Faculty of Biological Sciences, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Sara Mumtaz
- Department of Animal Sciences, Human Genetics Program, Faculty of Biological Sciences, Quaid-i-Azam University, 45320 Islamabad, Pakistan
| | - Nurten A Akarsu
- Department of Medical Genetics, Gene Mapping Laboratory, Hacettepe University Medical Faculty, Sihhiye, 06100 Ankara, Turkey
| | - Karl-Heinz Grzeschik
- Zentrum fuer Humangenetik, Philipps-Universitaet Marburg, 35033 Marburg, Germany.
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Hill MJ, Forrest MP, Martin-Rendon E, Blake DJ. Association of Transcription Factor 4 (TCF4) variants with schizophrenia and intellectual disability. Curr Behav Neurosci Rep 2014. [DOI: 10.1007/s40473-014-0027-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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129
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A new syndrome of intellectual disability with dysmorphism due toTBL1XR1deletion. Am J Med Genet A 2014; 167A:164-8. [DOI: 10.1002/ajmg.a.36759] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/08/2014] [Indexed: 11/07/2022]
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Redin C, Gérard B, Lauer J, Herenger Y, Muller J, Quartier A, Masurel-Paulet A, Willems M, Lesca G, El-Chehadeh S, Le Gras S, Vicaire S, Philipps M, Dumas M, Geoffroy V, Feger C, Haumesser N, Alembik Y, Barth M, Bonneau D, Colin E, Dollfus H, Doray B, Delrue MA, Drouin-Garraud V, Flori E, Fradin M, Francannet C, Goldenberg A, Lumbroso S, Mathieu-Dramard M, Martin-Coignard D, Lacombe D, Morin G, Polge A, Sukno S, Thauvin-Robinet C, Thevenon J, Doco-Fenzy M, Genevieve D, Sarda P, Edery P, Isidor B, Jost B, Olivier-Faivre L, Mandel JL, Piton A. Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing. J Med Genet 2014; 51:724-36. [PMID: 25167861 PMCID: PMC4215287 DOI: 10.1136/jmedgenet-2014-102554] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Intellectual disability (ID) is characterised by an extreme genetic heterogeneity. Several hundred genes have been associated to monogenic forms of ID, considerably complicating molecular diagnostics. Trio-exome sequencing was recently proposed as a diagnostic approach, yet remains costly for a general implementation. Methods We report the alternative strategy of targeted high-throughput sequencing of 217 genes in which mutations had been reported in patients with ID or autism as the major clinical concern. We analysed 106 patients with ID of unknown aetiology following array-CGH analysis and other genetic investigations. Ninety per cent of these patients were males, and 75% sporadic cases. Results We identified 26 causative mutations: 16 in X-linked genes (ATRX, CUL4B, DMD, FMR1, HCFC1, IL1RAPL1, IQSEC2, KDM5C, MAOA, MECP2, SLC9A6, SLC16A2, PHF8) and 10 de novo in autosomal-dominant genes (DYRK1A, GRIN1, MED13L, TCF4, RAI1, SHANK3, SLC2A1, SYNGAP1). We also detected four possibly causative mutations (eg, in NLGN3) requiring further investigations. We present detailed reasoning for assigning causality for each mutation, and associated patients’ clinical information. Some genes were hit more than once in our cohort, suggesting they correspond to more frequent ID-associated conditions (KDM5C, MECP2, DYRK1A, TCF4). We highlight some unexpected genotype to phenotype correlations, with causative mutations being identified in genes associated to defined syndromes in patients deviating from the classic phenotype (DMD, TCF4, MECP2). We also bring additional supportive (HCFC1, MED13L) or unsupportive (SHROOM4, SRPX2) evidences for the implication of previous candidate genes or mutations in cognitive disorders. Conclusions With a diagnostic yield of 25% targeted sequencing appears relevant as a first intention test for the diagnosis of ID, but importantly will also contribute to a better understanding regarding the specific contribution of the many genes implicated in ID and autism.
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Affiliation(s)
- Claire Redin
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Bénédicte Gérard
- Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Julia Lauer
- Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yvan Herenger
- Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jean Muller
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Angélique Quartier
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Alice Masurel-Paulet
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Marjolaine Willems
- Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Gaétan Lesca
- Département de Génétique Médicale, Hospices Civils de Lyon, Bron, France
| | - Salima El-Chehadeh
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Stéphanie Le Gras
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Serge Vicaire
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Muriel Philipps
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Michaël Dumas
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Véronique Geoffroy
- Plateforme de Bioinformatique de Strasbourg (BIPS), IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Claire Feger
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Nicolas Haumesser
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Yves Alembik
- Département de Génétique, CHU de Hautepierre, Strasbourg, France
| | - Magalie Barth
- Départment de Biochimie et de Génétique, CHU d'Angers, Angers, France
| | - Dominique Bonneau
- Départment de Biochimie et de Génétique, CHU d'Angers, Angers, France
| | - Estelle Colin
- Départment de Biochimie et de Génétique, CHU d'Angers, Angers, France
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, INSERM U1112, Faculté de Médecine de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Bérénice Doray
- Département de Génétique, CHU de Hautepierre, Strasbourg, France
| | - Marie-Ange Delrue
- CHU de Bordeaux, Génétique Médicale, Université de Bordeaux, Laboratoire MRGM, Bordeaux, France
| | | | - Elisabeth Flori
- Département de Génétique, CHU de Hautepierre, Strasbourg, France
| | - Mélanie Fradin
- Service de Génétique Médicale, Centre De Référence Anomalies du Développement, CHU de Rennes, Rennes, France
| | | | | | | | | | | | - Didier Lacombe
- CHU de Bordeaux, Génétique Médicale, Université de Bordeaux, Laboratoire MRGM, Bordeaux, France
| | - Gilles Morin
- Unité de Génétique Clinique, CHU d'Amiens, Amiens, France
| | - Anne Polge
- Laboratoire de Biochimie, CHU de Nîmes, Nîmes, France
| | - Sylvie Sukno
- Service de Neuropédiatrie, Hôpital Saint Vincent de Paul, Groupe Hospitalier de l'Institut Catholique Lillois, Faculté Libre de Médecine, Lille, France
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | | | - David Genevieve
- Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Pierre Sarda
- Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Patrick Edery
- Département de Génétique Médicale, Hospices Civils de Lyon, Bron, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - Bernard Jost
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Laurence Olivier-Faivre
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Jean-Louis Mandel
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Amélie Piton
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
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A girl with West syndrome and autistic features harboring a de novo TBL1XR1 mutation. J Hum Genet 2014; 59:581-3. [DOI: 10.1038/jhg.2014.71] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/07/2014] [Accepted: 07/17/2014] [Indexed: 11/08/2022]
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Watson CM, Crinnion LA, Tzika A, Mills A, Coates A, Pendlebury M, Hewitt S, Harrison SM, Daly C, Roberts P, Carr IM, Sheridan EG, Bonthron DT. Diagnostic whole genome sequencing and split-read mapping for nucleotide resolution breakpoint identification in CNTNAP2 deficiency syndrome. Am J Med Genet A 2014; 164A:2649-55. [PMID: 25045150 DOI: 10.1002/ajmg.a.36679] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 06/16/2014] [Indexed: 11/08/2022]
Abstract
Whole genome sequencing (WGS) has the potential to report on all types of genetic abnormality, thus converging diagnostic testing on a single methodology. Although WGS at sufficient depth for robust detection of point mutations is still some way from being affordable for diagnostic purposes, low-coverage WGS is already an excellent method for detecting copy number variants ("CNVseq"). We report on a family in which individuals presented with a presumed autosomal recessive syndrome of severe intellectual disability and epilepsy. Array comparative genomic hybridization (CGH) analysis had revealed a homozygous deletion apparently lying within intron 3 of CNTNAP2. Since this was too small for confirmation by FISH, CNVseq was used, refining the extent of this mutation to approximately 76.8 kb, encompassing CNTNAP2 exon 3 (an out-of-frame deletion). To characterize the precise breakpoints and provide a rapid molecular diagnostic test, we resequenced the CNVseq library at medium coverage and performed split read mapping. This yielded information for a multiplex polymerase chain reaction (PCR) assay, used for cascade screening and/or prenatal diagnosis in this family. This example demonstrates a rapid, low-cost approach to converting molecular cytogenetic findings into robust PCR-based tests.
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Affiliation(s)
- Christopher M Watson
- Yorkshire Regional Genetics Service, St. James's University Hospital, Leeds, United Kingdom; School of Medicine, University of Leeds, St. James's University Hospital, Leeds, United Kingdom
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Seltzer LE, Paciorkowski AR. Genetic disorders associated with postnatal microcephaly. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2014; 166C:140-55. [PMID: 24839169 DOI: 10.1002/ajmg.c.31400] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Several genetic disorders are characterized by normal head size at birth, followed by deceleration in head growth resulting in postnatal microcephaly. Among these are classic disorders such as Angelman syndrome and MECP2-related disorder (formerly Rett syndrome), as well as more recently described clinical entities associated with mutations in CASK, CDKL5, CREBBP, and EP300 (Rubinstein-Taybi syndrome), FOXG1, SLC9A6 (Christianson syndrome), and TCF4 (Pitt-Hopkins syndrome). These disorders can be identified clinically by phenotyping across multiple neurodevelopmental and neurobehavioral realms, and enough data are available to recognize these postnatal microcephaly disorders as separate diagnostic entities in their own right. A second diagnostic grouping, comprised of Warburg MICRO syndrome, Cockayne syndrome, and Cerebral-oculo-facial skeletal syndrome, share similar features of somatic growth failure, ophthalmologic, and dysmorphologic features. Many postnatal microcephaly syndromes are caused by mutations in genes important in the regulation of gene expression in the developing forebrain and hindbrain, although important synaptic structural genes also play a role. This is an emerging group of disorders with a fascinating combination of brain malformations, specific epilepsies, movement disorders, and other complex neurobehavioral abnormalities.
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Trakadis YJ, Buote C, Therriault JF, Jacques PÉ, Larochelle H, Lévesque S. PhenoVar: a phenotype-driven approach in clinical genomics for the diagnosis of polymalformative syndromes. BMC Med Genomics 2014; 7:22. [PMID: 24884844 PMCID: PMC4030287 DOI: 10.1186/1755-8794-7-22] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 04/24/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND We propose a phenotype-driven analysis of encrypted exome data to facilitate the widespread implementation of exome sequencing as a clinical genetic screening test.Twenty test-patients with varied syndromes were selected from the literature. For each patient, the mutation, phenotypic data, and genetic diagnosis were available. Next, control exome-files, each modified to include one of these twenty mutations, were assigned to the corresponding test-patients. These data were used by a geneticist blinded to the diagnoses to test the efficiency of our software, PhenoVar. The score assigned by PhenoVar to any genetic diagnosis listed in OMIM (Online Mendelian Inheritance in Man) took into consideration both the patient's phenotype and all variations present in the corresponding exome. The physician did not have access to the individual mutations. PhenoVar filtered the search using a cut-off phenotypic match threshold to prevent undesired discovery of incidental findings and ranked the OMIM entries according to diagnostic score. RESULTS When assigning the same weight to all variants in the exome, PhenoVar predicted the correct diagnosis in 10/20 patients, while in 15/20 the correct diagnosis was among the 4 highest ranked diagnoses. When assigning a higher weight to variants known, or bioinformatically predicted, to cause disease, PhenoVar's yield increased to 14/20 (18/20 in top 4). No incidental findings were identified using our cut-off phenotypic threshold. CONCLUSION The phenotype-driven approach described could render widespread use of ES more practical, ethical and clinically useful. The implications about novel disease identification, advancement of complex diseases and personalized medicine are discussed.
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Affiliation(s)
- Yannis J Trakadis
- Department of Medical Genetics, McGill University Health Centre, Montreal, Canada.
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Drosophila models of early onset cognitive disorders and their clinical applications. Neurosci Biobehav Rev 2014; 46 Pt 2:326-42. [PMID: 24661984 DOI: 10.1016/j.neubiorev.2014.01.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/28/2014] [Accepted: 01/31/2014] [Indexed: 12/28/2022]
Abstract
The number of genes known to cause human monogenic diseases is increasing rapidly. For the extremely large, genetically and phenotypically heterogeneous group of intellectual disability (ID) disorders, more than 600 causative genes have been identified to date. However, knowledge about the molecular mechanisms and networks disrupted by these genetic aberrations is lagging behind. The fruit fly Drosophila has emerged as a powerful model organism to close this knowledge gap. This review summarizes recent achievements that have been made in this model and envisions its future contribution to our understanding of ID genetics and neuropathology. The available resources and efficiency of Drosophila place it in a position to tackle the main challenges in the field: mapping functional modules of ID genes to provide conceptually novel insights into the genetic control of cognition, tailored functional studies to improve 'next-generation' diagnostics, and identification of reversible ID phenotypes and medication. Drosophila's behavioral repertoire and powerful genetics also open up perspectives for modeling genetically complex forms of ID and neuropsychiatric disorders, which overlap in their genetic etiologies. In conclusion, Drosophila provides many opportunities to advance future medical genomics of early onset cognitive disorders.
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hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex. PLoS One 2014; 9:e90957. [PMID: 24608264 PMCID: PMC3946611 DOI: 10.1371/journal.pone.0090957] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/05/2014] [Indexed: 02/05/2023] Open
Abstract
hCLE/C14orf166 is a nuclear and cytoplasmic protein that interacts with the RNAP II, modulates nuclear RNA metabolism and is present in cytoplasmic RNA granules involved in localized translation. Here we have studied whether hCLE shares common interactors in the nucleus and the cytosol, which could shed light on its participation in the sequential phases of RNA metabolism. Nuclear and cytoplasmic purified hCLE-associated factors were identified and proteins involved in mRNA metabolism, motor-related proteins, cytoskeletal and translation-related factors were found. Purified hCLE complexes also contain RNAs and as expected some hCLE-interacting proteins (DDX1, HSPC117, FAM98B) were found both in the nucleus and the cytoplasm. Moreover, endogenous hCLE fractionates in protein complexes together with DDX1, HSPC117 and FAM98B and silencing of hCLE down-regulates their nuclear and cytosolic accumulation levels. Using a photoactivatable hCLE-GFP protein, nuclear import and export of hCLE was observed indicating that hCLE is a shuttling protein. Interestingly, hCLE nuclear import required active transcription, as did the import of DDX1, HSPC117 and FAM98B proteins. The data indicate that hCLE probably as a complex with DDX1, HSPC117 and FAM98B shuttles between the nucleus and the cytoplasm transporting RNAs suggesting that this complex has a prominent role on nuclear and cytoplasmic RNA fate.
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137
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The emerging roles of TCF4 in disease and development. Trends Mol Med 2014; 20:322-31. [PMID: 24594265 DOI: 10.1016/j.molmed.2014.01.010] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 01/28/2014] [Accepted: 01/30/2014] [Indexed: 10/25/2022]
Abstract
Genome-wide association studies have identified common variants in transcription factor 4 (TCF4) as susceptibility loci for schizophrenia, Fuchs' endothelial corneal dystrophy, and primary sclerosing cholangitis. By contrast, rare TCF4 mutations cause Pitt-Hopkins syndrome, a disorder characterized by intellectual disability and developmental delay, and have also been described in patients with other neurodevelopmental disorders. TCF4 therefore sits at the nexus between common and rare disorders. TCF4 interacts with other basic helix-loop-helix proteins, forming transcriptional networks that regulate the differentiation of several distinct cell types. Here, we review the role of TCF4 in these seemingly diverse disorders and discuss recent data implicating TCF4 as an important regulator of neurodevelopment and epithelial-mesenchymal transition.
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138
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Abstract
Dendritic cells (DCs) are professional antigen presenting cells involved critically not only in provoking innate immune responses but also in establishing adaptive immune responses. Dendritic cells are heterogenous and divided into several subsets, including plasmactyoid DCs (pDCs) and several types of conventional DCs (cDCs), which show subset-specific functions. Plasmactyoid DCs are featured by their ability to produce large amounts of type I interferons (IFNs) in response to nucleic acid sensors, TLR7 and TLR9 and involved in anti-viral immunity and pathogenesis of certain autoimmune disorders such as psoriasis. Conventional DCs include the DC subsets with high crosspresentation activity, which contributes to anti-viral and anti-tumor immunity. These subsets are generated from hematopoietic stem cells (HSCs) via several intermediate progenitors and the development is regulated by the transcriptional mechanisms in which subset-specific transcription factors play major roles. We have recently found that an Ets family transcription factor, SPI-B, which is abundantly expressed in pDCs among DC subsets, plays critical roles in functions and late stage development of pDCs. SPI-B functions in cooperation with other transcription factors, especially, interferon regulatory factor (IRF) family members. Here we review the transcription factor-based molecular mechanisms for generation and functions of DCs, mainly by focusing on the roles of SPI-B and its relatives.
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139
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McCarroll SA, Hyman SE. Progress in the genetics of polygenic brain disorders: significant new challenges for neurobiology. Neuron 2013; 80:578-87. [PMID: 24183011 DOI: 10.1016/j.neuron.2013.10.046] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Advances in genome analysis, accompanied by the assembly of large patient cohorts, are making possible successful genetic analyses of polygenic brain disorders. If the resulting molecular clues, previously hidden in the genomes of affected individuals, are to yield useful information about pathogenesis and inform the discovery of new treatments, neurobiology will have to rise to many difficult challenges. Here we review the underlying logic of the genetic investigations, describe in more detail progress in schizophrenia and autism, and outline the challenges for neurobiology that lie ahead. We argue that technologies at the disposal of neuroscience are adequately advanced to begin to study the biology of common and devastating polygenic disorders.
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Affiliation(s)
- Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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140
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Inati A, Abbas HA, Korjian S, Daaboul Y, Harajeily M, Saab R. A case of Pitt-Hopkins syndrome with absence of hyperventilation. J Child Neurol 2013; 28:1698-701. [PMID: 23248353 DOI: 10.1177/0883073812468054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pitt-Hopkins syndrome is characterized by mental retardation, hyperventilation, and dysmorphic features due to TCF4 mutations. We report a case of Pitt-Hopkins syndrome in a 2½-year-old boy presenting with psychomotor retardation, recurrent respiratory tract infections, and dysmorphic features with absence of hyperventilation or other breathing abnormalities. Comparative genomic hybridization and quantitative real-time polymerase chain reaction were used to confirm TCF4 haploinsufficiency. Pitt-Hopkins syndrome is a rare debilitating disease that should be in the differential diagnosis of other neurodevelopmental disorders characterized by mental retardation and hypotonicity despite the absence of hyperapnea and seizures. Quantitative real-time polymerase chain reaction is another method to identify TCF4 and to confirm Pitt-Hopkins syndrome diagnosis.
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Affiliation(s)
- Adlette Inati
- 1Department of Pediatrics, Lebanese American University and University Medical Center Rizk Hospital, Beirut, Lebanon
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141
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Vulto-van Silfhout AT, Hehir-Kwa JY, van Bon BWM, Schuurs-Hoeijmakers JHM, Meader S, Hellebrekers CJM, Thoonen IJM, de Brouwer APM, Brunner HG, Webber C, Pfundt R, de Leeuw N, de Vries BBA. Clinical significance of de novo and inherited copy-number variation. Hum Mutat 2013; 34:1679-87. [PMID: 24038936 DOI: 10.1002/humu.22442] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 08/30/2013] [Indexed: 12/22/2022]
Abstract
Copy-number variations (CNVs) are a common cause of intellectual disability and/or multiple congenital anomalies (ID/MCA). However, the clinical interpretation of CNVs remains challenging, especially for inherited CNVs. Well-phenotyped patients (5,531) with ID/MCA were screened for rare CNVs using a 250K single-nucleotide polymorphism array platform in order to improve the understanding of the contribution of CNVs to a patients phenotype. We detected 1,663 rare CNVs in 1,388 patients (25.1%; range 0-5 per patient) of which 437 occurred de novo and 638 were inherited. The detected CNVs were analyzed for various characteristics, gene content, and genotype-phenotype correlations. Patients with severe phenotypes, including organ malformations, had more de novo CNVs (P < 0.001), whereas patient groups with milder phenotypes, such as facial dysmorphisms, were enriched for both de novo and inherited CNVs (P < 0.001), indicating that not only de novo but also inherited CNVs can be associated with a clinically relevant phenotype. Moreover, patients with multiple CNVs presented with a more severe phenotype than patients with a single CNV (P < 0.001), pointing to a combinatorial effect of the additional CNVs. In addition, we identified 20 de novo single-gene CNVs that directly indicate novel genes for ID/MCA, including ZFHX4, ANKH, DLG2, MPP7, CEP89, TRIO, ASTN2, and PIK3C3.
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Affiliation(s)
- Anneke T Vulto-van Silfhout
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences and Institute for Genetic and Metabolic Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
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142
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Spreiz A, Guilherme RS, Castellan C, Green A, Rittinger O, Wellek B, Utermann B, Erdel M, Fauth C, Haberlandt E, Kim CA, Kulikowski LD, Meloni VA, Utermann G, Zschocke J, Melaragno MI, Kotzot D. Single-nucleotide polymorphism array-based characterization of ring chromosome 18. J Pediatr 2013; 163:1174-8.e3. [PMID: 23876976 DOI: 10.1016/j.jpeds.2013.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 04/23/2013] [Accepted: 06/06/2013] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To study genotype-phenotype correlation of ring chromosome 18 [r(18)] in 9 patients with 46,XN karyotype. STUDY DESIGN In 9 patients with a de novo 46,XN,r(18) karyotype (7 females, 2 males), we performed high-resolution single-nucleotide polymorphism array analysis (Illumina Human Omni1-QuadV1 array in 6 patients, Affymetrix 6.0 array in 3 patients), investigation of parental origin, and genotype-phenotype correlation. RESULTS No breakpoint was recurrent. Single metaphases with loss of the ring, double rings, or secondarily rearranged rings were found in some cases, but true mosaicism was present in none of these cases. In 3 patients, additional duplications in 18p (of 1.4 Mb, 2 Mb, and 5.8 Mb) were detected. In 1 patient, an additional deletion of 472 kb in Xp22.33, including the SHOX gene, was found. Parental origin of r(18) was maternal in 2 patients and paternal in 4 patients, and formation was most likely meiotic. Karyotype was normal in all investigated parents (n = 15). At birth, mean maternal age was 30 years (n = 9) and mean paternal age was 34.4 years (n = 9). CONCLUSION Genotype-phenotype correlation revealed extensive clinical variability but no characteristic r(18) phenotype. Severity of clinical signs were generally correlated with the size of the deletion. Patients with large deletions in 18p and small deletions in 18q exhibited mainly symptoms related to 18p-, whereas those with large deletions in 18q and small deletions in 18p had symptoms of 18q-.
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Affiliation(s)
- Ana Spreiz
- Division of Human Genetics, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria
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143
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Autosomal recessive mutations in nuclear transport factor KPNA7 are associated with infantile spasms and cerebellar malformation. Eur J Hum Genet 2013; 22:587-93. [PMID: 24045845 DOI: 10.1038/ejhg.2013.196] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/21/2013] [Accepted: 07/24/2013] [Indexed: 11/08/2022] Open
Abstract
Nuclear import receptors of the KPNA family recognize the nuclear localization signal in proteins and together with importin-β mediate translocation into the nucleus. Accordingly, KPNA family members have a highly conserved architecture with domains that contact the nuclear localization signal and bind to importin-β. Here, we describe autosomal recessive mutations in KPNA7 found by whole exome sequencing in a sibling pair with severe developmental disability, infantile spasms, subsequent intractable epilepsy consistent with Lennox-Gastaut syndrome, partial agenesis of the corpus callosum, and cerebellar vermis hypoplasia. The mutations mapped to exon 7 in KPNA7 result in two amino-acid substitutions, Pro339Ala and Glu344Gln. On the basis of the crystal structure of the paralog KPNA2 bound to a bipartite nuclear localization signal from the retinoblastoma protein, the amino-acid substitutions in the affected subjects were predicted to occur within the seventh armadillo repeat that forms one of the two nuclear localization signal-binding sites in KPNA family members. Glu344 is conserved in all seven KPNA proteins, and we found that the Glu354Gln mutation in KPNA2 is sufficient to reduce binding to the retinoblastoma nuclear localization signal to approximately one-half that of wild-type protein. Our data show that compound heterozygous mutations in KPNA7 are associated with a human neurodevelopmental disease, and provide the first example of a human disease associated with mutation of a nuclear transport receptor.
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144
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Knockdown of human TCF4 affects multiple signaling pathways involved in cell survival, epithelial to mesenchymal transition and neuronal differentiation. PLoS One 2013; 8:e73169. [PMID: 24058414 PMCID: PMC3751932 DOI: 10.1371/journal.pone.0073169] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2013] [Accepted: 07/18/2013] [Indexed: 01/04/2023] Open
Abstract
Haploinsufficiency of TCF4 causes Pitt-Hopkins syndrome (PTHS): a severe form of mental retardation with phenotypic similarities to Angelman, Mowat-Wilson and Rett syndromes. Genome-wide association studies have also found that common variants in TCF4 are associated with an increased risk of schizophrenia. Although TCF4 is transcription factor, little is known about TCF4-regulated processes in the brain. In this study we used genome-wide expression profiling to determine the effects of acute TCF4 knockdown on gene expression in SH-SY5Y neuroblastoma cells. We identified 1204 gene expression changes (494 upregulated, 710 downregulated) in TCF4 knockdown cells. Pathway and enrichment analysis on the differentially expressed genes in TCF4-knockdown cells identified an over-representation of genes involved in TGF-β signaling, epithelial to mesenchymal transition (EMT) and apoptosis. Among the most significantly differentially expressed genes were the EMT regulators, SNAI2 and DEC1 and the proneural genes, NEUROG2 and ASCL1. Altered expression of several mental retardation genes such as UBE3A (Angelman Syndrome), ZEB2 (Mowat-Wilson Syndrome) and MEF2C was also found in TCF4-depleted cells. These data suggest that TCF4 regulates a number of convergent signaling pathways involved in cell differentiation and survival in addition to a subset of clinically important mental retardation genes.
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145
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Monozygotic twins discordant for 18q21.2qter deletion detected by array CGH in amniotic fluid. Eur J Med Genet 2013; 56:502-5. [PMID: 23832107 DOI: 10.1016/j.ejmg.2013.06.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 06/25/2013] [Indexed: 11/21/2022]
Abstract
Discordant chromosomal anomalies in monozygotic twins may be caused by various timing issues of erroneous mitosis and twinning events. Here, we report a prenatal diagnosis of heterokaryotypic monozygotic twins discordant for phenotype. In a 28-year-old woman, ultrasound examination performed at 26 weeks of gestation, detected intrauterine growth restriction and unilateral cleft lip and palate in twin B, whereas twin A had normal fluid, growth and anatomy. Molecular karyotyping in twin B identified a 18q21.2qter deletion, further confirmed by FISH analysis on amniocytes. Interestingly, in twin A, cytogenetic studies (FISH analysis and karyotype) on amniocytes were normal. Genotyping with microsatellite markers confirmed the monozygosity of the twins. At 32 weeks of gestation, selective termination of twin B was performed by umbilical cord coagulation and fetal blood samples were taken from the umbilical cord in both twins. FISH analyses detected mosaicism in both twins with 75% of cells being normal and 25% harboring the 18qter deletion. After genetic counseling, the parents elected to terminate the second twin at 36 weeks of gestation. In postmortem studies, FISH analyses revealed mosaicism on several tissues in both twins. Taking into account this observation, we discuss the difficulties of genetic counseling and management concerning heterokaryotypic monozygotic twins.
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146
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Kousoulidou L, Tanteles G, Moutafi M, Sismani C, Patsalis PC, Anastasiadou V. 263.4 kb deletion within the TCF4 gene consistent with Pitt–Hopkins syndrome, inherited from a mosaic parent with normal phenotype. Eur J Med Genet 2013; 56:314-8. [DOI: 10.1016/j.ejmg.2013.03.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Accepted: 03/09/2013] [Indexed: 12/23/2022]
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147
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Sweatt JD. Pitt-Hopkins Syndrome: intellectual disability due to loss of TCF4-regulated gene transcription. Exp Mol Med 2013; 45:e21. [PMID: 23640545 PMCID: PMC3674405 DOI: 10.1038/emm.2013.32] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 01/22/2023] Open
Abstract
TCF4 (transcription factor 4; E2-2, ITF2) is a transcription factor that when haplo-insufficient causes Pitt-Hopkins Syndrome (PTHS), an autism-spectrum disorder that is associated with pervasive developmental delay and severe intellectual disability. The TCF4 gene is also a risk factor with highly significant linkage to schizophrenia, presumably via overexpression of the TCF4 gene product in the central nervous system. This review will present an overview of the clinical manifestations of PTHS and relate those clinical attributes to the underlying molecular genetics of TCF4. In order to provide a molecular biological context for the loss of function of TCF4 in PTHS, the review will also present a brief overview of the basic biochemistry of TCF4-mediated regulation of cellular and neuronal gene expression. In the final section of this review, I will discuss and speculate upon possible roles for the TCF4 transcription factor in neuronal function and comment upon how understanding these roles may give new insights into the molecular neurobiology of human cognition.
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Affiliation(s)
- J David Sweatt
- Department of Neurobiology and Evelyn F. McKnight Brain Institute, Civitan International Research Center, University of Alabama at Birmingham, Birmingham, AL 35294-2182, USA.
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148
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Steinbusch CVM, van Roozendaal KEP, Tserpelis D, Smeets EEJ, Kranenburg-de Koning TJ, de Waal KH, Zweier C, Rauch A, Hennekam RCM, Blok MJ, Schrander-Stumpel CTRM. Somatic mosaicism in a mother of two children with Pitt-Hopkins syndrome. Clin Genet 2013; 83:73-7. [DOI: 10.1111/j.1399-0004.2012.01857.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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149
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Michaelson JJ, Shi Y, Gujral M, Zheng H, Malhotra D, Jin X, Jian M, Liu G, Greer D, Bhandari A, Wu W, Corominas R, Peoples A, Koren A, Gore A, Kang S, Lin GN, Estabillo J, Gadomski T, Singh B, Zhang K, Akshoomoff N, Corsello C, McCarroll S, Iakoucheva LM, Li Y, Wang J, Sebat J. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 2013; 151:1431-42. [PMID: 23260136 DOI: 10.1016/j.cell.2012.11.019] [Citation(s) in RCA: 383] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/05/2012] [Accepted: 10/30/2012] [Indexed: 02/06/2023]
Abstract
De novo mutation plays an important role in autism spectrum disorders (ASDs). Notably, pathogenic copy number variants (CNVs) are characterized by high mutation rates. We hypothesize that hypermutability is a property of ASD genes and may also include nucleotide-substitution hot spots. We investigated global patterns of germline mutation by whole-genome sequencing of monozygotic twins concordant for ASD and their parents. Mutation rates varied widely throughout the genome (by 100-fold) and could be explained by intrinsic characteristics of DNA sequence and chromatin structure. Dense clusters of mutations within individual genomes were attributable to compound mutation or gene conversion. Hypermutability was a characteristic of genes involved in ASD and other diseases. In addition, genes impacted by mutations in this study were associated with ASD in independent exome-sequencing data sets. Our findings suggest that regional hypermutation is a significant factor shaping patterns of genetic variation and disease risk in humans.
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Affiliation(s)
- Jacob J Michaelson
- Beyster Center for Genomics of Psychiatric Diseases, University of California, San Diego, La Jolla, CA 92093, USA
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150
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Navarrete K, Pedroso I, De Jong S, Stefansson H, Steinberg S, Stefansson K, Ophoff RA, Schalkwyk LC, Collier DA. TCF4 (e2-2; ITF2): a schizophrenia-associated gene with pleiotropic effects on human disease. Am J Med Genet B Neuropsychiatr Genet 2013; 162B:1-16. [PMID: 23129290 DOI: 10.1002/ajmg.b.32109] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2012] [Accepted: 09/27/2012] [Indexed: 12/22/2022]
Abstract
Common SNPs in the transcription factor 4 (TCF4; ITF2, E2-2, SEF-2) gene, which encodes a basic Helix-Loop-Helix (bHLH) transcription factor, are associated with schizophrenia, conferring a small increase in risk. Other common SNPs in the gene are associated with the common eye disorder Fuch's corneal dystrophy, while rare, mostly de novo inactivating mutations cause Pitt-Hopkins syndrome. In this review, we present a systematic bioinformatics and literature review of the genomics, biological function and interactome of TCF4 in the context of schizophrenia. The TCF4 gene is present in all vertebrates, and although protein length varies, there is high conservation of primary sequence, including the DNA binding domain. Humans have a unique leucine-rich nuclear export signal. There are two main isoforms (A and B), as well as complex splicing generating many possible N-terminal amino acid sequences. TCF4 is highly expressed in the brain, where plays a role in neurodevelopment, interacting with class II bHLH transcription factors Math1, HASH1, and neuroD2. The Ca(2+) sensor protein calmodulin interacts with the DNA binding domain of TCF4, inhibiting transcriptional activation. It is also the target of microRNAs, including mir137, which is implicated in schizophrenia. The schizophrenia-associated SNPs are in linkage disequilibrium with common variants within putative DNA regulatory elements, suggesting that regulation of expression may underlie association with schizophrenia. Combined gene co-expression analyses and curated protein-protein interaction data provide a network involving TCF4 and other putative schizophrenia susceptibility genes. These findings suggest new opportunities for understanding the molecular basis of schizophrenia and other mental disorders.
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Affiliation(s)
- Katherinne Navarrete
- Social, Genetic and Developmental Psychiatry Centre, King's College London, Institute of Psychiatry, London, UK
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