1
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Singh AK, Allington G, Viviano S, McGee S, Kiziltug E, Ma S, Zhao S, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 BAFopathy implicates neural progenitor epigenetic dysregulation in human hydrocephalus. Brain 2024; 147:1553-1570. [PMID: 38128548 PMCID: PMC10994532 DOI: 10.1093/brain/awad405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/01/2023] [Accepted: 10/26/2023] [Indexed: 12/23/2023] Open
Abstract
Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery in children. Recent studies have implicated SMARCC1, a component of the BRG1-associated factor (BAF) chromatin remodelling complex, as a candidate congenital hydrocephalus gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, congenital hydrocephalus-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo. Here, we aimed to assess the prevalence of SMARCC1 variants in an expanded patient cohort, describe associated clinical and radiographic phenotypes, and assess the impact of Smarcc1 depletion in a novel Xenopus tropicalis model of congenital hydrocephalus. To do this, we performed a genetic association study using whole-exome sequencing from a cohort consisting of 2697 total ventriculomegalic trios, including patients with neurosurgically-treated congenital hydrocephalus, that total 8091 exomes collected over 7 years (2016-23). A comparison control cohort consisted of 1798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents were sourced from the Simons Simplex Collection. Enrichment and impact on protein structure were assessed in identified variants. Effects on the human fetal brain transcriptome were examined with RNA-sequencing and Smarcc1 knockdowns were generated in Xenopus and studied using optical coherence tomography imaging, in situ hybridization and immunofluorescence. SMARCC1 surpassed genome-wide significance thresholds, yielding six rare, protein-altering de novo variants localized to highly conserved residues in key functional domains. Patients exhibited hydrocephalus with aqueductal stenosis; corpus callosum abnormalities, developmental delay, and cardiac defects were also common. Xenopus knockdowns recapitulated both aqueductal stenosis and cardiac defects and were rescued by wild-type but not patient-specific variant SMARCC1. Hydrocephalic SMARCC1-variant human fetal brain and Smarcc1-variant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2. These results suggest de novo variants in SMARCC1 cause a novel human BAFopathy we term 'SMARCC1-associated developmental dysgenesis syndrome', characterized by variable presence of cerebral ventriculomegaly, aqueductal stenosis, developmental delay and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodelling complex for human brain morphogenesis and provide evidence for a 'neural stem cell' paradigm of congenital hydrocephalus pathogenesis. These results highlight utility of trio-based whole-exome sequencing for identifying pathogenic variants in sporadic congenital structural brain disorders and suggest whole-exome sequencing may be a valuable adjunct in clinical management of congenital hydrocephalus patients.
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Affiliation(s)
- Amrita K Singh
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Garrett Allington
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Genetics, Yale University, New Haven, CT 06510, USA
| | - Stephen Viviano
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | | | - Emre Kiziltug
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shaojie Ma
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Shujuan Zhao
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - Kedous Y Mekbib
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John P Shohfi
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Phan Q Duy
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Tyrone DeSpenza
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - Charuta G Furey
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | - Benjamin C Reeves
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hannah Smith
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - André M M Sousa
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Adriana Cherskov
- Department of Neuroscience, Yale University, New Haven, CT 06510, USA
| | - August Allocco
- Department of Neurosurgery, Yale University, New Haven, CT 06510, USA
| | | | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London, WC1H 9RN, UK
| | - Syed R A Rizvi
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
| | - Seth L Alper
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Nephrology and Vascular Biology Research Center, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nenad Sestan
- Department of Genetics, Yale University, New Haven, CT 06510, USA
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Hermela Shimelis
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Lauren K Walsh
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Andres Moreno-De-Luca
- Department of Radiology, Neuroradiology section, Kingston Health Sciences Centre, Queen's University Faculty of Health Sciences, Kingston, Ontario, Canada
- Department of Radiology, Diagnostic Medicine Institute, Geisinger, Danville, PA, 17822, USA
| | - Sheng Chih Jin
- Departments of Genetics and Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA
| | | | - Engin Deniz
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
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Rojananuangnit K, Rojnueangnit K. Microspherophakic Angle Closure Glaucoma in a Patient with Coffin-Siris Syndrome: Case Report. Appl Clin Genet 2023; 16:165-170. [PMID: 37663124 PMCID: PMC10474847 DOI: 10.2147/tacg.s422312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 08/24/2023] [Indexed: 09/05/2023] Open
Abstract
Background Bilateral secondary angle closure glaucoma is a presenting symptom of microspherophakia and ectopia lentis. Characterizing the associated syndrome and confirmation by genetic testing can identify associated systemic abnormalities and provide appropriate genetic counseling. Case Presentation A 42-year-old woman with severe intellectual disability presented with light perception visual acuity and glaucoma, with intraocular pressure (IOP) in her right and left eyes of 69 and 70 mmHg, respectively. She underwent two sessions of 270-degree laser diode transscleral cytophotocoagulation treatment at a 6-month interval and was prescribed topical anti-glaucoma medication. Her family noticed a progressive decrease in her vision while on treatment for 2 years. She was diagnosed with apparent Weill-Marchesani syndrome, accompanied by angle closure glaucoma and microspherophakia. Cataract surgery and intraocular lens implantation were successful in both eyes and post-operative IOP was controlled with anti-glaucoma medication but her vision did not improve from severe glaucomatous optic neuropathy. Her underlying syndrome was investigated genetically by whole exome sequencing. Results Sequencing showed a pathogenic variant in ARID1B, c.3955dupC (p.Gln1319Profs*14), diagnostic of Coffin-Siris syndrome. This is the first report of Coffin-Siris syndrome associated with microspherophakia and angle closure glaucoma. Conclusion Bilateral angle closure glaucoma from ectopia lentis in patients with genetic syndromes could be an indicator of microspherophakia in adulthood. Ophthalmological surveillance is important in patients with Coffin-Siris syndrome.
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Affiliation(s)
- Kulawan Rojananuangnit
- Glaucoma Unit, Department of Ophthalmology, Mettapracharak (Wat Rai Khing) Hospital, Nakhon Pathom, Thailand
| | - Kitiwan Rojnueangnit
- Division of Genetics, Department of Pediatrics, Faculty of Medicine, Thammasat University, Pathumthani, Thailand
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Singh AK, Viviano S, Allington G, McGee S, Kiziltug E, Mekbib KY, Shohfi JP, Duy PQ, DeSpenza T, Furey CG, Reeves BC, Smith H, Ma S, Sousa AMM, Cherskov A, Allocco A, Nelson-Williams C, Haider S, Rizvi SRA, Alper SL, Sestan N, Shimelis H, Walsh LK, Lifton RP, Moreno-De-Luca A, Jin SC, Kruszka P, Deniz E, Kahle KT. A novel SMARCC1 -mutant BAFopathy implicates epigenetic dysregulation of neural progenitors in hydrocephalus. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.19.23287455. [PMID: 36993720 PMCID: PMC10055611 DOI: 10.1101/2023.03.19.23287455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Importance Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery. A few familial forms of congenital hydrocephalus (CH) have been identified, but the cause of most sporadic cases of CH remains elusive. Recent studies have implicated SMARCC1 , a component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, as a candidate CH gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, CH-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo . Objectives The aims of this study are to (i) assess the extent to which rare, damaging de novo mutations (DNMs) in SMARCC1 are associated with cerebral ventriculomegaly; (ii) describe the clinical and radiographic phenotypes of SMARCC1 -mutated patients; and (iii) assess the pathogenicity and mechanisms of CH-associated SMARCC1 mutations in vivo . Design setting and participants A genetic association study was conducted using whole-exome sequencing from a cohort consisting of 2,697 ventriculomegalic trios, including patients with neurosurgically-treated CH, totaling 8,091 exomes collected over 5 years (2016-2021). Data were analyzed in 2023. A comparison control cohort consisted of 1,798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents sourced from the Simons simplex consortium. Main outcomes and measures Gene variants were identified and filtered using stringent, validated criteria. Enrichment tests assessed gene-level variant burden. In silico biophysical modeling estimated the likelihood and extent of the variant impact on protein structure. The effect of a CH-associated SMARCC1 mutation on the human fetal brain transcriptome was assessed by analyzing RNA-sequencing data. Smarcc1 knockdowns and a patient-specific Smarcc1 variant were tested in Xenopus and studied using optical coherence tomography imaging, in situ hybridization, and immunofluorescence microscopy. Results SMARCC1 surpassed genome-wide significance thresholds in DNM enrichment tests. Six rare protein-altering DNMs, including four loss-of-function mutations and one recurrent canonical splice site mutation (c.1571+1G>A) were detected in unrelated patients. DNMs localized to the highly conserved DNA-interacting SWIRM, Myb-DNA binding, Glu-rich, and Chromo domains of SMARCC1 . Patients exhibited developmental delay (DD), aqueductal stenosis, and other structural brain and heart defects. G0 and G1 Smarcc1 Xenopus mutants exhibited aqueductal stenosis and cardiac defects and were rescued by human wild-type SMARCC1 but not a patient-specific SMARCC1 mutant. Hydrocephalic SMARCC1 -mutant human fetal brain and Smarcc1 -mutant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2 . Conclusions SMARCC1 is a bona fide CH risk gene. DNMs in SMARCC1 cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)", characterized by cerebral ventriculomegaly, aqueductal stenosis, DD, and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodeling complex for human brain morphogenesis and provide evidence for a "neural stem cell" paradigm of human CH pathogenesis. These results highlight the utility of trio-based WES for identifying risk genes for congenital structural brain disorders and suggest WES may be a valuable adjunct in the clinical management of CH patients. KEY POINTS Question: What is the role of SMARCC1 , a core component of the B RG1- a ssociated factor (BAF) chromatin remodeling complex, in brain morphogenesis and congenital hydrocephalus (CH)? Findings: SMARCC1 harbored an exome-wide significant burden of rare, protein-damaging de novo mutations (DNMs) (p = 5.83 × 10 -9 ) in the largest ascertained cohort to date of patients with cerebral ventriculomegaly, including treated CH (2,697 parent-proband trios). SMARCC1 contained four loss-of-function DNMs and two identical canonical splice site DNMs in a total of six unrelated patients. Patients exhibited developmental delay, aqueductal stenosis, and other structural brain and cardiac defects. Xenopus Smarcc1 mutants recapitulated core human phenotypes and were rescued by the expression of human wild-type but not patient-mutant SMARCC1 . Hydrocephalic SMARCC1 -mutant human brain and Smarcc1 -mutant Xenopus brain exhibited similar alterationsin the expression of key transcription factors that regulate neural progenitor cell proliferation. Meaning: SMARCC1 is essential for human brain morphogenesis and is a bona fide CH risk gene. SMARCC1 mutations cause a novel human BAFopathy we term " S MARCC1- a ssociated D evelopmental D ysgenesis S yndrome (SaDDS)". These data implicate epigenetic dysregulation of fetal neural progenitors in the pathogenesis of hydrocephalus, with diagnostic and prognostic implications for patients and caregivers.
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Simmers R, Goodwin A, Al Saif H, Couser N. Ophthalmologic and facial abnormalities of Nicolaides-Baraitser syndrome. Ophthalmic Genet 2022; 43:699-702. [PMID: 35762114 DOI: 10.1080/13816810.2022.2089358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND Nicolaides-Baraitser syndrome (NCBRS), first described in 1993, is a rare autosomal dominant disease caused by pathogenic variants in the SMARCA2 gene on chromosome 9p24.3. NCBRS typically presents with dysmorphic facial features, seizures, intellectual disability, and developmental delays. Abnormal findings of the eye and ocular adnexa associated with NCBRS have not been systematically evaluated and summarized in literature. This report presents the case of a 4-year-old male with NCBRS along with a systematic review of literature of the abnormal ophthalmologic and facial features of NCBRS cases. METHODS A systematic review of literature of published cases of molecularly confirmed NCBRS was performed and the frequencies of eye, ocular adnexa, and facial abnormalities were calculated. RESULTS Our patient's abnormal eye features include myopia, down slanting palpebral fissures, sagging inferior periorbital skin, hypertelorism, and long eyelashes. From the systemic review of literature, the most common abnormal eye and ocular adnexa features include prominent/long eyelashes, thick eyebrows, sagging periorbital skin, down slanting palpebral fissures, and ptosis. The most common facial dysmorphic features include thick/everted lower lip, coarse facial features, wide/large mouth, and thin upper lip. Dental abnormalities are also commonly reported. CONCLUSIONS NCBRS frequently presents with well-defined ophthalmic and facial abnormalities. Prompt ophthalmologic evaluation following NCBRS diagnosis may be recommended to screen for several eye disorders. Surgical correction of ptosis may be indicated for NCBRS patients. This report may help further delineate the phenotype of this condition, which may allow for more rapid identification of those affected and provide incentive for additional studies.
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Affiliation(s)
- Russell Simmers
- Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Allison Goodwin
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.,Department of Pediatrics, Virginia Commonwealth University School of Medicine, Children's Hospital of Richmond at VCU, Richmond, Virginia, USA
| | - Hind Al Saif
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.,Department of Pediatrics, Virginia Commonwealth University School of Medicine, Children's Hospital of Richmond at VCU, Richmond, Virginia, USA
| | - Natario Couser
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.,Department of Ophthalmology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA.,Department of Pediatrics, Virginia Commonwealth University School of Medicine, Children's Hospital of Richmond at VCU, Richmond, Virginia, USA
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5
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Akella R. SWI/SNF-Related SMARCA2 Gene Mutation Associated with Nicolaides–Baraitser's Syndrome: Follow-up Study. J Pediatr Genet 2022. [DOI: 10.1055/s-0041-1740458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractNicolaides–Baraitser's syndrome is a rare, dominantly inherited well-delineated syndrome caused by mutations in the SMARCA2 gene which is located on the small arm of chromosome 9. In this study, a de novo missense variant, which was identified in a 3-year-old boy by whole exome sequencing is reported. The de novo heterozygous V1198M missense variant in SMARCA2 gene in exon 25 is novel. Identifying the condition is crucial for the long-term management and family counseling. Follow-up over 4 years revealed improvements in overall performance.
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6
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Lu G, Peng Q, Wu L, Zhang J, Ma L. Identification of de novo mutations for ARID1B haploinsufficiency associated with Coffin-Siris syndrome 1 in three Chinese families via array-CGH and whole exome sequencing. BMC Med Genomics 2021; 14:270. [PMID: 34775996 PMCID: PMC8591803 DOI: 10.1186/s12920-021-01119-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/05/2021] [Indexed: 11/25/2022] Open
Abstract
Background Coffin–Siris syndrome (CSS) is a multiple malformation syndrome characterized by intellectual disability associated with coarse facial features, hirsutism, sparse scalp hair, and hypoplastic or absent fifth fingernails or toenails. CSS represents a small group of intellectual disability, and could be caused by at least twelve genes. The genetic background is quite heterogenous, making it difficult for clinicians and genetic consultors to pinpoint the exact disease types. Methods Array-Comparative Genomic Hybridization (array-CGH) and whole exome sequencing (WES) were applied for three trios affected with intellectual disability and clinical features similar with those of Coffin–Siris syndrome. Sanger sequencing was used to verify the detected single-nucleotide variants (SNVs). Results All of the three cases were female with normal karyotypes of 46, XX, born of healthy, non-consanguineous parents. A 6q25 microdeletion (arr[hg19]6q25.3(155,966,487–158,803,979) × 1) (2.84 Mb) (case 1) and two loss-of-function (LoF) mutations of ARID1B [c.2332 + 1G > A in case 2 and c.4741C > T (p.Q1581X) in case 3] were identified. All of the three pathogenic abnormalities were de novo, not inherited from their parents. After comparison of publicly available microdeletions containing ARID1B, four types of microdeletions leading to insufficient production of ARID1B were identified, namely deletions covering the whole region of ARID1B, deletions covering the promoter region, deletions covering the termination region or deletions covering enhancer regions. Conclusion Here we identified de novo ARID1B mutations in three Chinese trios. Four types of microdeletions covering ARID1B were identified. This study broadens current knowledge of ARID1B mutations for clinicians and genetic consultors.
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Affiliation(s)
- Guanting Lu
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang Key Laboratory of Tumor Molecular Research, Deyang People's Hospital, No. 173 First Section of TaishanBei Road, Jiangyang District, Deyang, 618000, China.
| | - Qiongling Peng
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, 56 Yulyu Road, Baoan District, Shenzhen, 518000, China
| | - Lianying Wu
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang Key Laboratory of Tumor Molecular Research, Deyang People's Hospital, No. 173 First Section of TaishanBei Road, Jiangyang District, Deyang, 618000, China
| | - Jian Zhang
- Department of Pathology, Laboratory of Translational Medicine Research, Deyang Key Laboratory of Tumor Molecular Research, Deyang People's Hospital, No. 173 First Section of TaishanBei Road, Jiangyang District, Deyang, 618000, China
| | - Liya Ma
- Department of Child Healthcare, Shenzhen Baoan Women's and Children's Hospital, Jinan University, 56 Yulyu Road, Baoan District, Shenzhen, 518000, China.
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Pan N, Chen S, Cai X, Li J, Yu T, Huang HF, Zhang J, Xu C. Low-level germline mosaicism of a novel SMARCA2 missense variant: Expanding the phenotypic spectrum and mode of genetic transmission. Mol Genet Genomic Med 2021; 9:e1763. [PMID: 34296532 PMCID: PMC8457699 DOI: 10.1002/mgg3.1763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/02/2022] Open
Abstract
Background Nicolaides–Baraitser syndrome (NCBRS) is a severe neurodevelopmental disorder with multiple abnormalities. To date, all pathogenic variants in SMARCA2 causing NCBRS are de novo and most are missense variants located in the ATPase domain of SMARCA2 protein. Methods In this study, a familial trio whole‐exome sequencing was performed on the proband presenting with intellectual disability, early‐onset epilepsy, and autistic features. A novel missense variant c.553C>G (p.Gln185Glu) in SMARCA2 was identified, which is located in the QLQ domain. The same variant was subsequently also found in the mother's ongoing pregnancy. Samples from accessible tissues such as saliva and sperm other than blood were collected from the parents, and the detection of the target variant was performed by amplicon‐based deep sequencing. Results Low‐level mosaicism of the target variant c.553C>G (p.Gln185Glu) was detected in the father's sperm with allele fraction of 2.8% by amplicon‐based deep sequencing, which was not detected in either parents’ blood or saliva specimens. Heterozygosity of this variant was confirmed in the proband. Conclusion This is the first report of paternal germline mosaicism for a SMARCA2 disease‐causing variant. In addition, the missense variant c.553C>G (p.Gln185Glu) in the QLQ domain causes mainly neurological and developmental phenotypes with unremarkable characteristic facial features and limb abnormalities. Our findings expand the phenotypic spectrum and mode of genetic transmission associated with the SMARCA2 variants.
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Affiliation(s)
- Nina Pan
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Songchang Chen
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering and MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xiaoqiang Cai
- Beijing BioBiggen Technology Co., Ltd.,, Beijing, China
| | - Jianli Li
- Beijing BioBiggen Technology Co., Ltd.,, Beijing, China
| | - Tao Yu
- Beijing BioBiggen Technology Co., Ltd.,, Beijing, China
| | - He-Feng Huang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Clinical Research Center for Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Key Laboratory of Reproductive Genetics, Ministry of Education, Zhejiang University, Hangzhou, China.,Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jinglan Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Beijing BioBiggen Technology Co., Ltd.,, Beijing, China.,Clinical Research Center for Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chenming Xu
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
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Hofmeister B, von Stülpnagel C, Betzler C, Mari F, Renieri A, Baldassarri M, Haberlandt E, Jansen K, Schilling S, Weber P, Ahlbory K, Tang S, Berweck S, Kluger G. Epilepsy in Nicolaides-Baraitser Syndrome: Review of Literature and Report of 25 Patients Focusing on Treatment Aspects. Neuropediatrics 2021; 52:109-122. [PMID: 33578439 DOI: 10.1055/s-0041-1722878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Nicolaides-Baraitser syndrome (NCBRS), caused by a mutation in the SMARCA2 gene, which goes along with intellectual disability, congenital malformations, especially of face and limbs, and often difficult-to-treat epilepsy, is surveyed focusing on epilepsy and its treatment. Patients were recruited via "Network Therapy of Rare Epilepsies (NETRE)" and an international NCBRS parent support group. Inclusion criterion is NCBRS-defining SMARCA2 mutation. Clinical findings including epilepsy classification, anticonvulsive treatment, electroencephalogram (EEG) findings, and neurodevelopmental outcome were collected with an electronic questionnaire. Inclusion of 25 NCBRS patients with epilepsy in 23 of 25. Overall, 85% of the participants (17/20) reported generalized seizures, the semiology varied widely. EEG showed generalized epileptogenic abnormalities in 53% (9/17), cranial magnetic resonance imaging (cMRI) was mainly inconspicuous. The five most frequently used anticonvulsive drugs were valproic acid (VPA [12/20]), levetiracetam (LEV [12/20]), phenobarbital (PB [8/20]), topiramate (TPM [5/20]), and carbamazepine (CBZ [5/20]). LEV (9/12), PB (6/8), TPM (4/5), and VPA (9/12) reduced the seizures' frequency in more than 50%. Temporary freedom of seizures (>6 months) was reached with LEV (4/12), PB (3/8), TPM (1/5, only combined with PB and nitrazepam [NZP]), and VPA (4/12). Seizures aggravation was observed under lamotrigine (LTG [2/4]), LEV (1/12), PB (1/8), and VPA (1/12). Ketogenic diet (KD) and vagal nerve stimulation (VNS) reduced seizures' frequency in one of two each. This first worldwide retrospective analysis of anticonvulsive therapy in NCBRS helps to treat epilepsy in NCBRS that mostly shows only initial response to anticonvulsive therapy, especially with LEV and VPA, but very rarely shows complete freedom of seizures in this, rather genetic than structural epilepsy.
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Affiliation(s)
- Benedikt Hofmeister
- Department of Gastroenterology, Hepatology and Gastrointestinal Oncology, Technical University of Munich, Bogenhausen Academic Teaching Hospital, Munich, Germany
| | - Celina von Stülpnagel
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Private Medical University of Salzburg, Salzburg, Austria.,Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Comprehensive Epilepsy Program for Children, University Hospital Munich, Munich, Germany
| | - Cornelia Betzler
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Private Medical University of Salzburg, Salzburg, Austria.,Clinic for Neuropediatrics and Neurological Rehabilitation, Epilepsy Center for Children and Adolescents, Schön Klinik Vogtareuth, Vogtareuth, Germany
| | - Francesca Mari
- Department of Medical Genetics, University of Siena, Sienna, Italy
| | | | | | - Edda Haberlandt
- Department of Pediatrics, Krankenhaus der Stadt Dornbirn, Dornbirn, Austria
| | - Katrien Jansen
- Department of Development and Regeneration, University Hospitals of Leuven, Leuven, Belgium
| | - Stefan Schilling
- Department of Neuropediatrics, Krankenhaus Barmherzige Brüder Regensburg, Regensburg, Germany
| | - Peter Weber
- Department of Neuro- and Developmental Pediatrics, University Children's Hospital Basel, Basel, Switzerland
| | - Katja Ahlbory
- Department of Neuropediatrics, Children's Hospital Amsterdamer Straße, Kliniken Köln, Cologne, Germany
| | - Shan Tang
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London, United Kingdom
| | - Steffen Berweck
- Clinic for Neuropediatrics and Neurological Rehabilitation, Epilepsy Center for Children and Adolescents, Schön Klinik Vogtareuth, Vogtareuth, Germany.,Department of Pediatrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Gerhard Kluger
- Institute for Transition, Rehabilitation and Palliation, Paracelsus Private Medical University of Salzburg, Salzburg, Austria.,Clinic for Neuropediatrics and Neurological Rehabilitation, Epilepsy Center for Children and Adolescents, Schön Klinik Vogtareuth, Vogtareuth, Germany
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9
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Cappuccio G, Sayou C, Tanno PL, Tisserant E, Bruel AL, Kennani SE, Sá J, Low KJ, Dias C, Havlovicová M, Hančárová M, Eichler EE, Devillard F, Moutton S, Van-Gils J, Dubourg C, Odent S, Gerard B, Piton A, Yamamoto T, Okamoto N, Firth H, Metcalfe K, Moh A, Chapman KA, Aref-Eshghi E, Kerkhof J, Torella A, Nigro V, Perrin L, Piard J, Le Guyader G, Jouan T, Thauvin-Robinet C, Duffourd Y, George-Abraham JK, Buchanan CA, Williams D, Kini U, Wilson K, Sousa SB, Hennekam RCM, Sadikovic B, Thevenon J, Govin J, Vitobello A, Brunetti-Pierri N. De novo SMARCA2 variants clustered outside the helicase domain cause a new recognizable syndrome with intellectual disability and blepharophimosis distinct from Nicolaides-Baraitser syndrome. Genet Med 2020; 22:1838-1850. [PMID: 32694869 DOI: 10.1038/s41436-020-0898-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Nontruncating variants in SMARCA2, encoding a catalytic subunit of SWI/SNF chromatin remodeling complex, cause Nicolaides-Baraitser syndrome (NCBRS), a condition with intellectual disability and multiple congenital anomalies. Other disorders due to SMARCA2 are unknown. METHODS By next-generation sequencing, we identified candidate variants in SMARCA2 in 20 individuals from 18 families with a syndromic neurodevelopmental disorder not consistent with NCBRS. To stratify variant interpretation, we functionally analyzed SMARCA2 variants in yeasts and performed transcriptomic and genome methylation analyses on blood leukocytes. RESULTS Of 20 individuals, 14 showed a recognizable phenotype with recurrent features including epicanthal folds, blepharophimosis, and downturned nasal tip along with variable degree of intellectual disability (or blepharophimosis intellectual disability syndrome [BIS]). In contrast to most NCBRS variants, all SMARCA2 variants associated with BIS are localized outside the helicase domains. Yeast phenotype assays differentiated NCBRS from non-NCBRS SMARCA2 variants. Transcriptomic and DNA methylation signatures differentiated NCBRS from BIS and those with nonspecific phenotype. In the remaining six individuals with nonspecific dysmorphic features, clinical and molecular data did not permit variant reclassification. CONCLUSION We identified a novel recognizable syndrome named BIS associated with clustered de novo SMARCA2 variants outside the helicase domains, phenotypically and molecularly distinct from NCBRS.
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Affiliation(s)
- Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, Naples, Italy
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Camille Sayou
- Inserm U1209, CNRS UMR 5309, Univ. Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Pauline Le Tanno
- Department of Genetics and Reproduction, Centre Hospitalo-Universitaire Grenoble-Alpes, Grenoble, France
| | - Emilie Tisserant
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Ange-Line Bruel
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Sara El Kennani
- Inserm U1209, CNRS UMR 5309, Univ. Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Joaquim Sá
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Karen J Low
- University Hospitals Bristol NHS Foundation Trust, University of Bristol, Bristol, UK
| | - Cristina Dias
- Department of Medical and Molecular Genetics, King's College, London, UK
- The Francis Crick Institute, London, UK
- Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Markéta Havlovicová
- Department of Biology and Medical Genetics, Charles University Prague 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Miroslava Hančárová
- Department of Biology and Medical Genetics, Charles University Prague 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Françoise Devillard
- Department of Genetics and Reproduction, Centre Hospitalo-Universitaire Grenoble-Alpes, Grenoble, France
| | - Sébastien Moutton
- CPDPN, Pôle mère enfant, Maison de Santé Protestante Bordeaux Bagatelle, Talence, France
| | - Julien Van-Gils
- Reference Center for Developmental Anomalies, Department of Medical Genetics, Bordeaux University Hospital, Bordeaux, France
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, BMT-HC « Jean Dausset », Rennes, France
| | - Sylvie Odent
- Service de Génétique clinique, CHU de Rennes, Univ. Rennes, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
| | - Bénédicte Gerard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
- Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Helen Firth
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, Manchester, UK
| | - Anna Moh
- Department of Genetics and Metabolism, Children's National Medical Center, Washington, DC, USA
| | - Kimberly A Chapman
- Department of Genetics and Metabolism, Children's National Medical Center, Washington, DC, USA
| | - Erfan Aref-Eshghi
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Laurence Perrin
- Department of Genetics, Robert Debré Hospital, AP-HP, Paris, France
| | - Juliette Piard
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France
| | - Gwenaël Le Guyader
- Department of Medical Genetics, Poitiers University Hospital, Poitiers, France
| | - Thibaud Jouan
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Christel Thauvin-Robinet
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, CHU Dijon, Dijon, France
- UF Innovation en diagnostic génomique des maladies rares, CHU Dijon, Dijon, France
| | - Yannis Duffourd
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France
| | - Jaya K George-Abraham
- Dell Children's Medical Group, Austin, TX, USA
- Department of Pediatrics, The University of Texas at Austin Dell Medical School, Austin, TX, USA
| | | | | | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Kate Wilson
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sérgio B Sousa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
- University Clinic of Genetics, Faculty of Medicine, Universidade de Coimbra, Coimbra, Portugal
| | - Raoul C M Hennekam
- Department of Pediatrics and Translational Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Victoria Hospital, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Julien Thevenon
- Department of Genetics and Reproduction, Centre Hospitalo-Universitaire Grenoble-Alpes, Grenoble, France
| | - Jérôme Govin
- Inserm U1209, CNRS UMR 5309, Univ. Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France.
| | - Antonio Vitobello
- Inserm UMR 1231 GAD, Genetics of Developmental disorders, Université de Bourgogne-Franche Comté, FHU TRANSLAD, Dijon, France.
- UF Innovation en diagnostic génomique des maladies rares, CHU Dijon, Dijon, France.
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Naples, Italy.
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.
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10
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Curcio MR, Ferranti S, Lotti F, Grosso S. Coffin-Siris syndrome and epilepsy. Neurol Sci 2020; 42:727-729. [PMID: 33006724 DOI: 10.1007/s10072-020-04782-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 09/26/2020] [Indexed: 10/23/2022]
Abstract
Coffin-Siris syndrome is a rare genetic disorder defined by the presence of particular facial traits, congenital malformations, intellectual disability, and speech impairment. Epilepsy in Coffin-Siris syndrome has only occasionally been reported, and its features are poorly defined. We provide a detailed description of the clinical and instrumental findings of three patients with Coffin-Siris syndrome and epilepsy. The clinical diagnosis in our patients was confirmed by molecular analysis, which identified the presence of de novo mutations of ARID1B and SMARCB1 genes, in two patients and one patient, respectively. All the patients presented with epilepsy, with a mean age of seizure onset of 5.5 years. Seizures were brief and had a focal onset with secondary generalization. Electroencephalographic recording documented a unilateral, and less commonly bilateral, paroxysmal activity in the temporal, parietal, and occipital regions. Clinical response to anticonvulsive therapy was satisfactory, with a low rate of seizure recurrence. Our case series contributes to delineate the phenotype of Coffin-Siris syndrome. We wish this report could pave the way for further studies that will better define the prevalence and clinical manifestations of epilepsy in this rare syndrome.
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Affiliation(s)
- Maria Rosaria Curcio
- Dipartimento di Medicina Molecolare e dello Sviluppo, Universita' degli Studi di Siena, viale Bracci 16, 53100, Siena, Italy
| | - Silvia Ferranti
- Dipartimento di Medicina Molecolare e dello Sviluppo, Universita' degli Studi di Siena, viale Bracci 16, 53100, Siena, Italy.
| | - Federica Lotti
- U.O.C. Pediatria, Azienda Ospedaliera Universitaria Senese, viale Bracci 16, 53100, Siena, Italy
| | - Salvatore Grosso
- Dipartimento di Medicina Molecolare e dello Sviluppo, Universita' degli Studi di Siena, viale Bracci 16, 53100, Siena, Italy.,U.O.C. Pediatria, Azienda Ospedaliera Universitaria Senese, viale Bracci 16, 53100, Siena, Italy
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11
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Sato A, Suzuki T, Ikeno M, Takeda J, Yamamoto Y, Shinohara M, Makino S, Takeda S, Shimizu T, Itakura A. Pure 9p duplication syndrome with aplasia of the middle phalanges of the fifth fingers. Eur J Med Genet 2020; 63:104005. [PMID: 32693209 DOI: 10.1016/j.ejmg.2020.104005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/12/2020] [Accepted: 07/07/2020] [Indexed: 11/29/2022]
Abstract
9p duplication syndrome is a common congenital anomaly syndrome with specific facial features, mental and developmental retardations, and characteristic fingers. Pure 9p duplication without other chromosomal structural variations is very rare. It has recently been reported that cases with partial 9p duplication including SMARCA2 have phenotypes overlapping with Coffin-Siris syndrome (CSS). Herein, we present a family with pure 9p duplication syndrome in which phenotypes partially characteristic of CSS were identified. In one of two siblings, X-ray examination revealed hypoplasia of the distal phalanges of the fifth fingers, aplasia of the middle phalanges of the fifth fingers, and aplasia of the distal phalanges of the second to fifth toes. In pure 9p duplication together with our one affected case, 9 out of 14 cases (64.3%), excluding cases whose clinical data were unavailable, presented the absence or hypoplasia of the middle phalanges of fingers or toes. Interestingly, there are no reports on CSS with aplasia or hypoplasia of the middle phalanx. Therefore, this family might suggest that the aplasia or hypoplasia of the middle phalanges of the fifth fingers or toes is a distinct finding that can distinguish between pure 9p duplication and CSS.
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Affiliation(s)
- Anna Sato
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Toshifumi Suzuki
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan; Department of Obstetrics and Gynecology, Keiai Hospital, Saitama, Japan.
| | - Mitsuru Ikeno
- Department of Pediatrics, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Jun Takeda
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Yuka Yamamoto
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Mitsuko Shinohara
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Shintaro Makino
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan; Aiiku Research Institute for Maternal, Child Health and Welfare, Tokyo, Japan
| | - Toshiaki Shimizu
- Department of Pediatrics, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, Juntendo University Faculty of Medicine, Tokyo, Japan
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12
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Abstract
Nicolaides-Baraitser syndrome (NCBRS) (OMIM 601358) is an uncommon but well-recognized autosomal dominant entity that is characterized by sparse scalp hair, characteristic coarse facies, microcephaly, seizures, developmental delay, intellectual disability (ID) and prominence of the interphalangeal joints and distal phalanges. Seizures are also common finding besides developmental delay and ID, which is severe approximately in half, moderate in one third and mild in the remainder. Here, we report two Turkish patients with NCBRS. One has a novel variant [NM_003070.5:c.3389G>T p.(Gly1130Val)] and a mild-moderate phenotype, and the other has a known variant [NM_003070.5:c.2554G>A p.(Glu852Lys)] correlated with severe phenotype.
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13
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Corpus callosum metrics predict severity of visuospatial and neuromotor dysfunctions in ARID1B mutations with Coffin-Siris syndrome. Psychiatr Genet 2020; 29:237-242. [PMID: 30933046 DOI: 10.1097/ypg.0000000000000225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ARID1B mutations in Coffin-Siris syndrome are a cause of intellectual disability (0.5-1%), with various degrees of autism and agenesis of the corpus callosum (10%). Little is known regarding the cognitive and motor consequences of ARID1B mutations in humans and no link has been made between corpus callosum anomalies and visuospatial and neuromotor dysfunctions. We have investigated the visuospatial and neuromotor phenotype in eight patients with ARID1B mutations. A paramedian sagittal section of the brain MRI was selected, and corpus callosum was measured in anteroposterior length, genu and trunk width. Spearman's rank order coefficients were used to explore correlations between visuospatial and social cognitive variables and dimensions of the corpus callosum. A significant correlation between genu width size and visual cognition was observed. Retrocerebellar cysts were associated with corpus callosum anomalies. Here, we show that corpus callosum anomalies caused in ARID1B mutations may be predictive of the visuospatial and motor phenotype in Coffin-Siris syndrome.
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14
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Yamamoto T, Imaizumi T, Yamamoto-Shimojima K, Lu Y, Yanagishita T, Shimada S, Chong PF, Kira R, Ueda R, Ishiyama A, Takeshita E, Momosaki K, Ozasa S, Akiyama T, Kobayashi K, Oomatsu H, Kitahara H, Yamaguchi T, Imai K, Kurahashi H, Okumura A, Oguni H, Seto T, Okamoto N. Genomic backgrounds of Japanese patients with undiagnosed neurodevelopmental disorders. Brain Dev 2019; 41:776-782. [PMID: 31171384 DOI: 10.1016/j.braindev.2019.05.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/08/2019] [Accepted: 05/21/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND Recently, many genes related to neurodevelopmental disorders have been identified by high-throughput genomic analysis; however, a comprehensive understanding of the mechanism underlying neurodevelopmental disorders remains to be established. To further understand these underlying mechanisms, we performed a comprehensive genomic analysis of patients with undiagnosed neurodevelopmental disorders. METHODS Genomic analysis using next-generation sequencing with a targeted panel was performed for a total of 133 Japanese patients (male/female, 81/52) with previously undiagnosed neurodevelopmental disorders, including developmental delay (DD), intellectual disability (ID), autism spectrum disorder (ASD), and epilepsy. Genomic copy numbers were also analyzed using the eXome Hidden Markov Model (XHMM). RESULTS Thirty-nine patients (29.3%) exhibited pathogenic or likely pathogenic findings with single-gene variants or chromosomal aberrations. Among them, 20 patients were presented here. Pathogenic or likely pathogenic variants were identified in 18 genes, including ACTG1, CACNA1A, CHD2, CDKL5, DNMT3A, EHMT1, GABRB3, GABRG2, GRIN2B, KCNQ3, KDM5C, MED13L, SCN2A, SHANK3, SMARCA2, STXBP1, SYNGAP1, and TBL1XR1. CONCLUSION A diagnostic yield of 29.3% in this study was nearly the same as that previously reported from other countries. Thus, we suggest that there is no difference in genomic backgrounds in Japanese patients with undiagnosed neurodevelopmental disabilities. Although most of the patients possessed de novo variants, one of the patients showed an X-linked inheritance pattern. As X-linked recessive disorders exhibit the possibility of recurrent occurrence in the family, comprehensive molecular diagnosis is important for genetic counseling.
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Affiliation(s)
- Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan.
| | - Taichi Imaizumi
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Department of Pediatrics, St. Mariannna University School of Medicine, Kawasaki, Japan
| | - Keiko Yamamoto-Shimojima
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Tokyo Women's Medical University Institute of Integrated Medical Sciences, Tokyo, Japan
| | - Yongping Lu
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Tomoe Yanagishita
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan; Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Shino Shimada
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Pin Fee Chong
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Riyo Ueda
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Akihiko Ishiyama
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Eri Takeshita
- Department of Child Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Ken Momosaki
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Shiro Ozasa
- Department of Pediatrics, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Tomoyuki Akiyama
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Katsuhiro Kobayashi
- Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroo Oomatsu
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | - Hikaru Kitahara
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | - Tokito Yamaguchi
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | - Katsumi Imai
- Department of Pediatrics, National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, Japan
| | | | - Akihisa Okumura
- Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Hirokazu Oguni
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Toshiyuki Seto
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
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15
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Pascolini G, Valiante M, Bottillo I, Laino L, Fleischer N, Ferraris A, Grammatico P. Striking phenotypic overlap between Nicolaides-Baraitser and Coffin-Siris syndromes in monozygotic twins with ARID1B intragenic deletion. Eur J Med Genet 2019; 63:103739. [PMID: 31421289 DOI: 10.1016/j.ejmg.2019.103739] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/05/2019] [Accepted: 08/13/2019] [Indexed: 11/15/2022]
Abstract
The chromatin remodeling AT-Rich interaction domain containing 1B protein (ARID1B) also known as BAF-associated factor, 250-KD, B (BAF250B) codified by the ARID1B gene (MIM#614556), is a small subunit of the mammalian SWI/SNF or BAF complex, an ATP-dependent protein machinery which is able to activate or repress gene transcription, allowing protein access to histones through DNA relaxed conformation. ARID1B gene mutations have been associated with two hereditary syndromic conditions, namely Coffin-Siris (CSS, MIM#135900) and Nicolaides-Baraitser syndromes (NCBRS, MIM#601358), characterized by neurodevelopment delay, craniofacial dysmorphisms and skeletal anomalies. Furthermore, intellectual impairment and central nervous system (CNS) alterations, comprising abnormal corpus callosum, have been associated with mutations in this gene. Moreover, ARID1B anomalies resulted to be involved in neoplastic events and Hirschprung disease. Here we report on two monozygotic male twins, displaying clinical appearance strikingly resembling NCBRS and CSS phenotype, who resulted carriers of a novel 6q25.3 microdeletion, encompassing only part of the ARID1B gene. The deleted segment was not inherited from the only parent tested and afflicted the first exons of the gene, coding for protein disordered region. We also provide, for the first time, a review of previously published ARID1B mutated patients with NCBRS and CSS phenotype and a computer-assisted dysmorphology analysis of NCBRS and ARID1B related CSS individuals, through the Face2Gene suite, confirming the existence of highly overlapping facial gestalt of both conditions. The present findings indicate that ARID1B could be considered a contributing gene not only in CSS but also in NCBRS phenotype, although the main gene related to this latter condition is the SMARCA2 gene (MIM#600014), another component of the BAF complex. So, ARID1B study should be considered in such individuals.
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Affiliation(s)
- Giulia Pascolini
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy.
| | - Michele Valiante
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Irene Bottillo
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Luigi Laino
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | | | - Alessandro Ferraris
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Paola Grammatico
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
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16
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Chater-Diehl E, Ejaz R, Cytrynbaum C, Siu MT, Turinsky A, Choufani S, Goodman SJ, Abdul-Rahman O, Bedford M, Dorrani N, Engleman K, Flores-Daboub J, Genevieve D, Mendoza-Londono R, Meschino W, Perrin L, Safina N, Townshend S, Scherer SW, Anagnostou E, Piton A, Deardorff M, Brudno M, Chitayat D, Weksberg R. New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome. BMC Med Genomics 2019; 12:105. [PMID: 31288860 PMCID: PMC6617651 DOI: 10.1186/s12920-019-0555-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/30/2019] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. Pathogenic variants in genes that encode epigenetic regulators have been associated with genome-wide changes in DNA methylation (DNAm) in affected individuals termed DNAm signatures. METHODS Genome-wide DNAm was assessed in whole-blood samples from the individuals with pathogenic SMARCA2 variants and NCBRS diagnosis (n = 8) compared to neurotypical controls (n = 23) using the Illumina MethylationEPIC array. Differential methylated CpGs between groups (DNAm signature) were identified and used to generate a model enabling classification variants of uncertain significance (VUS; n = 9) in SMARCA2 as "pathogenic" or "benign". A validation cohort of NCBRS cases (n = 8) and controls (n = 96) demonstrated 100% model sensitivity and specificity. RESULTS We identified a DNAm signature of 429 differentially methylated CpG sites in individuals with NCBRS. The genes to which these CpG sites map are involved in cell differentiation, calcium signaling, and neuronal function consistent with NCBRS pathophysiology. DNAm model classifications of VUS were concordant with the clinical phenotype; those within the SMARCA2 ATPase/helicase domain classified as "pathogenic". A patient with a mild neurodevelopmental NCBRS phenotype and a VUS distal to the ATPase/helicase domain did not score as pathogenic, clustering away from cases and controls. She demonstrated an intermediate DNAm profile consisting of one subset of signature CpGs with methylation levels characteristic of controls and another characteristic of NCBRS cases; each mapped to genes with ontologies consistent with the patient's unique clinical presentation. CONCLUSIONS Here we find that a DNAm signature of SMARCA2 pathogenic variants in NCBRS maps to CpGs relevant to disorder pathophysiology, classifies VUS, and is sensitive to the position of the variant in SMARCA2. The patient with an intermediate model score demonstrating a unique genotype-epigenotype-phenotype correlation underscores the potential utility of this signature as a functionally relevant VUS classification system scalable beyond binary "benign" versus "pathogenic" scoring. This is a novel feature of DNAm signatures that could enable phenotypic predictions from genotype data. Our findings also demonstrate that DNAm signatures can be domain-specific, highlighting the precision with which they can reflect genotypic variation.
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Affiliation(s)
- Eric Chater-Diehl
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Resham Ejaz
- Division of Genetics, Department of Pediatrics, McMaster University, Hamilton, Ontario L8S 4L8 Canada
| | - Cheryl Cytrynbaum
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Michelle T. Siu
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Andrei Turinsky
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Sanaa Choufani
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Sarah J. Goodman
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
| | - Omar Abdul-Rahman
- Department of Genetic Medicine, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE USA
| | - Melanie Bedford
- Genetics Program, North York General Hospital, Toronto, Ontario M2K 1E1 Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario M5S 3H7 Canada
| | | | - Kendra Engleman
- Division of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 66111 USA
| | - Josue Flores-Daboub
- Division of Pediatric Clinical Genetics, University of Utah School of Medicine, Salt Lake City, UT 84132 USA
| | - David Genevieve
- Service de génétique clinique, Département de génétique médicale, maladies rares, médecine personnalisée, Unité INSERM U1183, Université Montpellier, CHU Montpellier, 34000 Montpellier, France
| | - Roberto Mendoza-Londono
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Pediatrics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Wendy Meschino
- Genetics Program, North York General Hospital, Toronto, Ontario M2K 1E1 Canada
| | - Laurence Perrin
- AP-HP, Department of Genetics, Hôpital Robert Debré, 75019 Paris, France
| | - Nicole Safina
- University of Missouri Kansas City, School of Medicine, Kansas City, MO 64108 USA
- Division of Clinical Genetics, Children’s Mercy Hospital, Kansas City, MO 64108 USA
- Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO 64108 USA
| | - Sharron Townshend
- Department of Health, Government of Western Australia, Genetic Services of Western Australia, Perth, WA Australia
| | - Stephen W. Scherer
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- McLaughlin Centre, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Evdokia Anagnostou
- Holland Bloorview Kids Rehabilitation Hospital Toronto, Toronto, Ontario M4G 1R8 Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - Amelie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
- Laboratoire de Diagnostic Génétique, Nouvel Hôpital Civil, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
| | - Matthew Deardorff
- Division of Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- The Department of Pediatrics, The Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Michael Brudno
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario M5S 1A1 Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
- Prenatal Diagnosis and Medical Genetics Program, Mount Sinai Hospital, Toronto, Ontario M5G 1X5 Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario M5G 1X8 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1 Canada
- Institute of Medical Sciences, University of Toronto, Toronto, Ontario M5S 1A8 Canada
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17
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Bell S, Rousseau J, Peng H, Aouabed Z, Priam P, Theroux JF, Jefri M, Tanti A, Wu H, Kolobova I, Silviera H, Manzano-Vargas K, Ehresmann S, Hamdan FF, Hettige N, Zhang X, Antonyan L, Nassif C, Ghaloul-Gonzalez L, Sebastian J, Vockley J, Begtrup AG, Wentzensen IM, Crunk A, Nicholls RD, Herman KC, Deignan JL, Al-Hertani W, Efthymiou S, Salpietro V, Miyake N, Makita Y, Matsumoto N, Østern R, Houge G, Hafström M, Fassi E, Houlden H, Klein Wassink-Ruiter JS, Nelson D, Goldstein A, Dabir T, van Gils J, Bourgeron T, Delorme R, Cooper GM, Martinez JE, Finnila CR, Carmant L, Lortie A, Oegema R, van Gassen K, Mehta SG, Huhle D, Abou Jamra R, Martin S, Brunner HG, Lindhout D, Au M, Graham JM, Coubes C, Turecki G, Gravel S, Mechawar N, Rossignol E, Michaud JL, Lessard J, Ernst C, Campeau PM. Mutations in ACTL6B Cause Neurodevelopmental Deficits and Epilepsy and Lead to Loss of Dendrites in Human Neurons. Am J Hum Genet 2019; 104:815-834. [PMID: 31031012 PMCID: PMC6507050 DOI: 10.1016/j.ajhg.2019.03.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 03/01/2019] [Indexed: 02/04/2023] Open
Abstract
We identified individuals with variations in ACTL6B, a component of the chromatin remodeling machinery including the BAF complex. Ten individuals harbored bi-allelic mutations and presented with global developmental delay, epileptic encephalopathy, and spasticity, and ten individuals with de novo heterozygous mutations displayed intellectual disability, ambulation deficits, severe language impairment, hypotonia, Rett-like stereotypies, and minor facial dysmorphisms (wide mouth, diastema, bulbous nose). Nine of these ten unrelated individuals had the identical de novo c.1027G>A (p.Gly343Arg) mutation. Human-derived neurons were generated that recaptured ACTL6B expression patterns in development from progenitor cell to post-mitotic neuron, validating the use of this model. Engineered knock-out of ACTL6B in wild-type human neurons resulted in profound deficits in dendrite development, a result recapitulated in two individuals with different bi-allelic mutations, and reversed on clonal genetic repair or exogenous expression of ACTL6B. Whole-transcriptome analyses and whole-genomic profiling of the BAF complex in wild-type and bi-allelic mutant ACTL6B neural progenitor cells and neurons revealed increased genomic binding of the BAF complex in ACTL6B mutants, with corresponding transcriptional changes in several genes including TPPP and FSCN1, suggesting that altered regulation of some cytoskeletal genes contribute to altered dendrite development. Assessment of bi-alleic and heterozygous ACTL6B mutations on an ACTL6B knock-out human background demonstrated that bi-allelic mutations mimic engineered deletion deficits while heterozygous mutations do not, suggesting that the former are loss of function and the latter are gain of function. These results reveal a role for ACTL6B in neurodevelopment and implicate another component of chromatin remodeling machinery in brain disease.
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Affiliation(s)
- Scott Bell
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Justine Rousseau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Huashan Peng
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Zahia Aouabed
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Pierre Priam
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Jean-Francois Theroux
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Malvin Jefri
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Arnaud Tanti
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Hanrong Wu
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Ilaria Kolobova
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Heika Silviera
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Karla Manzano-Vargas
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Sophie Ehresmann
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Fadi F Hamdan
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Nuwan Hettige
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Xin Zhang
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Lilit Antonyan
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Christina Nassif
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Lina Ghaloul-Gonzalez
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jessica Sebastian
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Jerry Vockley
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | | | | | | | - Robert D Nicholls
- Department of Pediatrics, Division of Medical Genetics, University of Pittsburgh, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Kristin C Herman
- University of California at Davis Medical Center, Section of Medical Genomics, Sacramento, CA 95817, USA
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Walla Al-Hertani
- Departments of Medical Genetics and Paediatrics, Cumming School of Medicine, Alberta Children's Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Stephanie Efthymiou
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Vincenzo Salpietro
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Yoshio Makita
- Education Center, Asahikawa Medical University, Asahikawa 078-8510, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Rune Østern
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, 5021 Bergen, Norway
| | - Maria Hafström
- Department of Pediatrics, St. Olav's Hospital, Trondheim University Hospital, Postbox 3250, Sluppen 7006 Trondheim, Norway
| | - Emily Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, WC1N 3BG London, UK
| | - Jolien S Klein Wassink-Ruiter
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Dominic Nelson
- McGill University, Department of Human Genetics, Montreal, QC H3G 0B1, Canada
| | - Amy Goldstein
- Division of Child Neurology, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Belfast Health and Social Care Trust, Belfast City Hospital, Lisburn Road, Belfast BT9 7AB, UK
| | - Julien van Gils
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, University Paris Diderot, Paris 75015, France
| | - Richard Delorme
- Assistance Publique Hôpitaux de Paris (APHP), Robert Debré Hospital, Child and Adolescent Psychiatry Department, Paris, France
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | | | | | - Lionel Carmant
- Children's Rehabilitation Service, Mobile, AL 36604, USA
| | - Anne Lortie
- Department of Neurology, University of Montreal, Montreal, QC, Canada
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Koen van Gassen
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Sarju G Mehta
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Dagmar Huhle
- Department of Clinical Genetics, Addenbrookes Hospital, Cambridge CB2 0QQ, UK
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Sonja Martin
- Institute of Human Genetics, University Medical Center Leipzig, 04103 Leipzig, Germany
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Nijmegen 6500 GA, the Netherlands; Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands
| | - Dick Lindhout
- Department of Genetics, University Medical Center Utrecht, Utrecht & Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede, the Netherlands
| | - Margaret Au
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - John M Graham
- Medical Genetics, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Christine Coubes
- Service de génétique clinique, Département de génétique médicale, Maladies rares et médecine personnalisée, Centre de Référence Anomalies du développement et Syndromes malformatifs du Sud-Ouest Occitanie Réunion, CHU de Montpellier, 34295 Montpellier Cedex 5, France
| | - Gustavo Turecki
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Simon Gravel
- Department of Genetics, University of Groningen and University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Naguib Mechawar
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada
| | - Elsa Rossignol
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Jacques L Michaud
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada
| | - Julie Lessard
- Institute for Research in Immunology and Cancer (IRIC), University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Carl Ernst
- Psychiatric Genetics Group, Douglas Hospital Research Institute, McGill University, Montreal, QC H4H 1R3, Canada.
| | - Philippe M Campeau
- CHU-Sainte Justine Research Centre, University of Montreal, Montreal, QC H3T 1C5, Canada.
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18
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Chubak MC, Nixon KCJ, Stone MH, Raun N, Rice SL, Sarikahya M, Jones SG, Lyons TA, Jakub TE, Mainland RLM, Knip MJ, Edwards TN, Kramer JM. Individual components of the SWI/SNF chromatin remodelling complex have distinct roles in memory neurons of the Drosophila mushroom body. Dis Model Mech 2019; 12:12/3/dmm037325. [PMID: 30923190 PMCID: PMC6451433 DOI: 10.1242/dmm.037325] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/23/2019] [Indexed: 12/13/2022] Open
Abstract
Technology has led to rapid progress in the identification of genes involved in neurodevelopmental disorders such as intellectual disability (ID), but our functional understanding of the causative genes is lagging. Here, we show that the SWI/SNF chromatin remodelling complex is one of the most over-represented cellular components disrupted in ID. We investigated the role of individual subunits of this large protein complex using targeted RNA interference in post-mitotic memory-forming neurons of the Drosophila mushroom body (MB). Knockdown flies were tested for defects in MB morphology, short-term memory and long-term memory. Using this approach, we identified distinct roles for individual subunits of the Drosophila SWI/SNF complex. Bap60, Snr1 and E(y)3 are required for pruning of the MBγ neurons during pupal morphogenesis, while Brm and Osa are required for survival of MBγ axons during ageing. We used the courtship conditioning assay to test the effect of MB-specific SWI/SNF knockdown on short- and long-term memory. Several subunits, including Brm, Bap60, Snr1 and E(y)3, were required in the MB for both short- and long-term memory. In contrast, Osa knockdown only reduced long-term memory. Our results suggest that individual components of the SWI/SNF complex have different roles in the regulation of structural plasticity, survival and functionality of post-mitotic MB neurons. This study highlights the many possible processes that might be disrupted in SWI/SNF-related ID disorders. Our broad phenotypic characterization provides a starting point for understanding SWI/SNF-mediated gene regulatory mechanisms that are important for development and function of post-mitotic neurons. Summary: The SWI/SNF chromatin remodelling complex is the most over-represented protein complex in the intellectual disability. Different components of this complex have distinct roles in development and function of memory-forming neurons in the Drosophila mushroom body.
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Affiliation(s)
- Melissa C Chubak
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada
| | - Kevin C J Nixon
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Max H Stone
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada.,Division of Genetics and Development, Children's Health Research Institute, London, ON N6C 2V5, Canada
| | - Nicholas Raun
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada.,Division of Genetics and Development, Children's Health Research Institute, London, ON N6C 2V5, Canada
| | - Shelby L Rice
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada
| | - Mohammed Sarikahya
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Spencer G Jones
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Taylor A Lyons
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Taryn E Jakub
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Roslyn L M Mainland
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Maria J Knip
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Tara N Edwards
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Jamie M Kramer
- Department of Biology, Faculty of Science, Western University, London, ON N6A 5B7, Canada .,Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada.,Division of Genetics and Development, Children's Health Research Institute, London, ON N6C 2V5, Canada
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19
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Khazanchi R, Ronspies CA, Smith SC, Starr LJ. Patient with anomalous skin pigmentation expands the phenotype of ARID2 loss-of-function disorder, a SWI/SNF-related intellectual disability. Am J Med Genet A 2019; 179:808-812. [PMID: 30838730 DOI: 10.1002/ajmg.a.61075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 12/12/2018] [Accepted: 12/13/2018] [Indexed: 12/20/2022]
Abstract
ARID2 loss-of-function is associated with a rare genetic disorder characterized in 14 reported patients to date. ARID2 encodes a member of the SWItch/sucrose non-fermentable chromatin remodeling complex. Other genes encoding subunits of this complex, such as ARID1A, ARID1B, and SMARCA2, are mutated in association with Coffin-Siris syndrome (CSS) and Nicolaides Baraitser syndrome (NCBRS) phenotypes. Previously reported ARID2 mutations manifested clinically with a CSS-like phenotype including intellectual disability, coarsened facial features, fifth toenail hypoplasia, and other recognizable dysmorphisms. However, heterogeneity exists between previously reported patients with some patients showing more overlapping features with NCBRS. Herein, we present a patient with a novel disease-causing ARID2 loss-of-function mutation. His clinical features included intellectual disability, coarse and dysmorphic facial features, toenail hypoplasia, ADHD, short stature, and delayed development consistent with prior reports. Our patient also presented with previously unreported clinical findings including ophthalmologic involvement, persistent fetal fingertip and toetip pads, and diffuse hyperpigmentary and hypopigmentary changes sparing his face, palms, and soles. The anomalous skin findings are particularly of interest given prior literature outlining the role of ARID2 in melanocyte homeostasis and melanoma. This clinical report and review of the literature is further affirming of the characteristic symptoms and expands the phenotype of this newly described and rare syndrome.
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Affiliation(s)
- Rohan Khazanchi
- College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska
| | - Carey A Ronspies
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska
| | - Scott C Smith
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska
| | - Lois J Starr
- Munroe-Meyer Institute for Genetics & Rehabilitation, University of Nebraska Medical Center, Omaha, Nebraska
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van der Sluijs PJ, Jansen S, Vergano SA, Adachi-Fukuda M, Alanay Y, AlKindy A, Baban A, Bayat A, Beck-Wödl S, Berry K, Bijlsma EK, Bok LA, Brouwer AFJ, van der Burgt I, Campeau PM, Canham N, Chrzanowska K, Chu YWY, Chung BHY, Dahan K, De Rademaeker M, Destree A, Dudding-Byth T, Earl R, Elcioglu N, Elias ER, Fagerberg C, Gardham A, Gener B, Gerkes EH, Grasshoff U, van Haeringen A, Heitink KR, Herkert JC, den Hollander NS, Horn D, Hunt D, Kant SG, Kato M, Kayserili H, Kersseboom R, Kilic E, Krajewska-Walasek M, Lammers K, Laulund LW, Lederer D, Lees M, López-González V, Maas S, Mancini GMS, Marcelis C, Martinez F, Maystadt I, McGuire M, McKee S, Mehta S, Metcalfe K, Milunsky J, Mizuno S, Moeschler JB, Netzer C, Ockeloen CW, Oehl-Jaschkowitz B, Okamoto N, Olminkhof SNM, Orellana C, Pasquier L, Pottinger C, Riehmer V, Robertson SP, Roifman M, Rooryck C, Ropers FG, Rosello M, Ruivenkamp CAL, Sagiroglu MS, Sallevelt SCEH, Sanchis Calvo A, Simsek-Kiper PO, Soares G, Solaeche L, Sonmez FM, Splitt M, Steenbeek D, Stegmann APA, Stumpel CTRM, Tanabe S, Uctepe E, Utine GE, Veenstra-Knol HE, Venkateswaran S, Vilain C, Vincent-Delorme C, Vulto-van Silfhout AT, Wheeler P, Wilson GN, Wilson LC, Wollnik B, Kosho T, Wieczorek D, Eichler E, Pfundt R, de Vries BBA, Clayton-Smith J, Santen GWE. The ARID1B spectrum in 143 patients: from nonsyndromic intellectual disability to Coffin-Siris syndrome. Genet Med 2018; 21:1295-1307. [PMID: 30349098 PMCID: PMC6752273 DOI: 10.1038/s41436-018-0330-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 09/26/2018] [Indexed: 01/09/2023] Open
Abstract
Purpose Pathogenic variants in ARID1B are one of the most frequent causes of intellectual disability (ID) as determined by large-scale exome sequencing studies. Most studies published thus far describe clinically diagnosed Coffin–Siris patients (ARID1B-CSS) and it is unclear whether these data are representative for patients identified through sequencing of unbiased ID cohorts (ARID1B-ID). We therefore sought to determine genotypic and phenotypic differences between ARID1B-ID and ARID1B-CSS. In parallel, we investigated the effect of different methods of phenotype reporting. Methods Clinicians entered clinical data in an extensive web-based survey. Results 79 ARID1B-CSS and 64 ARID1B-ID patients were included. CSS-associated dysmorphic features, such as thick eyebrows, long eyelashes, thick alae nasi, long and/or broad philtrum, small nails and small or absent fifth distal phalanx and hypertrichosis, were observed significantly more often (p < 0.001) in ARID1B-CSS patients. No other significant differences were identified. Conclusion There are only minor differences between ARID1B-ID and ARID1B-CSS patients. ARID1B-related disorders seem to consist of a spectrum, and patients should be managed similarly. We demonstrated that data collection methods without an explicit option to report the absence of a feature (such as most Human Phenotype Ontology-based methods) tended to underestimate gene-related features.
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Affiliation(s)
| | - Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Samantha A Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of the King's Daughters, Norfolk, VA, USA
| | - Miho Adachi-Fukuda
- Department of Pediatrics, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Yasemin Alanay
- School of Medicine, Department of Pediatrics, Pediatric Genetics Unit, Acibadem University, Istanbul, Turkey
| | - Adila AlKindy
- Department of Genetics, Sultan Qaboos University Hospital, Muscat, Oman
| | - Anwar Baban
- Pediatric Cardiology and Cardiac Surgery Department, Bambino Gesù Children Hospital and Research Institute, IRCCS, Rome, Italy
| | - Allan Bayat
- Copenhagen University Hospital Hvidovre, Copenhagen, Denmark
| | - Stefanie Beck-Wödl
- Department of Molecular Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Katherine Berry
- Department of Medical Genetics, Shodair Hospital, Helena, MT, USA
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Levinus A Bok
- Department of Pediatrics, Màxima Medical Centre, Veldhoven, The Netherlands
| | - Alwin F J Brouwer
- Department of Paediatrics, Nij Smellinghe Hospital, Drachten, The Netherlands
| | - Ineke van der Burgt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philippe M Campeau
- Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Natalie Canham
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, United Kingdom.,Cheshire and Merseyside Regional Genetics Service, Liverpool Women's Hospital, Crown Street, Liverpool, United Kingdom
| | - Krystyna Chrzanowska
- Department of Medical Genetics, The Children's Memorial Health Institute, Warsaw, Poland
| | - Yoyo W Y Chu
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Brain H Y Chung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Karin Dahan
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | | | - Anne Destree
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Tracy Dudding-Byth
- Hunter Genetics and University of Newcastle, GrowUpWell Priority Research Centre, Newcastle, Australia
| | - Rachel Earl
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Nursel Elcioglu
- Department of Pediatric Genetics, Marmara University Pendik Hospital, Istanbul, Turkey
| | - Ellen R Elias
- Department of Pediatrics and Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Christina Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Alice Gardham
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow, United Kingdom
| | - Blanca Gener
- Department of Genetics, Cruces University Hospital, Biocruces Health Research Institute, Vizcayam, Spain
| | - Erica H Gerkes
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Ute Grasshoff
- Department of Molecular Genetics and Applied Genomics, University Hospital Tübingen, Tübingen, Germany
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Karin R Heitink
- Department of Rehabilitation Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Johanna C Herkert
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | | | - Denise Horn
- Institute for Medical Genetics and Human Genetics, Charité Universitätsmedizin, Berlin, Germany
| | - David Hunt
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, United Kingdom
| | - Sarina G Kant
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Hülya Kayserili
- Medical Genetics Department, Koç University School of Medicine (KUSoM), İstanbul, Turkey
| | - Rogier Kersseboom
- Department of Clinical Genetics, Sophia Children's Hospital, Erasmus MC, Rotterdam, The Netherlands
| | - Esra Kilic
- Department of Pediatric Genetics, Hematology Oncology Research & Training Children's Hospital, Ankara, Turkey
| | | | - Kylin Lammers
- Department of Medical Genetics, Dayton Children's Hospital, Dayton, OH, USA
| | - Lone W Laulund
- Department of Paediatrics, Odense University Hospital, Odense, Denmark
| | - Damien Lederer
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Melissa Lees
- Department of Clinical Genetics, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Vanesa López-González
- Sección de Genética Médica, Servicio de Pediatria, Hospital Clinico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, CIBERER-ISCIII, Murcia, Spain
| | - Saskia Maas
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Grazia M S Mancini
- Department of Clinical Genetics, Sophia Children's Hospital, Erasmus MC, Rotterdam, The Netherlands
| | - Carlo Marcelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Francisco Martinez
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Isabelle Maystadt
- Center for Human Genetics, Institute of Pathology and Genetics, Gosselies, Belgium
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Shane McKee
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, Ireland
| | - Sarju Mehta
- East Anglian Regional Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | | | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Kasugai, Aichi, Japan
| | - John B Moeschler
- Department of Pediatrics, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Christian Netzer
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Charlotte W Ockeloen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Sharon N M Olminkhof
- Willem Alexander Children's Hospital, Leiden University Medical Center, Leiden, The Netherlands
| | - Carmen Orellana
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Laurent Pasquier
- CRMR Déficiences intellectuelles, Service de Génétique Médicale, CLAD Ouest CHU Hôpital Sud, Rennes, France
| | - Caroline Pottinger
- All Wales Medical Genetics Service, Glan Clwyd Hospital, Rhyl, United Kingdom
| | - Vera Riehmer
- Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | | | - Maian Roifman
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Fabienne G Ropers
- Department of Pediatrics, Leiden University Medical Center, Leiden, The Netherlands
| | - Monica Rosello
- Unidad de Genética, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Suzanne C E H Sallevelt
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | | | - Pelin O Simsek-Kiper
- Department of Pediatric Genetics, Ihsan Dogramaci Children's Hospital, Hacettepe University School of Medicine, Ankara, Turkey
| | - Gabriela Soares
- Jacinto de Magalhães Medical Genetics Center, Centro Hospitalar do Porto, Porto, Portugal
| | - Lucia Solaeche
- Departamento de neurometabólicas, Hospital Universitario Son Espases, Palma de Mallorca, Spain
| | - Fatma Mujgan Sonmez
- Karadeniz Technical University, Faculty of Medicine, Dept of Child Neurology, Retired Professor, Trabzon, Turkey
| | - Miranda Splitt
- Northern Genetics Service, Institute of Genetics Medicine, Newcastle upon Tyne, United Kingdom
| | - Duco Steenbeek
- Department of Rehabilitation Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Constance T R M Stumpel
- Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Saori Tanabe
- Division of Pediatrics, Yamagata Prefectural and Sakata Munici pal Hospital Organization Nihon-Kai General Hospital, Sakata, Japan
| | | | - G Eda Utine
- Department of Pediatric Genetics, Ihsan Dogramaci Children's Hospital, Hacettepe University School of Medicine, Ankara, Turkey
| | - Hermine E Veenstra-Knol
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Sunita Venkateswaran
- Division of Neurology, Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON, Canada
| | - Catheline Vilain
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Medical Genetics, Université Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme. ULB Center of Medical Genetics, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Anneke T Vulto-van Silfhout
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Golder N Wilson
- KinderGenome Genetics, Medical City Hospital Dallas, Dallas, TX, USA
| | - Louise C Wilson
- Department of Clinical Genetics, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Tomoki Kosho
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Japan
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany
| | - Evan Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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21
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Bögershausen N, Wollnik B. Mutational Landscapes and Phenotypic Spectrum of SWI/SNF-Related Intellectual Disability Disorders. Front Mol Neurosci 2018; 11:252. [PMID: 30123105 PMCID: PMC6085491 DOI: 10.3389/fnmol.2018.00252] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/03/2018] [Indexed: 12/29/2022] Open
Abstract
Mutations in genes that encode proteins of the SWI/SNF complex, called BAF complex in mammals, cause a spectrum of disorders that ranges from syndromic intellectual disability to Coffin-Siris syndrome (CSS) to Nicolaides-Baraitser syndrome (NCBRS). While NCBRS is known to be a recognizable and restricted phenotype, caused by missense mutations in SMARCA2, the term CSS has been used lately for a more heterogeneous group of phenotypes that are caused by mutations in either of the genes ARID1B, ARID1A, ARID2, SMARCA4, SMARCB1, SMARCE1, SOX11, or DPF2. In this review, we summarize the current knowledge on the phenotypic traits and molecular causes of the above named conditions, consider the question whether a clinical distinction of the phenotypes is still adequate, and suggest the term "SWI/SNF-related intellectual disability disorders" (SSRIDDs). We will also outline important features to identify the ARID1B-related phenotype in the absence of classic CSS features, and discuss distinctive and overlapping features of the SSRIDD subtypes. Moreover, we will briefly review the function of the SWI/SNF complex in development and describe the mutational landscapes of the genes involved in SSRIDD.
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Affiliation(s)
- Nina Bögershausen
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
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22
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A SMARCA2 Mutation in the First Case Report of Nicolaides-Baraitser Syndrome in Latin America: Genotype-Phenotype Correlation. Case Rep Genet 2017; 2017:8639617. [PMID: 28948053 PMCID: PMC5602489 DOI: 10.1155/2017/8639617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/06/2017] [Indexed: 01/10/2023] Open
Abstract
Nicolaides-Baraitser syndrome (NCBRS) is a rare and well-recognized entity that was first described in 1993, with a prevalence that is currently not known. It is recognized as a distinctive entity, with some variability in its signs and symptoms. The most important characteristics include intellectual disability, peculiar facial features including sparse scalp hair, coarse facial features, low frontal hairline, and microcephaly, and seizures. Additional features may include epicanthic folds, thin upper lip vermilion with thick lower lip vermilion, skeletal abnormalities, and severe language impairment. The disorder is inherited in an autosomal dominant manner caused by de novo mutations in the SMARCA2 gene, with most being missense mutations. We report a young adult patient with NCBRS and, to our knowledge, the first case report of the syndrome in Latin America with a confirmed molecular diagnosis and a mild-to-moderate phenotype.
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23
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Sokpor G, Xie Y, Rosenbusch J, Tuoc T. Chromatin Remodeling BAF (SWI/SNF) Complexes in Neural Development and Disorders. Front Mol Neurosci 2017; 10:243. [PMID: 28824374 PMCID: PMC5540894 DOI: 10.3389/fnmol.2017.00243] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 07/18/2017] [Indexed: 12/26/2022] Open
Abstract
The ATP-dependent BRG1/BRM associated factor (BAF) chromatin remodeling complexes are crucial in regulating gene expression by controlling chromatin dynamics. Over the last decade, it has become increasingly clear that during neural development in mammals, distinct ontogenetic stage-specific BAF complexes derived from combinatorial assembly of their subunits are formed in neural progenitors and post-mitotic neural cells. Proper functioning of the BAF complexes plays critical roles in neural development, including the establishment and maintenance of neural fates and functionality. Indeed, recent human exome sequencing and genome-wide association studies have revealed that mutations in BAF complex subunits are linked to neurodevelopmental disorders such as Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, Kleefstra's syndrome spectrum, Hirschsprung's disease, autism spectrum disorder, and schizophrenia. In this review, we focus on the latest insights into the functions of BAF complexes during neural development and the plausible mechanistic basis of how mutations in known BAF subunits are associated with certain neurodevelopmental disorders.
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Affiliation(s)
- Godwin Sokpor
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany
| | - Yuanbin Xie
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany
| | - Joachim Rosenbusch
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany
| | - Tran Tuoc
- Institute of Neuroanatomy, University Medical Center, Georg-August-University GoettingenGoettingen, Germany.,DFG Center for Nanoscale Microscopy and Molecular Physiology of the BrainGoettingen, Germany
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24
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Marom R, Jain M, Burrage LC, Song IW, Graham BH, Brown CW, Stevens SJC, Stegmann APA, Gunter AT, Kaplan JD, Gavrilova RH, Shinawi M, Rosenfeld JA, Bae Y, Tran AA, Chen Y, Lu JT, Gibbs RA, Eng C, Yang Y, Rousseau J, de Vries BBA, Campeau PM, Lee B. Heterozygous variants in ACTL6A, encoding a component of the BAF complex, are associated with intellectual disability. Hum Mutat 2017. [PMID: 28649782 DOI: 10.1002/humu.23282] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pathogenic variants in genes encoding components of the BRG1-associated factor (BAF) chromatin remodeling complex have been associated with intellectual disability syndromes. We identified heterozygous, novel variants in ACTL6A, a gene encoding a component of the BAF complex, in three subjects with varying degrees of intellectual disability. Two subjects have missense variants affecting highly conserved amino acid residues within the actin-like domain. Missense mutations in the homologous region in yeast actin were previously reported to be dominant lethal and were associated with impaired binding of the human ACTL6A to β-actin and BRG1. A third subject has a splicing variant that creates an in-frame deletion. Our findings suggest that the variants identified in our subjects may have a deleterious effect on the function of the protein by disturbing the integrity of the BAF complex. Thus, ACTL6A gene mutation analysis should be considered in patients with intellectual disability, learning disabilities, or developmental language disorder.
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Affiliation(s)
- Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Mahim Jain
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - I-Wen Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Brett H Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Chester W Brown
- Department of Pediatrics/Genetics Division, University of Tennessee Health Science Center Memphis, Memphis, Tennessee
| | - Servi J C Stevens
- Department of Human Genetics, Maastricht University Hospital, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Human Genetics, Maastricht University Hospital, Maastricht, The Netherlands
| | - Andrew T Gunter
- Department of Pediatrics, Division of Medical Genetics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Julie D Kaplan
- Department of Pediatrics, Division of Medical Genetics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Ralitza H Gavrilova
- Department of Medical Genetics, Mayo Clinic, Rochester, Minnesota.,Department of Neurology, Mayo Clinic, Rochester, Minnesota
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yangjin Bae
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alyssa A Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yuqing Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justine Rousseau
- Department of Pediatrics, CHU Ste-Justine and University of Montreal, Montreal, Canada
| | - Bert B A de Vries
- Department of Human Genetics and Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Philippe M Campeau
- Department of Pediatrics, CHU Ste-Justine and University of Montreal, Montreal, Canada
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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25
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Bidart M, El Atifi M, Miladi S, Rendu J, Satre V, Ray PF, Bosson C, Devillard F, Lehalle D, Malan V, Amiel J, Mencarelli MA, Baldassarri M, Renieri A, Clayton-Smith J, Vieville G, Thevenon J, Amblard F, Berger F, Jouk PS, Coutton C. Microduplication of the ARID1A gene causes intellectual disability with recognizable syndromic features. Genet Med 2016; 19:701-710. [PMID: 27906199 DOI: 10.1038/gim.2016.180] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/04/2016] [Indexed: 12/13/2022] Open
Abstract
PURPOSE To determine whether duplication of the ARID1A gene is responsible for a new recognizable syndrome. METHODS We describe four patients with a 1p36.11 microduplication involving ARID1A as identified by array-comparative genomic hybridization . We performed comparative transcriptomic analysis of patient-derived fibroblasts using RNA sequencing and evaluated the impact of ARID1A duplication on the cell cycle using fluorescence-activated cell sorting. Functional relationships between differentially expressed genes were investigated with ingenuity pathway analysis (IPA). RESULTS Combining the genomic data, we defined a small (122 kb), minimally critical region that overlaps the full ARID1A gene. The four patients shared a strikingly similar phenotype that included intellectual disability and microcephaly. Transcriptomic analysis revealed the deregulated expression of several genes previously linked to microcephaly and developmental disorders as well as the involvement of signaling pathways relevant to microcephaly, among which the polo-like kinase (PLK) pathway was especially notable. Cell-cycle analysis of patient-derived fibroblasts showed a significant increase in the proportion of cells in G1 phase at the expense of G2-M cells. CONCLUSION Our study reports a new microduplication syndrome involving the ARID1A gene. This work is the first step in clarifying the pathophysiological mechanism that links changes in the gene dosage of ARID1A with intellectual disability and microcephaly.Genet Med advance online publication 01 December 2016.
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Affiliation(s)
- Marie Bidart
- UF Clinatec, Pôle Recherche, INSERM UMR 1205, CHU de Grenoble, Grenoble, France.,Université Grenoble-Alpes, Grenoble, France
| | - Michèle El Atifi
- UF Clinatec, Pôle Recherche, INSERM UMR 1205, CHU de Grenoble, Grenoble, France.,Université Grenoble-Alpes, Grenoble, France
| | - Sarra Miladi
- UF Clinatec, Pôle Recherche, INSERM UMR 1205, CHU de Grenoble, Grenoble, France.,Université Grenoble-Alpes, Grenoble, France
| | - John Rendu
- Université Grenoble-Alpes, Grenoble, France.,Département de Biochimie Toxicologie et Pharmacologie, Département de Biochimie Génétique et Moléculaire, Centre Hospitalier Universitaire de Grenoble, Grenoble, France
| | - Véronique Satre
- Université Grenoble-Alpes, Grenoble, France.,Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France.,Equipe "Genetics Epigenetics and Therapies of Infertility," Institut Albert Bonniot, INSERM U823, La Tronche, France
| | - Pierre F Ray
- Université Grenoble-Alpes, Grenoble, France.,Département de Biochimie Toxicologie et Pharmacologie, Département de Biochimie Génétique et Moléculaire, Centre Hospitalier Universitaire de Grenoble, Grenoble, France.,Equipe "Genetics Epigenetics and Therapies of Infertility," Institut Albert Bonniot, INSERM U823, La Tronche, France
| | - Caroline Bosson
- Département de Biochimie Toxicologie et Pharmacologie, Département de Biochimie Génétique et Moléculaire, Centre Hospitalier Universitaire de Grenoble, Grenoble, France
| | - Françoise Devillard
- Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France
| | - Daphné Lehalle
- Service de Génétique, INSERM U781, Hôpital Necker-Enfants Malades, Institut Imagine, University Sorbonne-Paris-Cité, Paris, France
| | - Valérie Malan
- Service de Cytogénétique et UMR_S1163, IHU Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | - Jeanne Amiel
- Service de Génétique, INSERM U781, Hôpital Necker-Enfants Malades, Institut Imagine, University Sorbonne-Paris-Cité, Paris, France
| | | | - Margherita Baldassarri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.,Medical Genetics, University of Siena, Siena, Italy
| | - Alessandra Renieri
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy.,Medical Genetics, University of Siena, Siena, Italy
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Gaëlle Vieville
- Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence "Anomalies du Développement et Syndromes Malformatifs," Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Florence Amblard
- Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France
| | - François Berger
- UF Clinatec, Pôle Recherche, INSERM UMR 1205, CHU de Grenoble, Grenoble, France.,Université Grenoble-Alpes, Grenoble, France
| | - Pierre-Simon Jouk
- Université Grenoble-Alpes, Grenoble, France.,Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France
| | - Charles Coutton
- Université Grenoble-Alpes, Grenoble, France.,Département de Génétique et Procréation, Hôpital Couple-Enfant, CHU de Grenoble, Grenoble, France.,Equipe "Genetics Epigenetics and Therapies of Infertility," Institut Albert Bonniot, INSERM U823, La Tronche, France
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26
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Poynter ST, Kadoch C. Polycomb and trithorax opposition in development and disease. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2016; 5:659-688. [PMID: 27581385 DOI: 10.1002/wdev.244] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 05/07/2016] [Accepted: 06/02/2016] [Indexed: 01/08/2023]
Abstract
Early discoveries in chromatin biology and epigenetics heralded new insights into organismal development. From these studies, two mediators of cellular differentiation were discovered: the Polycomb group (PcG) of transcriptional repressors, and the trithorax group (trxG) of transcriptional activators. These protein families, while opposed in function, work together to coordinate the appropriate cellular developmental programs that allow for both embryonic stem cell self-renewal and differentiation. Recently, both the PcG and trxG chromatin modulators have been observed to be deregulated in a wide spectrum diseases including developmental disorders and cancer. To understand the impact of these findings we outline the past, present, and future. WIREs Dev Biol 2016, 5:659-688. doi: 10.1002/wdev.244 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Steven T Poynter
- Chemical Biology Program, Harvard Medical School, Boston, MA, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. .,Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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27
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Pretegiani E, Mari F, Renieri A, Penco S, Dotti MT. Nicolaides-Baraitser syndrome: defining a phenotype. J Neurol 2016; 263:1659-60. [PMID: 27286846 DOI: 10.1007/s00415-016-8194-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Elena Pretegiani
- Laboratory of Sensorimotor Research, IRP, National Eye Institute, National Institutes of Health, 49 Convent Dr., Room 2A50, Bethesda, MD, 20892-4435, USA.
- Neurodegenerative Disease Unit, Department of Medical, Surgical, and Neurological Sciences, University of Siena, Siena, Italy.
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Silvana Penco
- Medical Genetics, A.O. Niguarda Ca' Granda, Milan, Italy
| | - Maria Teresa Dotti
- Neurodegenerative Disease Unit, Department of Medical, Surgical, and Neurological Sciences, University of Siena, Siena, Italy
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28
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Darbro BW, Singh R, Zimmerman MB, Mahajan VB, Bassuk AG. Autism Linked to Increased Oncogene Mutations but Decreased Cancer Rate. PLoS One 2016; 11:e0149041. [PMID: 26934580 PMCID: PMC4774916 DOI: 10.1371/journal.pone.0149041] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/25/2016] [Indexed: 12/20/2022] Open
Abstract
Autism spectrum disorder (ASD) is one phenotypic aspect of many monogenic, hereditary cancer syndromes. Pleiotropic effects of cancer genes on the autism phenotype could lead to repurposing of oncology medications to treat this increasingly prevalent neurodevelopmental condition for which there is currently no treatment. To explore this hypothesis we sought to discover whether autistic patients more often have rare coding, single-nucleotide variants within tumor suppressor and oncogenes and whether autistic patients are more often diagnosed with neoplasms. Exome-sequencing data from the ARRA Autism Sequencing Collaboration was compared to that of a control cohort from the Exome Variant Server database revealing that rare, coding variants within oncogenes were enriched for in the ARRA ASD cohort (p<1.0 x 10(-8)). In contrast, variants were not significantly enriched in tumor suppressor genes. Phenotypically, children and adults with ASD exhibited a protective effect against cancer, with a frequency of 1.3% vs. 3.9% (p<0.001), but the protective effect decreased with age. The odds ratio of neoplasm for those with ASD relative to controls was 0.06 (95% CI: 0.02, 0.19; p<0.0001) in the 0 to 14 age group; 0.35 (95% CI: 0.14, 0.87; p = 0.024) in the 15 to 29 age group; 0.41 (95% CI: 0.15, 1.17; p = 0.095) in the 30 to 54 age group; and 0.49 (95% CI: 0.14, 1.74; p = 0.267) in those 55 and older. Both males and females demonstrated the protective effect. These findings suggest that defects in cellular proliferation, and potentially senescence, might influence both autism and neoplasm, and already approved drugs targeting oncogenic pathways might also have therapeutic value for treating autism.
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Affiliation(s)
- Benjamin W. Darbro
- Department of Pediatrics, Division of Medical Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- The Holden Comprehensive Cancer Center, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail: (BD); (AB)
| | - Rohini Singh
- Department of Pediatrics, Division of Medical Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Pediatrics, Division of Pediatric Hematology/Oncology/BMT, University of Iowa, Iowa City, Iowa, United States of America
| | - M. Bridget Zimmerman
- Department of Biostatistics, University of Iowa College of Public Health, Iowa City, Iowa, United States of America
| | - Vinit B. Mahajan
- Department of Ophthalmology and Visual Sciences, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Alexander G. Bassuk
- Interdisciplinary Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
- Department of Pediatrics, Division of Neurology, University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Graduate Program in Molecular and Cellular Biology, University of Iowa, Iowa City, Iowa, United States of America
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, Iowa, United States of America
- University of Iowa eHealth and eNovation Center, University of Iowa, Iowa City, Iowa, United States of America
- * E-mail: (BD); (AB)
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29
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Ejaz R, Babul-Hirji R, Chitayat D. The evolving features of Nicolaides-Baraitser syndrome - a clinical report of a 20-year follow-up. Clin Case Rep 2016; 4:351-5. [PMID: 27099726 PMCID: PMC4831382 DOI: 10.1002/ccr3.425] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/24/2015] [Accepted: 09/29/2015] [Indexed: 11/06/2022] Open
Abstract
Nicolaides–Baraitser syndrome (NCBRS) is a rare genetic condition associated with SMARCA2 gene mutations. Clinical diagnosis is challenging as its features evolve with time. The 20 years follow‐up of our NCBRS patient, with a previously unreported SMARCA2 mutation, illustrates the syndrome's natural history and its clinical variability, especially in a milder form.
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Affiliation(s)
- Resham Ejaz
- Department of Pediatrics Division of Clinical & Metabolic Genetics The Hospital for Sick Children University of Toronto Toronto ON Canada
| | - Riyana Babul-Hirji
- Department of Pediatrics Division of Clinical & Metabolic Genetics The Hospital for Sick Children University of Toronto Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON Canada
| | - David Chitayat
- Department of Pediatrics Division of Clinical & Metabolic Genetics The Hospital for Sick Children University of Toronto Toronto ON Canada; Department of Molecular Genetics University of Toronto Toronto ON Canada; The Prenatal Diagnosis and Medical Genetics Program Department of Obstetrics and Gynecology Mount Sinai Hospital University of Toronto Toronto ON Canada
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30
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Pezzani L, Milani D, Tadini G. Intellectual Disability: When the Hypertrichosis Is a Clue. J Pediatr Genet 2015; 4:154-8. [PMID: 27617126 DOI: 10.1055/s-0035-1564442] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 01/18/2023]
Abstract
The skin and the central and peripheral nervous system both derive from the ectoderm ridge. Therefore, several syndromes characterized by the presence of intellectual disability (ID) can be associated with specific congenital cutaneous manifestations. In this review, we list some of the most frequent diseases characterized by the presence of ID associated with hirsutism, which might be an incentive for the clinicians to pay attention to the ectodermal annexes in patients with ID.
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Affiliation(s)
- Lidia Pezzani
- Pathology Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Gianluca Tadini
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy; Unit of Dermatology, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
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31
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Ben-Salem S, Sobreira N, Akawi NA, Al-Shamsi AM, John A, Pramathan T, Valle D, Ali BR, Al-Gazali L. Gonadal mosaicism in ARID1B gene causes intellectual disability and dysmorphic features in three siblings. Am J Med Genet A 2015; 170A:156-61. [PMID: 26395437 PMCID: PMC5448135 DOI: 10.1002/ajmg.a.37405] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/03/2015] [Indexed: 02/05/2023]
Abstract
The gene encoding the AT-rich interaction domain-containing protein 1B (ARID1B) has recently been shown to be one of the most frequently mutated genes in patients with intellectual disability (ID). The phenotypic spectrums associated with variants in this gene vary widely ranging for mild to severe non-specific ID to Coffin-Siris syndrome. In this study, we evaluated three children from a consanguineous Emirati family affected with ID and dysmorphic features. Genomic DNA from all affected siblings was analyzed using CGH array and whole-exome sequencing (WES). Based on a recessive mode of inheritance, homozygous or compound heterozygous variants shared among all three affected children could not be identified. However, further analysis revealed a heterozygous variant (c.4318C>T; p.Q1440*) in the three affected children in an autosomal dominant ID causing gene, ARID1B. This variant was absent in peripheral blood samples obtained from both parents and unaffected siblings. Therefore, we propose that the most likely explanation for this situation is that one of the parents is a gonadal mosaic for the variant. To the best of our knowledge, this is the first report of a gonadal mosaicism inheritance of an ARID1B variant leading to familial ID recurrence.
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Affiliation(s)
- Salma Ben-Salem
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Nara Sobreira
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nadia A Akawi
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Aisha M Al-Shamsi
- Department of Paediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Anne John
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Thachillath Pramathan
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - David Valle
- Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Paediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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