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Wu R, Tang W, Li P, Meng Z, Li X, Liang L. Identification of a novel phenotype of external ear deformity related to Coffin-Siris syndrome-9 and literature review. Am J Med Genet A 2024; 194:e63626. [PMID: 38591849 DOI: 10.1002/ajmg.a.63626] [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: 10/09/2023] [Revised: 02/13/2024] [Accepted: 03/29/2024] [Indexed: 04/10/2024]
Abstract
De novo germline variants of the SRY-related HMG-box 11 gene (SOX11) have been reported to cause Coffin-Siris syndrome-9 (CSS-9), a rare congenital disorder associated with multiple organ malformations, including ear anomalies. Previous clinical and animal studies have found that intragenic pathogenic variant or haploinsufficiency in the SOX11 gene could cause inner ear malformation, but no studies to date have documented the external ear malformation caused by SOX11 deficiency. Here, we reported a Chinese male with unilateral microtia and bilateral sensorineural deafness who showed CSS-like manifestations, including dysmorphic facial features, impaired neurodevelopment, and fingers/toes malformations. Using trio-based whole-exome sequencing, a de novo missense variant in SOX11 (NM_003108.4: c.347A>G, p.Y116C) was identified and classified as pathogenic variant as per American College of Medical Genetics guidelines. Moreover, a systematic search of the literature yielded 12 publications that provided data of 55 SOX11 intragenic variants affecting various protein-coding regions of SOX11 protein. By quantitatively analyzing phenotypic spectrum information related to these 56 SOX11 variants (including our case), we found variants affecting different regions of SOX11 protein (high-mobility group [HMG] domain and non-HMG regions) appear to influence the phenotypic spectrum of organ malformations in CSS-9; variants altering the HMG domain were more likely to cause the widest range of organ anomalies. In summary, this is the first report of CSS with external ear malformation caused by pathogenic variant in SOX11, indicating that the SOX11 gene may be not only essential for the development of the inner ear but also critical for the morphogenesis of the external ear. In addition, thorough clinical examination is recommended for patients who carry pathogenic SOX11 variants that affect the HMG domain, as these variants may cause the widest range of organ anomalies underlying this condition.
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Affiliation(s)
- Ruohao Wu
- Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenting Tang
- Department of Research and Molecular Diagnostics, Sun Yat-sen University Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pinggan Li
- Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhe Meng
- Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xiaojuan Li
- Department of Cellular and Molecular Diagnostics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liyang Liang
- Department of Children's Neuroendocrinology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
- Children's Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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Baccas M, Ganesan V, Leung A, Pineiro L, McKillop AN, Liu J. SEM-2/SoxC regulates multiple aspects of C. elegans postembryonic mesoderm development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.04.602042. [PMID: 39005444 PMCID: PMC11245110 DOI: 10.1101/2024.07.04.602042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Development of multicellular organisms requires well-orchestrated interplay between cell-intrinsic transcription factors and cell-cell signaling. One set of highly conserved transcription factors that plays diverse roles in development is the SoxC group. C. elegans contains a sole SoxC protein, SEM-2. SEM-2 is essential for embryonic development, and for specifying the sex myoblast (SM) fate in the postembryonic mesoderm, the M lineage. We have identified a novel partial loss-of-function sem-2 allele that has a proline to serine change in the C-terminal tail of the highly conserved DNA-binding domain. Detailed analyses of mutant animals harboring this point mutation uncovered new functions of SEM-2 in the M lineage. First, SEM-2 functions antagonistically with LET-381, the sole C. elegans FoxF/C forkhead transcription factor, to regulate dorsoventral patterning of the M lineage. Second, in addition to specifying the SM fate, SEM-2 is essential for the proliferation and diversification of the SM lineage. Finally, SEM-2 appears to directly regulate the expression of hlh-8 , which encodes a basic helix-loop-helix Twist transcription factor and plays critical roles in proper patterning of the M lineage. Our data, along with previous studies, suggest an evolutionarily conserved relationship between SoxC and Twist proteins. Furthermore, our work identified new interactions in the gene regulatory network (GRN) underlying C. elegans postembryonic development and adds to the general understanding of the structure-function relationship of SoxC proteins. AUTHOR SUMMARY SoxC transcription factors play important roles in metazoan development. Abnormal expression or function of SoxC factors has been linked to a variety of developmental disorders and cancers. It is therefore critical to understand the functions of SoxC proteins in vivo. C. elegans has a single SoxC transcription factor, SEM-2, that is known to regulate a fate decision between a proliferative progenitor cell vs. a terminally differentiated cell during postembryonic mesoderm development. In this study, we report new functions of SEM-2 in postembryonic mesoderm development via our studies of a partial loss-of-function allele of sem-2 . Our work uncovers new regulatory relationships between SEM-2/SoxC and the FoxF/C transcription factor LET-381, and between SEM-2/SoxC and the C. elegans Twist ortholog HLH-8. Our findings suggest that the SoxC-Twist axis, including the downstream targets of Twist, represents an evolutionarily conserved regulatory cassette important in metazoan development.
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Smith H, Al-Jawahiri R, Stokes L, Freeth M, Fricke S, Matthews D, McNeill A. Impaired communication ability in SOX11 syndrome. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2024; 68:285-292. [PMID: 37916390 DOI: 10.1111/jir.13105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/29/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023]
Abstract
BACKGROUND Speech and language skills are important for social interaction and learning. This study characterised the communication abilities of verbal individuals with SOX11 syndrome using a standardised parent/carer questionnaire, the Children's Communication Checklist (CCC-2). METHOD Thirteen parent/carers of verbal individuals (aged 5-19 years) diagnosed with SOX11 syndrome completed the CCC-2. In order to contextualise findings, responses were compared to norms and to data from Noonan syndrome, a relatively well-known genetic diagnosis associated with communication impairment. RESULTS For all individuals, the CCC-2 composite score indicated significant communication difficulties. Language structure (speech, syntax, semantics and coherence), pragmatic language (inappropriate initiation, stereotyped language use of context and non-verbal communication) and autistic features (social relations and interests) scores were lower than typically developing norms. Subscale comparisons revealed relative difference in use of context compared to other pragmatic domains (stereotyped language and inappropriate initiation). Individual scores showed substantial variation, particularly in regard to language structure profile. Differences were more pronounced than for Noonan syndrome, specifically in domains of speech, syntax, non-verbal communication and social relations. CONCLUSIONS SOX11 syndrome is associated with communication impairment. It is important to assess communication abilities as part of the management of individuals with SOX11 syndrome and understand individual strengths and difficulties in order to provide targeted support.
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Affiliation(s)
- H Smith
- Division of Neuroscience, The University of Sheffield, Sheffield, UK
- Department of Psychology, The University of Sheffield, Sheffield, UK
| | - R Al-Jawahiri
- Division of Neuroscience, The University of Sheffield, Sheffield, UK
| | - L Stokes
- Division of Neuroscience, The University of Sheffield, Sheffield, UK
| | - M Freeth
- Department of Psychology, The University of Sheffield, Sheffield, UK
| | - S Fricke
- Human Communication Sciences, School of Allied Health Professions, Nursing and Midwifery, The University of Sheffield, Sheffield, UK
| | - D Matthews
- Human Communication Sciences, School of Allied Health Professions, Nursing and Midwifery, The University of Sheffield, Sheffield, UK
| | - A McNeill
- Division of Neuroscience, The University of Sheffield, Sheffield, UK
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Grippa M, Graziano C. Landscape of Constitutional SOX4 Variation in Human Disorders. Genes (Basel) 2024; 15:158. [PMID: 38397148 PMCID: PMC10887744 DOI: 10.3390/genes15020158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
SOX proteins are transcription factors which play a role in regulating the development of progenitor cells and tissue differentiation. Twenty members are known, clustered in eight groups named A through H and sharing a common DNA-binding domain called the HMG (high-mobility-group) box. Eleven of the SOX genes have been associated with genetic disorders so far, covering a broad spectrum of developmental diseases. SOX4 is a single-exon gene and belongs to the SOXC group, together with SOX11 and SOX12. SOX4 variants have been recently described to cause a highly penetrant but heterogeneous disorder, with a phenotypic spectrum ranging from mild developmental delays and learning difficulties to intellectual disabilities with congenital anomalies. Nineteen pathogenic variants have been reported to date, generally de novo, heterozygous, and inactivating, either stop-gain or missense, the latter ones primarily targeting the HMG domain. Further, a bi-allelic variant was reported in a single consanguineous family. Copy number variants leading to whole gene deletion or duplication are rare and not clearly associated with any neurodevelopmental disorder. Many open questions remain regarding the definition of variants of unknown significance, a possible role of missense variants outside the HMG domain, genotype-phenotype correlation, the range of phenotypic spectrum and modifying factors, and treatment options.
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Affiliation(s)
- Mina Grippa
- SSD Genetica Medica, Dipartimento Materno Infantile, AOU Policlinico Modena, 41125 Modena, Italy;
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Al-Jawahiri R, Stokes L, Smith H, McNeill A, Freeth M. Short report: Behavioural characterisation of SOX11 syndrome. RESEARCH IN DEVELOPMENTAL DISABILITIES 2023; 143:104623. [PMID: 37924570 DOI: 10.1016/j.ridd.2023.104623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/06/2023] [Accepted: 10/18/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND SOX11 syndrome is a rare condition caused by deletions or de novo point mutations of the SOX11 gene. SOX11 is a transcription factor gene that plays an important role in brain development. AIMS The aim of this study was to quantitatively evaluate the behavioural profiles of individuals with SOX11 syndrome. METHODS AND PROCEDURES The Vineland Adaptive Behaviour Scales 3 (VABS-3) and the Social Responsiveness Scale 2 (SRS-2) were completed by parents of 21 children and young adults with SOX11 syndrome. OUTCOMES AND RESULTS Most were found to have borderline (33 %) or mild (39 %) impairment in adaptive behaviour, with more difficulties in communication and daily living than socialisation in the cohort overall. Most (90 %) were found to exhibit clinically relevant levels of autistic traits, with 62 % scoring in the "severe" range, though social motivation was observed to be a relative strength in the cohort overall. CONCLUSIONS AND IMPLICATIONS This study presents the first standardised evaluation of adaptive behaviour and autistic traits of individuals with SOX11 syndrome. This will improve clinicians, educators and parents' understanding of SOX11 syndrome.
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Affiliation(s)
| | - Louis Stokes
- University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Harriet Smith
- University of Sheffield, Sheffield S10 2TN, United Kingdom
| | | | - Megan Freeth
- University of Sheffield, Sheffield S10 2TN, United Kingdom.
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Lim Y. Transcription factors in microcephaly. Front Neurosci 2023; 17:1302033. [PMID: 38094004 PMCID: PMC10716367 DOI: 10.3389/fnins.2023.1302033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 02/01/2024] Open
Abstract
Higher cognition in humans, compared to other primates, is often attributed to an increased brain size, especially forebrain cortical surface area. Brain size is determined through highly orchestrated developmental processes, including neural stem cell proliferation, differentiation, migration, lamination, arborization, and apoptosis. Disruption in these processes often results in either a small (microcephaly) or large (megalencephaly) brain. One of the key mechanisms controlling these developmental processes is the spatial and temporal transcriptional regulation of critical genes. In humans, microcephaly is defined as a condition with a significantly smaller head circumference compared to the average head size of a given age and sex group. A growing number of genes are identified as associated with microcephaly, and among them are those involved in transcriptional regulation. In this review, a subset of genes encoding transcription factors (e.g., homeobox-, basic helix-loop-helix-, forkhead box-, high mobility group box-, and zinc finger domain-containing transcription factors), whose functions are important for cortical development and implicated in microcephaly, are discussed.
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Affiliation(s)
- Youngshin Lim
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, United States
- Department of Biomedical Science Education, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
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van der Laan L, Rooney K, Haghshenas S, Silva A, McConkey H, Relator R, Levy MA, Valenzuela I, Trujillano L, Lasa-Aranzasti A, Campos B, Castells N, Verberne EA, Maas S, Alders M, Mannens MMAM, van Haelst MM, Sadikovic B, Henneman P. Functional Insight into and Refinement of the Genomic Boundaries of the JARID2-Neurodevelopmental Disorder Episignature. Int J Mol Sci 2023; 24:14240. [PMID: 37762546 PMCID: PMC10531903 DOI: 10.3390/ijms241814240] [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: 08/17/2023] [Revised: 09/15/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
JARID2 (Jumonji, AT-rich interactive domain 2) haploinsufficiency is associated with a clinically distinct neurodevelopmental syndrome. It is characterized by intellectual disability, developmental delay, autistic features, behavior abnormalities, cognitive impairment, hypotonia, and dysmorphic features. JARID2 acts as a transcriptional repressor protein that is involved in the regulation of histone methyltransferase complexes. JARID2 plays a role in the epigenetic machinery, and the associated syndrome has an identified DNA methylation episignature derived from sequence variants and intragenic deletions involving JARID2. For this study, our aim was to determine whether patients with larger deletions spanning beyond JARID2 present a similar DNA methylation episignature and to define the critical region involved in aberrant DNA methylation in 6p22-p24 microdeletions. We examined the DNA methylation profiles of peripheral blood from 56 control subjects, 13 patients with (likely) pathogenic JARID2 variants or patients carrying copy number variants, and three patients with JARID2 VUS variants. The analysis showed a distinct and strong differentiation between patients with (likely) pathogenic variants, both sequence and copy number, and controls. Using the identified episignature, we developed a binary model to classify patients with the JARID2-neurodevelopmental syndrome. DNA methylation analysis indicated that JARID2 is the driver gene for aberrant DNA methylation observed in 6p22-p24 microdeletions. In addition, we performed analysis of functional correlation of the JARID2 genome-wide methylation profile with the DNA methylation profiles of 56 additional neurodevelopmental disorders. To conclude, we refined the critical region for the presence of the JARID2 episignature in 6p22-p24 microdeletions and provide insight into the functional changes in the epigenome observed when regulation by JARID2 is lost.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Ananília Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
| | - Irene Valenzuela
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Laura Trujillano
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Berta Campos
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Neus Castells
- Medicine Genetics Group, Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d’Hebron Barcelona Hospital Campus, Vall d’Hebron Hospital Universitari, 129, 08035 Barcelona, Spain
| | - Eline A. Verberne
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Saskia Maas
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Mieke M. van Haelst
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada (R.R.)
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam University Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and genomic analyses of Drosophila melanogaster models of chromatin modification disorders. Genetics 2023; 224:iyad061. [PMID: 37036413 PMCID: PMC10411607 DOI: 10.1093/genetics/iyad061] [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: 11/10/2022] [Revised: 11/10/2022] [Accepted: 03/30/2023] [Indexed: 04/11/2023] Open
Abstract
Switch/sucrose nonfermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 associated factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce the expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration), and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, an SSRIDD-associated BAF component. k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in the behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in the discovery of drugs that ameliorate deleterious phenotypic effects.
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Affiliation(s)
- Rebecca A MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R H Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F C Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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9
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MacPherson RA, Shankar V, Anholt RRH, Mackay TFC. Genetic and Genomic Analyses of Drosophila melanogaster Models of Chromatin Modification Disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534923. [PMID: 37034595 PMCID: PMC10081333 DOI: 10.1101/2023.03.30.534923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
Switch/Sucrose Non-Fermentable (SWI/SNF)-related intellectual disability disorders (SSRIDDs) and Cornelia de Lange syndrome are rare syndromic neurodevelopmental disorders with overlapping clinical phenotypes. SSRIDDs are associated with the BAF (Brahma-Related Gene-1 Associated Factor) complex, whereas CdLS is a disorder of chromatin modification associated with the cohesin complex. Here, we used RNA interference in Drosophila melanogaster to reduce expression of six genes (brm, osa, Snr1, SMC1, SMC3, vtd) orthologous to human genes associated with SSRIDDs and CdLS. These fly models exhibit changes in sleep, activity, startle behavior (a proxy for sensorimotor integration) and brain morphology. Whole genome RNA sequencing identified 9,657 differentially expressed genes (FDR < 0.05), 156 of which are differentially expressed in both sexes in SSRIDD- and CdLS-specific analyses, including Bap60, which is orthologous to SMARCD1, a SSRIDD-associated BAF component, k-means clustering reveals genes co-regulated within and across SSRIDD and CdLS fly models. RNAi-mediated reduction of expression of six genes co-regulated with focal genes brm, osa, and/or Snr1 recapitulated changes in behavior of the focal genes. Based on the assumption that fundamental biological processes are evolutionarily conserved, Drosophila models can be used to understand underlying molecular effects of variants in chromatin-modification pathways and may aid in discovery of drugs that ameliorate deleterious phenotypic effects.
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Affiliation(s)
- Rebecca A. MacPherson
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Vijay Shankar
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Robert R. H. Anholt
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
| | - Trudy F. C. Mackay
- Center for Human Genetics and Department of Genetics and Biochemistry, Clemson University, 114 Gregor Mendel Circle, Greenwood, SC 29646, USA
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Rimoldi M, Rinaldi B, Villa R, Cerasani J, Beltrami B, Iascone M, Silipigni R, Boito S, Gangi S, Colombo L, Porro M, Cesaretti C, Bedeschi MF. Congenital diaphragmatic hernia in Coffin Siris syndrome: Further evidence from two cases. Am J Med Genet A 2023; 191:605-611. [PMID: 36416235 DOI: 10.1002/ajmg.a.63054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/08/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
Coffin-Siris Syndrome (CSS) is a rare multi-system dominant condition with a variable clinical presentation mainly characterized by hypoplasia/aplasia of the nail and/or distal phalanx of the fifth digit, coarse facies, hirsutism/hypertrichosis, developmental delay and intellectual disability of variable degree and growth impairment. Congenital anomalies may include cardiac, genitourinary and central nervous system malformations whereas congenital diaphragmatic hernia (CDH) is rarely reported. The genes usually involved in CSS pathogenesis are ARID1B (most frequently), SMARCA4, SMARCB1, ARID1A, SMARCE1, DPF2, and PHF6. Here, we present two cases of CSS presenting with CDH, for whom Whole Exome Sequencing (WES) identified two distinct de novo heterozygous causative variants, one in ARID1B (case 1) and one in SMARCA4 (case 2). Due to the rarity of CDH in CSS, in both cases the occurrence of CDH did not represent a predictive sign of CSS but, on the other hand, prompted genetic testing before (case 1) or independently (case 2) from the clinical hypothesis of CSS. We provide further evidence of the association between CSS and CDH, reviewed previous cases from literature and discuss possible functional links to related conditions.
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Affiliation(s)
- Martina Rimoldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Berardo Rinaldi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Roberta Villa
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Jacopo Cerasani
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Benedetta Beltrami
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
| | - Maria Iascone
- Ospedale Papa Giovanni XXIII, Laboratory of Medical Genetics, Bergamo, Italy
| | - Rosamaria Silipigni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Laboratory of Medical Genetics, Milan, Italy
| | - Simona Boito
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Fetal Medicine and Surgery Service, Milan, Italy
| | - Silvana Gangi
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Colombo
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Neonatal Intensive Care Unit (NICU), Department of Clinical Science and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Matteo Porro
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Pediatric Physical Medicine and Rehabilitation Unit, Milan, Italy
| | - Claudia Cesaretti
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Medical Genetics Unit, Milan, Italy
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11
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Chromosomal Microarray Analysis Identifies a Novel SALL1 Deletion, Supporting the Association of Haploinsufficiency with a Mild Phenotype of Townes-Brocks Syndrome. Genes (Basel) 2023; 14:genes14020258. [PMID: 36833185 PMCID: PMC9956891 DOI: 10.3390/genes14020258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
SALL1 heterozygous pathogenic variants cause Townes-Brocks syndrome (TBS), a condition with variable clinical presentation. The main features are a stenotic or imperforate anus, dysplastic ears, and thumb malformations, and other common concerns are hearing impairments, foot malformations, and renal and heart defects. Most of the pathogenic SALL1 variants are nonsense and frameshift, likely escaping nonsense-mediated mRNA decay and causing disease via a dominant-negative mechanism. Haploinsufficiency may result in mild phenotypes, but only four families with distinct SALL1 deletions have been reported to date, with a few more being of larger size and also affecting neighboring genes. We report on a family with autosomal dominant hearing impairment and mild anal and skeletal anomalies, in whom a novel 350 kb SALL1 deletion, spanning exon 1 and the upstream region, was identified by array comparative genomic hybridization. We review the clinical findings of known individuals with SALL1 deletions and point out that the overall phenotype is milder, especially when compared with individuals who carry the recurrent p.Arg276Ter mutation, but with a possible higher risk of developmental delay. Chromosomal microarray analysis is still a valuable tool in the identification of atypical/mild TBS cases, which are likely underestimated.
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12
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Wang Q, Wu J, Yang J, Huang S, Yuan Y, Dai P. Two SOX11 variants cause Coffin-Siris syndrome with a new feature of sensorineural hearing loss. Am J Med Genet A 2023; 191:183-189. [PMID: 36369738 PMCID: PMC10100107 DOI: 10.1002/ajmg.a.63011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022]
Abstract
Coffin-Siris syndrome (CSS, OMIM#135900) is a rare congenital disorder associated with neurodevelopmental and dysmorphic features. The primary cause of CSS is pathogenic variants in any of 9 BAF chromatin-remodeling complex encoding genes or the genes SOX11 and PHF6. Herein, we performed whole-exome sequencing (WES) and a series of analyses of growth-related, auditory, and radiological findings in two probands with syndromic sensorineural hearing loss and inner ear malformations who exhibited distinctive facial features, intellectual disability, growth retardation, and fifth finger malformation. Two de novo variants in the SOX11 gene (c.148A>C:p.Lys50Asn; c.811_814del:p.Asn271Serfs*10) were detected in these probands and were identified as pathogenic variants as per ACMG guidelines. These probands were diagnosed as having CSS based upon clinical and genetic findings. This is the first report of CSS caused by variants in SOX11 gene in Chinese individuals. Deleterious SOX11 variants can result in sensorineural hearing loss with inner ear malformation, potentially extending the array of phenotypes associated with these pathogenic variants. We suggest that both genetic and clinical findings be considered when diagnosing syndromic hearing loss.
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Affiliation(s)
- Qiuquan Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Jie Wu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Jinyuan Yang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Yongyi Yuan
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Beijing, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, China.,Beijing Key Lab of hearing loss Prevention and Treatment, Beijing, China
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13
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van der Laan L, Rooney K, Alders M, Relator R, McConkey H, Kerkhof J, Levy MA, Lauffer P, Aerden M, Theunis M, Legius E, Tedder ML, Vissers LELM, Koene S, Ruivenkamp C, Hoffer MJV, Wieczorek D, Bramswig NC, Herget T, González VL, Santos-Simarro F, Tørring PM, Denomme-Pichon AS, Isidor B, Keren B, Julia S, Schaefer E, Francannet C, Maillard PY, Misra-Isrie M, Van Esch H, Mannens MMAM, Sadikovic B, van Haelst MM, Henneman P. Episignature Mapping of TRIP12 Provides Functional Insight into Clark-Baraitser Syndrome. Int J Mol Sci 2022; 23:ijms232213664. [PMID: 36430143 PMCID: PMC9690904 DOI: 10.3390/ijms232213664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Clark-Baraitser syndrome is a rare autosomal dominant intellectual disability syndrome caused by pathogenic variants in the TRIP12 (Thyroid Hormone Receptor Interactor 12) gene. TRIP12 encodes an E3 ligase in the ubiquitin pathway. The ubiquitin pathway includes activating E1, conjugating E2 and ligating E3 enzymes which regulate the breakdown and sorting of proteins. This enzymatic pathway is crucial for physiological processes. A significant proportion of TRIP12 variants are currently classified as variants of unknown significance (VUS). Episignatures have been shown to represent a powerful diagnostic tool to resolve inconclusive genetic findings for Mendelian disorders and to re-classify VUSs. Here, we show the results of DNA methylation episignature analysis in 32 individuals with pathogenic, likely pathogenic and VUS variants in TRIP12. We identified a specific and sensitive DNA methylation (DNAm) episignature associated with pathogenic TRIP12 variants, establishing its utility as a clinical biomarker for Clark-Baraitser syndrome. In addition, we performed analysis of differentially methylated regions as well as functional correlation of the TRIP12 genome-wide methylation profile with the profiles of 56 additional neurodevelopmental disorders.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Peter Lauffer
- Department of Pediatric Endocrinology, Emma Children’s Hospital, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Mio Aerden
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Miel Theunis
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | | | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Mariette J. V. Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Nuria C. Bramswig
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Vanesa López González
- Sección Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, CIBERER, 30120 Murcia, Spain
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, 28029 Madrid, Spain
| | - Pernille M. Tørring
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Anne-Sophie Denomme-Pichon
- UF6254 Innovation en Diagnostic Genomique des Maladies Rares, 21070 Dijon, France
- Équipe Génétique des Anomalies du Développement (GAD), CHU Dijon-Bourgogne, 21000 Dijon, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France
| | - Boris Keren
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne Université, 75013 Paris, France
| | - Sophie Julia
- Service de Génétique Clinique, CHU Toulouse, 31300 Toulouse, France
| | - Elise Schaefer
- Service de Génétique Clinique, CHU Toulouse, 31300 Toulouse, France
| | - Christine Francannet
- Service de Genetique Medicale, CHU de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | | | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Hilde Van Esch
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
- Correspondence: (B.S.); (P.H.)
| | - Mieke M. van Haelst
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Correspondence: (B.S.); (P.H.)
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14
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Schneider SA, Mueller C, Biskup S, Fietzek UM, Schroeder AS. Neurodevelopmental disorder with dystonia due to SOX6 mutations. Mol Genet Genomic Med 2022; 10:e2051. [PMID: 36069193 PMCID: PMC9747553 DOI: 10.1002/mgg3.2051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/30/2022] [Accepted: 08/18/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mutations in SOX6 have recently been recognized as a new molecular cause of neurodevelopmental disorders characterized by intellectual disability, behavioral changes, and nonspecific facial and digital skeletal abnormalities. To date, <25 cases have been reported in the literature. METHODS AND FINDINGS Here we report a new case of SOX6-associated neurodegeneration and expand the phenotype to include ceratoconus. The clinical picture consisted of early onset mildly reduced intellectual function, facial asymmetry, and dystonic tremor of hands and neck, substantially improved by levodopa. Skeletal abnormalities included scoliosis and hypertrophy of the mandibular coronoid process. A heterozygous de novo loss-of-function variant in SOX6 (c.277 C>T. p.Arg93*) was molecularly confirmed which leads to truncation of the SOX6 protein in its N-terminus, upstream of any known functional domain. CONCLUSION SOX6-associated neurodevelopmental delayis ultrarare with less than 25 cases described in the literature. We report a new case who presented with early-onset mildly reduced intellectual function, facial asymmetry, skeletal abnormalities and dystonic tremor of hands and neck, substantially improved by levodopa. Given the therapeutic implications, SOX6 mutations should be considered in patients with complex dystonia parkinsonism.
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Affiliation(s)
- Susanne A. Schneider
- Department of NeurologyUniversity Hospital, Ludwig Maximilians UniversitätMunichGermany
| | - Christine Mueller
- Department of Pediatric Neurology, Developmental Medicine, Social Pediatrics, Dr. von Hauner Children's HospitalLMU ‐ University Hospital, Ludwig Maximilians UniversitätMunichGermany
| | - Saskia Biskup
- Center for Genomics and Transcriptomics CeGaT GmbH and Praxis für Humangenetik TübingenTübingenGermany
| | - Urban M. Fietzek
- Department of NeurologyUniversity Hospital, Ludwig Maximilians UniversitätMunichGermany,Department of Neurology and Clinical NeurophysiologySchön Klinik München SchwabingMunichGermany
| | - Andreas Sebastian Schroeder
- Department of Pediatric Neurology, Developmental Medicine, Social Pediatrics, Dr. von Hauner Children's HospitalLMU ‐ University Hospital, Ludwig Maximilians UniversitätMunichGermany
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15
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Ding Y, Chen J, Tang Y, Chen LN, Yao RE, Yu T, Yin Y, Wang X, Wang J, Li N. Identification and functional analysis of novel SOX11 variants in Chinese patients with Coffin-Siris syndrome 9. Front Genet 2022; 13:940776. [PMID: 35938035 PMCID: PMC9354949 DOI: 10.3389/fgene.2022.940776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
SOX11 is a transcription factor belonging to the sex determining region Y-related high-mobility group box family that plays a vital role in early embryogenesis and neurogenesis. De novo variants in SOX11 have been initially reported to cause a rare neurodevelopmental disorder, mainly referred to Coffin-siris syndrome 9 (CSS9, OMIM# 615866) which is characterized with growth deficiency, intellectual disability (ID), microcephaly, coarse facies, and hypoplastic nails of the fifth fingers and/or toes. A recent large-scale cohort study suggests that SOX11 variation would result in a clinically and molecularly distinct disease from CSS. Here, we describe three unrelated Chinese cases with variable phenotype, mainly involving developmental delay, ID, short statute, microcephaly, facial deformities (i.e., prominent forehead, arched eye brow, flat nasal bridge, broad nose and short philtrum), and cryptorchidism. Whole-exome sequencing (WES) revealed three novel heterozygous variants in the SOX11 gene, including two missense variants of c.337T>C (p.Y113H) and c.425C>G (p.A142G), and one nonsense variant of c.820A>T (p. K142*). Luciferase reporting assay shows that the two missense variants impair the transcriptional activity of the SOX11 target gene GDF5. Additionally, WES uncovered a 4,300 kb deletion involving the region of 1q24.2-q25.1 (hg19,chr1:169,433,149-173,827,682) in patient 1, which also contributes to the condition of the patient. In summary, this is the first report of Chinese cases with de novo variants of SOX11. Our study partially supports the previous observation that the phenotype caused by SOX11 variants somewhat differs from classical CSS.
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Affiliation(s)
- Yu Ding
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiande Chen
- Department of Respiratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yijun Tang
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li-Na Chen
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ru-En Yao
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
- Shanghai Clinical Research Center for Rare Pediatric Diseases, Shanghai, China
| | - Tingting Yu
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
- Shanghai Clinical Research Center for Rare Pediatric Diseases, Shanghai, China
| | - Yong Yin
- Department of Respiratory Medicine, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiumin Wang
- Department of Endocrinology and Metabolism, Shanghai Children’s Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
- Shanghai Clinical Research Center for Rare Pediatric Diseases, Shanghai, China
- *Correspondence: Niu Li, ; Jian Wang,
| | - Niu Li
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China
- Shanghai Clinical Research Center for Rare Pediatric Diseases, Shanghai, China
- *Correspondence: Niu Li, ; Jian Wang,
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16
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Al-Jawahiri R, Foroutan A, Kerkhof J, McConkey H, Levy M, Haghshenas S, Rooney K, Turner J, Shears D, Holder M, Lefroy H, Castle B, Reis LM, Semina EV, Lachlan K, Chandler K, Wright T, Clayton-Smith J, Hug FP, Pitteloud N, Bartoloni L, Hoffjan S, Park SM, Thankamony A, Lees M, Wakeling E, Naik S, Hanker B, Girisha KM, Agolini E, Giuseppe Z, Alban Z, Tessarech M, Keren B, Afenjar A, Zweier C, Reis A, Smol T, Tsurusaki Y, Nobuhiko O, Sekiguchi F, Tsuchida N, Matsumoto N, Kou I, Yonezawa Y, Ikegawa S, Callewaert B, Freeth M, Kleinendorst L, Donaldson A, Alders M, De Paepe A, Sadikovic B, McNeill A. SOX11 variants cause a neurodevelopmental disorder with infrequent ocular malformations and hypogonadotropic hypogonadism and with distinct DNA methylation profile. Genet Med 2022; 24:1261-1273. [PMID: 35341651 PMCID: PMC9245088 DOI: 10.1016/j.gim.2022.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 12/28/2022] Open
Abstract
PURPOSE This study aimed to undertake a multidisciplinary characterization of the phenotype associated with SOX11 variants. METHODS Individuals with protein altering variants in SOX11 were identified through exome and genome sequencing and international data sharing. Deep clinical phenotyping was undertaken by referring clinicians. Blood DNA methylation was assessed using Infinium MethylationEPIC array. The expression pattern of SOX11 in developing human brain was defined using RNAscope. RESULTS We reported 38 new patients with SOX11 variants. Idiopathic hypogonadotropic hypogonadism was confirmed as a feature of SOX11 syndrome. A distinctive pattern of blood DNA methylation was identified in SOX11 syndrome, separating SOX11 syndrome from other BAFopathies. CONCLUSION SOX11 syndrome is a distinct clinical entity with characteristic clinical features and episignature differentiating it from BAFopathies.
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Affiliation(s)
- Reem Al-Jawahiri
- Department of Psychology, The University of Sheffield, Sheffield, United Kingdom
| | - Aidin Foroutan
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Michael Levy
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Sadegheh Haghshenas
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada; The Archie and Irene Verspeeten Clinical Genome Centre, London Health Sciences Foundation, London Health Sciences Centre, London, Ontario, Canada
| | - Jasmin Turner
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Debbie Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Muriel Holder
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
| | - Henrietta Lefroy
- Peninsula Clinical Genetics Service, RD&E Heavitree Hospital, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Bruce Castle
- Peninsula Clinical Genetics Service, RD&E Heavitree Hospital, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Linda M Reis
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Children's Wisconsin, Milwaukee, WI
| | - Elena V Semina
- Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin, Children's Wisconsin, Milwaukee, WI
| | - Katherine Lachlan
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Kate Chandler
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Thomas Wright
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Franziska Phan Hug
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Nelly Pitteloud
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Lucia Bartoloni
- Service of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, Lausanne, Switzerland
| | - Sabine Hoffjan
- Ruhr-Universitat Bochum, Abteilung für Humangenetik, Bochum, Germany
| | - Soo-Mi Park
- Clinical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ajay Thankamony
- Clinical Genetics, Addenbrooke's Treatment Centre, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Melissa Lees
- Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Emma Wakeling
- Clinical Genetics, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Swati Naik
- West Midlands Regional Clinical Genetics Centre and Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Britta Hanker
- Ambulanzzentrum UKSH, Institut für Humangenetik, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Emanuele Agolini
- Medical Genetics Laboratory, Bambino Gesu Children's Hospital, Rome, Italy
| | - Zampino Giuseppe
- Paediatric Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | | | | | - Boris Keren
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Alexandra Afenjar
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Christiane Zweier
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andre Reis
- Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Thomas Smol
- EA7364 RADEME, Institute of Medical Genetics, Lille University Hospital, Lille University, Lille, France
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Okamoto Nobuhiko
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Ikuyo Kou
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Yoshiro Yonezawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan; Department of Orthopedic Surgery, Keio University School of Medicine, Keio University, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Megan Freeth
- Department of Psychology, The University of Sheffield, Sheffield, United Kingdom
| | - Lotte Kleinendorst
- Centrum voor Medische Genetica - UZ Gent, Ghent University Hospital, Gent, Belgium
| | - Alan Donaldson
- Department of Clinical Genetics Service, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Anne De Paepe
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.
| | - Alisdair McNeill
- Department of Neuroscience, The Medical School, The University of Sheffield, Sheffield, United Kingdom; Department of Clinical Genetics, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, United Kingdom.
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17
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Alburaiky S, Taylor J, O'Grady G, Thomson G, Perry D, England EM, Yap P. Cochlear nerve deficiency in SOX11-related Coffin-Siris syndrome. Am J Med Genet A 2022; 188:2460-2465. [PMID: 35642566 DOI: 10.1002/ajmg.a.62851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/01/2022] [Accepted: 04/23/2022] [Indexed: 11/10/2022]
Abstract
The phenotypic spectrum of SOX11-related Coffin-Siris syndrome (CSS) is expanding with reports of new associations. SOX11 is implicated in neurogenesis and inner ear development. Cochlear nerve deficiency, absence or hypoplasia, is commonly associated with cochlear canal stenosis or with CHARGE syndrome, a monogenic condition that affects inner ear development. SOX11 is a transcription factor essential for neuronal identity, highly correlated with the expression of CHD7, which regulates SOX11. We present two unrelated probands, each with novel de novo SOX11 likely pathogenic variants and phenotypic manifestations of CSS including global developmental delay, growth deficiency, and hypoplastic nails. They have unilateral sensorineural hearing loss due to cochlear nerve deficiency confirmed on MRI. SOX11 is implicated in sensory neuron survival and maturation. It is highly expressed in the developing inner ear. Homozygous ablation of SOX11 in a mouse model resulted in a reduction in sensory neuron survival and decreased axonal growth. A heterozygous knockout mice model had hearing impairment with grossly normal inner ear structures like the two probands reported. We propose cochlear nerve deficiency as a new phenotypic feature of SOX11-related CSS. Magnetic resonance imaging is useful in delineating the cochlear nerve deficiency and other CSS-related brain malformations.
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Affiliation(s)
- Salam Alburaiky
- Genetic Health Service New Zealand-Northern Hub, Auckland, New Zealand
| | - Juliet Taylor
- Genetic Health Service New Zealand-Northern Hub, Auckland, New Zealand
| | - Gina O'Grady
- Department of Paediatric Neurology, Starship Children's Hospital, Auckland, New Zealand
| | - Glen Thomson
- Department of Paediatric Radiology, Starship Children's Hospital, Auckland, New Zealand
| | - David Perry
- Department of Paediatric Radiology, Starship Children's Hospital, Auckland, New Zealand
| | - Eleina M England
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Patrick Yap
- Genetic Health Service New Zealand-Northern Hub, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
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18
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Liu M, Wan L, Wang C, Yuan H, Peng Y, Wan N, Tang Z, Yuan X, Chen D, Long Z, Shi Y, Qiu R, Tang B, Jiang H, Chen Z. Coffin-Siris syndrome in two chinese patients with novel pathogenic variants of ARID1A and SMARCA4. Genes Genomics 2022; 44:1061-1070. [PMID: 35353340 DOI: 10.1007/s13258-022-01231-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/05/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Coffin-Siris syndrome (CSS) is a rare congenital syndrome characterized by developmental delay, intellectual disability, microcephaly, coarse face and hypoplastic nail of the fifth digits. Heterozygous variants of different BAF complex-related genes were reported to cause CSS, including ARID1A and SMARCA4. So far, no CSS patients with ARID1A and SMARCA4 variants have been reported in China. OBJECTIVE The aim of the current study was to identify the causes of two Chinese patients with congenital growth deficiency and intellectual disability. METHODS Genomic DNA was extracted from the peripheral venous blood of patients and their family members. Genetic analysis included whole-exome and Sanger sequencing. Pathogenicity assessments of variants were performed according to the guideline of the American College of Medical Genetics and Genomics. The phenotypic characteristics of all CSS subtypes were summarized through literature review. RESULTS We identified two Chinese CSS patients carrying novel variants of ARID1A and SMARCA4 respectively. The cases presented most core symptoms of CSS except for the digits involvement. Additionally, we performed a review of the phenotypic characteristics in CSS, highlighting phenotypic varieties and related potential causes. CONCLUSIONS We reported the first Chinese CSS2 and CSS4 patients with novel variants of ARID1A and SMARCA4. Our study expanded the genetic and phenotypic spectrum of CSS, providing a comprehensive overview of genotype-phenotype correlations of CSS.
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Affiliation(s)
- Mingjie Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Linlin Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chunrong Wang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongyu Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yun Peng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Na Wan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhichao Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xinrong Yuan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Daji Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhe Long
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuting Shi
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Rong Qiu
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China
- Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China
- National International Collaborative Research Center for Medical Metabolomics, Central South University, Changsha, Hunan, China
| | - Zhao Chen
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Key Laboratory of Hunan Province in Neurodegenerative Disorders, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Diseases, Central South University, Changsha, Hunan, China.
- Hunan International Scientific and Technological Cooperation Base of Neurodegenerative and Neurogenetic Diseases, Changsha, China.
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19
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Angelozzi M, Karvande A, Molin AN, Ritter AL, Leonard JMM, Savatt JM, Douglass K, Myers SM, Grippa M, Tolchin D, Zackai E, Donoghue S, Hurst ACE, Descartes M, Smith K, Velasco D, Schmanski A, Crunk A, Tokita MJ, de Lange IM, van Gassen K, Robinson H, Guegan K, Suri M, Patel C, Bournez M, Faivre L, Tran-Mau-Them F, Baker J, Fabie N, Weaver K, Shillington A, Hopkin RJ, Barge-Schaapveld DQCM, Ruivenkamp CA, Bökenkamp R, Vergano S, Seco Moro MN, Díaz de Bustamante A, Misra VK, Kennelly K, Rogers C, Friedman J, Wigby KM, Lenberg J, Graziano C, Ahrens-Nicklas RC, Lefebvre V. Consolidation of the clinical and genetic definition of a SOX4-related neurodevelopmental syndrome. J Med Genet 2022; 59:1058-1068. [PMID: 35232796 DOI: 10.1136/jmedgenet-2021-108375] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/13/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND A neurodevelopmental syndrome was recently reported in four patients with SOX4 heterozygous missense variants in the high-mobility-group (HMG) DNA-binding domain. The present study aimed to consolidate clinical and genetic knowledge of this syndrome. METHODS We newly identified 17 patients with SOX4 variants, predicted variant pathogenicity using in silico tests and in vitro functional assays and analysed the patients' phenotypes. RESULTS All variants were novel, distinct and heterozygous. Seven HMG-domain missense and five stop-gain variants were classified as pathogenic or likely pathogenic variant (L/PV) as they precluded SOX4 transcriptional activity in vitro. Five HMG-domain and non-HMG-domain missense variants were classified as of uncertain significance (VUS) due to negative results from functional tests. When known, inheritance was de novo or from a mosaic unaffected or non-mosaic affected parent for patients with L/PV, and from a non-mosaic asymptomatic or affected parent for patients with VUS. All patients had neurodevelopmental, neurological and dysmorphic features, and at least one cardiovascular, ophthalmological, musculoskeletal or other somatic anomaly. Patients with L/PV were overall more affected than patients with VUS. They resembled patients with other neurodevelopmental diseases, including the SOX11-related and Coffin-Siris (CSS) syndromes, but lacked the most specific features of CSS. CONCLUSION These findings consolidate evidence of a fairly non-specific neurodevelopmental syndrome due to SOX4 haploinsufficiency in neurogenesis and multiple other developmental processes.
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Affiliation(s)
- Marco Angelozzi
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Anirudha Karvande
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Arnaud N Molin
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Alyssa L Ritter
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jacqueline M M Leonard
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Juliann M Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Kristen Douglass
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Scott M Myers
- Autism & Developmental Medicine Institute, Geisinger, Danville, Pennsylvania, USA
| | - Mina Grippa
- U.O. Genetica Medica, Universita di Bologna, Bologna, Italy
| | - Dara Tolchin
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Elaine Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Sarah Donoghue
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Anna C E Hurst
- Department of Genetics, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Maria Descartes
- Department of Genetics, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Kirstin Smith
- Department of Genetics, The University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, USA
| | - Danita Velasco
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Andrew Schmanski
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Amy Crunk
- GeneDx Inc, Gaithersburg, Maryland, USA
| | | | - Iris M de Lange
- Department of Medical Genetics, University Medical Centre Utrecht Brain Centre, Utrecht, The Netherlands
| | - Koen van Gassen
- Department of Medical Genetics, University Medical Centre Utrecht Brain Centre, Utrecht, The Netherlands
| | - Hannah Robinson
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Katie Guegan
- Exeter Genomics Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Mohnish Suri
- Clinical Genetics, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Chirag Patel
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
| | - Marie Bournez
- Centres de référence Anomalies du Développement et Syndrome Malformatifs, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Laurence Faivre
- Centre de Génétique, Centre Hospitalier Universitaire de Dijon Hôpital d'Enfants, Dijon, France
| | - Frédéric Tran-Mau-Them
- Genetics of Developmental Disorders, INSERM - Bourgogne Franche-Comté University, UMR 1231 GAD Team, Dijon, France.,Functional Unit 6254 Innovation in Genomic Diagnosis of Rare Diseases, CHU Dijon Bourgogne, Dijon, France
| | - Janice Baker
- Genomics and Genetic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Noelle Fabie
- Genomics and Genetic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | - K Weaver
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Amelle Shillington
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Robert J Hopkin
- Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Claudia Al Ruivenkamp
- Laboratory for Diagnostic Genome Analyses, Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Regina Bökenkamp
- Department of Pediatric Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Samantha Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia, USA
| | | | | | - Vinod K Misra
- Department of Pediatrics, Division of Genetic, Genomic, and Metabolic Disorders, Children's Hospital of Michigan, Detroit, Michigan, USA.,Discipline of Pediatrics, Central Michigan University, Mount Pleasant, Michigan, USA
| | - Kelly Kennelly
- Department of Pediatrics, Children's Hospital of Michigan, Detroit, Michigan, USA
| | - Caleb Rogers
- Department of Molecular and Medical Genetics, Oregon Health & Science University School of Medicine, Portland, Oregon, USA
| | - Jennifer Friedman
- Department of Pediatrics, University of California San Diego, San Diego, California, USA.,Division of Genetics/Dysmorphology and Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA.,Department of Neurosciences, University of California San Diego, San Diego, California, USA.,Division of Neurology, Rady Children's Hospital, San Diego, California, USA
| | - Kristen M Wigby
- Department of Pediatrics, University of California San Diego, San Diego, California, USA.,Division of Genetics/Dysmorphology and Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Jerica Lenberg
- Division of Genetics/Dysmorphology and Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA
| | - Claudio Graziano
- Department of Pediatrics, University of California San Diego, San Diego, California, USA .,Division of Genetics/Dysmorphology and Institute for Genomic Medicine, Rady Children's Hospital, San Diego, California, USA.,Department of Neurosciences, University of California San Diego, San Diego, California, USA.,Division of Neurology, Rady Children's Hospital, San Diego, California, USA.,U.O. Genetica Medica, AUSL della Romagna Rimini, Cesena, Italy
| | - Rebecca C Ahrens-Nicklas
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Veronique Lefebvre
- Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
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20
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Vasko A, Schrier Vergano SA. Language Impairments in Individuals With Coffin-Siris Syndrome. Front Neurosci 2022; 15:802583. [PMID: 35126043 PMCID: PMC8811135 DOI: 10.3389/fnins.2021.802583] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 12/03/2022] Open
Abstract
Coffin-Siris syndrome (CSS, MIM 135900) is a now well-described, multiple congenital anomaly/intellectual disability syndrome classically characterized by fifth digit/nail hypoplasia, coarse facial features, and a range of organ-system related anomalies. Since its initial description in 1970, and the discovery of associated genes in 2011, CSS now encompasses a wide range of phenotypes and abilities caused by pathogenic variants in the BAF complex (often referred to as “BAFopathy”). It appears that the BAF complex leads to speech and language impairments in this population, and subsequently we have reviewed individuals in the CSS/BAF registry to understand the prevalence and degree of this particular learning difference. We have examined the frequency of delayed language acquisition, augmented communication device use, and speech intervention therapies. To aid in language progression, childhood speech interventions are necessary in children with a diagnosis of CSS. While the majority of children with pathogenic variants in the BAF complex have language-related struggles, the exact mechanism is not yet fully understood. At the time of writing, there are 284 individuals in the CSS/BAF registry with known variants in the following genes; ARID1B (n = 174), SMARCA4 (n = 41), ARID1A (n = 20), SMARCB1 (n = 20), ARID2 (n = 14), SOX11 (n = 10), and SMARCE1 (n = 5). While speech delays in individuals with CSS are expected, a full analysis of these delays has yet to be detailed. In the CSS/BAF registry, we identified 183 (64%) individuals with language-related challenges and 90 (32%) individuals that are non-verbal.
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Affiliation(s)
- Ashley Vasko
- Clinical Research Unit, Children’s Hospital of the King’s Daughters, Norfolk, VA, United States
| | - Samantha A. Schrier Vergano
- Division of Medical Genetics and Metabolism, Children’s Hospital of the King’s Daughters, Norfolk, VA, United States
- Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, United States
- *Correspondence: Samantha A. Schrier Vergano,
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21
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Turan S, Boerstler T, Kavyanifar A, Loskarn S, Reis A, Winner B, Lie DC. A novel human stem cell model for Coffin-Siris syndrome-like syndrome reveals the importance of SOX11 dosage for neuronal differentiation and survival. Hum Mol Genet 2021; 28:2589-2599. [PMID: 31035284 DOI: 10.1093/hmg/ddz089] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 04/03/2019] [Accepted: 04/17/2019] [Indexed: 11/14/2022] Open
Abstract
The SOXC transcription factors Sox4, Sox11 and Sox12, are critical neurodevelopmental regulators that are thought to function in a highly redundant fashion. Surprisingly, heterozygous missense mutations or deletions of SOX11 were recently detected in patients with Coffin-Siris syndrome-like syndrome (CSSLS), a neurodevelopmental disorder associated with intellectual disability, demonstrating that in humans SOX11 haploinsufficiency cannot be compensated and raising the question of the function of SOX11 in human neurodevelopment. Here, we describe the generation of SOX11+/- heterozygous human embryonic stem cell (hESC) lines by CRISPR/Cas9 genome engineering. SOX11 haploinsufficiency impaired the generation of neurons and resulted in a proliferation/differentiation imbalance of neural precursor cells and enhanced neuronal cell death. Using the SOX11+/- hESC model we provide for the first time experimental evidence that SOX11 haploinsufficiency is sufficient to impair key processes of human neurodevelopment, giving a first insight into the pathophysiology of CSSLS and SOX11 function in human neurodevelopment.
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Affiliation(s)
- Soeren Turan
- Institute of Biochemistry.,Department of Stem Cell Biology
| | | | | | | | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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22
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23
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Wittmann MT, Katada S, Sock E, Kirchner P, Ekici AB, Wegner M, Nakashima K, Lie DC, Reis A. scRNA sequencing uncovers a TCF4-dependent transcription factor network regulating commissure development in mouse. Development 2021; 148:269257. [PMID: 34184026 PMCID: PMC8327186 DOI: 10.1242/dev.196022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 06/15/2021] [Indexed: 01/21/2023]
Abstract
Transcription factor 4 (TCF4) is a crucial regulator of neurodevelopment and has been linked to the pathogenesis of autism, intellectual disability and schizophrenia. As a class I bHLH transcription factor (TF), it is assumed that TCF4 exerts its neurodevelopmental functions through dimerization with proneural class II bHLH TFs. Here, we aim to identify TF partners of TCF4 in the control of interhemispheric connectivity formation. Using a new bioinformatic strategy integrating TF expression levels and regulon activities from single cell RNA-sequencing data, we find evidence that TCF4 interacts with non-bHLH TFs and modulates their transcriptional activity in Satb2+ intercortical projection neurons. Notably, this network comprises regulators linked to the pathogenesis of neurodevelopmental disorders, e.g. FOXG1, SOX11 and BRG1. In support of the functional interaction of TCF4 with non-bHLH TFs, we find that TCF4 and SOX11 biochemically interact and cooperatively control commissure formation in vivo, and regulate the transcription of genes implicated in this process. In addition to identifying new candidate interactors of TCF4 in neurodevelopment, this study illustrates how scRNA-Seq data can be leveraged to predict TF networks in neurodevelopmental processes. Summary: Single-cell RNA sequencing identifies interactions of TCF4 with non-bHLH transcription factors linked to neurodevelopmental and neuropsychiatric disease in the regulation of interhemispheric projection neuron development.
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Affiliation(s)
- Marie-Theres Wittmann
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany.,Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Sayako Katada
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Elisabeth Sock
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Philipp Kirchner
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Michael Wegner
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Dieter Chichung Lie
- Institute of Biochemistry, Emil Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
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24
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Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome. Genes (Basel) 2021; 12:genes12060937. [PMID: 34205270 PMCID: PMC8233770 DOI: 10.3390/genes12060937] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 01/18/2023] Open
Abstract
Coffin-Siris syndrome (CSS, MIM 135900) is a multi-system intellectual disability syndrome characterized by classic dysmorphic features, developmental delays, and organ system anomalies. Genes in the BRG1(BRM)-associated factors (BAF, Brahma associated factor) complex have been shown to be causative, including ARID1A, ARID1B, ARID2, DPF2, SMARCA4, SMARCB1, SMARCC2, SMARCE1, SOX11, and SOX4. In order to describe more robust genotype-phenotype correlations, we collected data from 208 individuals from the CSS/BAF complex registry with pathogenic variants in seven of these genes. Data were organized into cohorts by affected gene, comparing genotype groups across a number of binary and quantitative phenotypes. We determined that, while numerous phenotypes are seen in individuals with variants in the BAF complex, hypotonia, hypertrichosis, sparse scalp hair, and hypoplasia of the distal phalanx are still some of the most common features. It has been previously proposed that individuals with ARID-related variants are thought to have more learning and developmental struggles, and individuals with SMARC-related variants, while they also have developmental delay, tend to have more severe organ-related complications. SOX-related variants also have developmental differences and organ-related complications but are most associated with neurodevelopmental differences. While these generalizations still overall hold true, we have found that all individuals with BAF-related conditions are at risk of many aspects of the phenotype, and management and surveillance should be broad.
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25
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Maternal transmission of a mild Coffin-Siris syndrome phenotype caused by a SOX11 missense variant. Eur J Hum Genet 2021; 30:126-132. [PMID: 33785884 PMCID: PMC8738766 DOI: 10.1038/s41431-021-00865-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 02/19/2021] [Accepted: 03/10/2021] [Indexed: 11/08/2022] Open
Abstract
Here we report for the first time on the maternal transmission of mild Coffin-Siris syndrome (CSS) caused by a SOX11 missense variant. We present two sisters with intellectual disability and muscular hypotonia born to non-consanguineous parents. Cogan ocular motor apraxia was present in both sisters. Body measurements were in a normal range. The mother and both daughters showed hypoplastic nails of the fifth toes. A missense variant in SOX11 [c.139 G > A; p.(Gly47Ser)] in both sisters and their mother was identified. Since 2014, variants in SOX11 are known to cause mild CSS. Most described patients showed intellectual disability, especially concerning acquired language. All of them had hypoplastic nails of the fifth toes. It is of note, that some of these patients show Cogan ocular motor apraxia. The facial dysmorphic features seem not to be specific. We suggest that the combination of Cogan ocular motor apraxia, hypoplastic nails of fifth toes, and developmental delay give the important diagnostic clue for a variant in the SOX11 gene (OMIM 615866, MR 27).
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26
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Cho CY, Tsai WY, Lee CT, Liu SY, Huang SY, Chien YH, Hwu WL, Lee NC, Tung YC. Clinical and molecular features of idiopathic hypogonadotropic hypogonadism in Taiwan: A single center experience. J Formos Med Assoc 2021; 121:218-226. [PMID: 33775534 DOI: 10.1016/j.jfma.2021.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/08/2021] [Accepted: 03/08/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Idiopathic (isolated) hypogonadotropic hypogonadism (IHH) is a rare disease that can be classified as Kallmann syndrome (KS) or normosmic IHH (nIHH). This study investigated the phenotype and genotype of IHH in Taiwanese patients. METHODS Twenty-six unrelated IHH patients were included in this study and their clinical, hormonal, and radiological findings were analyzed retrospectively. Whole exome sequencing (WES) was performed to identify the etiology. RESULTS The 26 patients (M:F = 19:7) were divided into a KS group (n = 11) and a nIHH group (n = 15). The diagnosis was earlier in boys than in girls. Fifteen patients were found to have pathogenic/likely pathogenic (P/LP) variants of IHH-associated genes, and the mutation detection rate was 58%. CHD7, FGFR1, and ANOS1 were the most common genetic etiologies identified in this group. Two patients with nIHH were found to have de novo SOX11 mutations and Coffin-Siris syndrome features. After treatment, the height outcomes and secondary sexual characteristics were significantly improved. There were no obvious differences between the genetically resolved (GR), variants of uncertain significance (VUS) and genetically unresolved groups (GUR). CONCLUSION Whole exome sequencing is useful in patients with IHH, and we identified the SOX11 gene as a causal factor in this study. We described the clinical, hormonal, and molecular characteristics, and the treatment outcomes, of Taiwanese patients with IHH, which should aid therapeutic planning and further research.
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Affiliation(s)
- Chih-Yi Cho
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wen-Yu Tsai
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Cheng-Ting Lee
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shih-Yao Liu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Yuan Huang
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Yin-Hsiu Chien
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ni-Chung Lee
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan.
| | - Yi-Ching Tung
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan.
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27
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Mossink B, Negwer M, Schubert D, Nadif Kasri N. The emerging role of chromatin remodelers in neurodevelopmental disorders: a developmental perspective. Cell Mol Life Sci 2021; 78:2517-2563. [PMID: 33263776 PMCID: PMC8004494 DOI: 10.1007/s00018-020-03714-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022]
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID) and autism spectrum disorders (ASD), are a large group of disorders in which early insults during brain development result in a wide and heterogeneous spectrum of clinical diagnoses. Mutations in genes coding for chromatin remodelers are overrepresented in NDD cohorts, pointing towards epigenetics as a convergent pathogenic pathway between these disorders. In this review we detail the role of NDD-associated chromatin remodelers during the developmental continuum of progenitor expansion, differentiation, cell-type specification, migration and maturation. We discuss how defects in chromatin remodelling during these early developmental time points compound over time and result in impaired brain circuit establishment. In particular, we focus on their role in the three largest cell populations: glutamatergic neurons, GABAergic neurons, and glia cells. An in-depth understanding of the spatiotemporal role of chromatin remodelers during neurodevelopment can contribute to the identification of molecular targets for treatment strategies.
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Affiliation(s)
- Britt Mossink
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Moritz Negwer
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Geert Grooteplein 10, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Department of Cognitive Neuroscience, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, 6500 HB, Nijmegen, The Netherlands.
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28
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Chiang SY, Wu HC, Lin SY, Chen HY, Wang CF, Yeh NH, Shih JH, Huang YS, Kuo HC, Chou SJ, Chen RH. Usp11 controls cortical neurogenesis and neuronal migration through Sox11 stabilization. SCIENCE ADVANCES 2021; 7:7/7/eabc6093. [PMID: 33579706 PMCID: PMC7880594 DOI: 10.1126/sciadv.abc6093] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/23/2020] [Indexed: 06/01/2023]
Abstract
The role of protein stabilization in cortical development remains poorly understood. A recessive mutation in the USP11 gene is found in a rare neurodevelopmental disorder with intellectual disability, but its pathogenicity and molecular mechanism are unknown. Here, we show that mouse Usp11 is expressed highly in embryonic cerebral cortex, and Usp11 deficiency impairs layer 6 neuron production, delays late-born neuronal migration, and disturbs cognition and anxiety behaviors. Mechanistically, these functions are mediated by a previously unidentified Usp11 substrate, Sox11. Usp11 ablation compromises Sox11 protein accumulation in the developing cortex, despite the induction of Sox11 mRNA. The disease-associated Usp11 mutant fails to stabilize Sox11 and is unable to support cortical neurogenesis and neuronal migration. Our findings define a critical function of Usp11 in cortical development and highlight the importance of orchestrating protein stabilization mechanisms into transcription regulatory programs for a robust induction of cell fate determinants during early brain development.
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Affiliation(s)
- Shang-Yin Chiang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 100, Taiwan
| | - Hsin-Chieh Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Shu-Yu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Hsin-Yi Chen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Chia-Fang Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | - Nai-Hsing Yeh
- Insititute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Jou-Ho Shih
- Insititute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yi-Shuian Huang
- Insititute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | - Shen-Ju Chou
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan.
| | - Ruey-Hwa Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
- Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 100, Taiwan
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29
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Diel H, Ding C, Grehn F, Chronopoulos P, Bartsch O, Hoffmann EM. First observation of secondary childhood glaucoma in Coffin-Siris syndrome: a case report and literature review. BMC Ophthalmol 2021; 21:28. [PMID: 33430815 PMCID: PMC7802219 DOI: 10.1186/s12886-020-01788-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Severe congenital ophthalmological malformations and glaucoma might be an important occasional feature in patients with Coffin-Siris syndrome (CSS), especially Coffin-Siris syndrome 9 (CSS9, OMIM #615866) caused by SOX11 mutation. Recently, primary (open-angle) glaucoma was described in two children with the most common form of Coffin-Siris syndrome, CSS1 (OMIM #135900) by ARID1B (AT-rich interaction domain-containing protein 1B) gene mutation. In this article, we present the first report of glaucoma with Coffin-Siris syndrome 9 as well as the first report of secondary glaucoma with any form of Coffin-Siris syndrome. These findings indicate that secondary glaucoma is an occasional finding in patients with Coffin-Siris syndrome. CASE PRESENTATION A child with secondary childhood glaucoma and additional ocular manifestations was evaluated and treated at the childhood glaucoma centre in Mainz, Germany. Examination under general anaesthesia revealed ocular anterior segment dysgenesis (ASD) (Peters type iridocorneal dysgenesis) in combination with congenital limbal stem cell deficiency (LSCD), aniridia, and cataract. The patient also had multiple other congenital anomalies and severe developmental delay. To explain his combination of anomalies, molecular genetic analysis from peripheral blood was performed in late 2018 and early 2019. Following normal findings with a panel diagnostic of 18 genes associated with congenital glaucoma, whole exome sequencing was performed and revealed a novel likely pathogenic heterozygous variant c.251G>T, p.(Gly84Val) in the SOX11 gene (SRY-related HMG-box gene 11). The variant had occurred de novo. Thus, the multiple congenital anomalies and developmental delay of the patient represented Coffin-Siris syndrome 9 (CSS9, OMIM #615866). CONCLUSIONS When eye diseases occur in combination with other systemic features, genetic analysis can be seminal. Results indicate that glaucoma is an occasional feature of patients with Coffin-Siris syndrome. As early treatment may improve the visual outcome of patients with glaucoma, we suggest that patients with Coffin-Siris syndrome should receive specific ophthalmological screening.
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Affiliation(s)
- Heidi Diel
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D – 55131 Mainz, Germany
| | - Can Ding
- Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Franz Grehn
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D – 55131 Mainz, Germany
| | - Panagiotis Chronopoulos
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D – 55131 Mainz, Germany
| | - Oliver Bartsch
- Institute of Human Genetics, University Medical Centre of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Esther M. Hoffmann
- Department of Ophthalmology, University Medical Centre of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, D – 55131 Mainz, Germany
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30
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Innella G, Greco D, Carli D, Magini P, Giorgio E, Galesi O, Ferrero GB, Romano C, Brusco A, Graziano C. Clinical spectrum and follow-up in six individuals with Lamb-Shaffer syndrome (SOX5). Am J Med Genet A 2020; 185:608-613. [PMID: 33296143 DOI: 10.1002/ajmg.a.62001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/19/2020] [Accepted: 11/14/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Giovanni Innella
- Medical Genetics Unit, Policlinico di S. Orsola, University of Bologna, Bologna, Italy
| | | | - Diana Carli
- Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy
| | - Pamela Magini
- Medical Genetics Unit, Policlinico di S. Orsola, University of Bologna, Bologna, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Turin, Turin, Italy
| | | | | | | | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy.,Unit of Medical Genetics, "Città della Salute e della Scienza" University Hospital, Turin, Italy
| | - Claudio Graziano
- Medical Genetics Unit, Policlinico di S. Orsola, University of Bologna, Bologna, Italy
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31
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Schock EN, LaBonne C. Sorting Sox: Diverse Roles for Sox Transcription Factors During Neural Crest and Craniofacial Development. Front Physiol 2020; 11:606889. [PMID: 33424631 PMCID: PMC7793875 DOI: 10.3389/fphys.2020.606889] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022] Open
Abstract
Sox transcription factors play many diverse roles during development, including regulating stem cell states, directing differentiation, and influencing the local chromatin landscape. Of the twenty vertebrate Sox factors, several play critical roles in the development the neural crest, a key vertebrate innovation, and the subsequent formation of neural crest-derived structures, including the craniofacial complex. Herein, we review the specific roles for individual Sox factors during neural crest cell formation and discuss how some factors may have been essential for the evolution of the neural crest. Additionally, we describe how Sox factors direct neural crest cell differentiation into diverse lineages such as melanocytes, glia, and cartilage and detail their involvement in the development of specific craniofacial structures. Finally, we highlight several SOXopathies associated with craniofacial phenotypes.
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Affiliation(s)
- Elizabeth N Schock
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States
| | - Carole LaBonne
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States.,NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, United States
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32
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Brauner R, Bignon-Topalovic J, Bashamboo A, McElreavey K. Pituitary stalk interruption syndrome is characterized by genetic heterogeneity. PLoS One 2020; 15:e0242358. [PMID: 33270637 PMCID: PMC7714207 DOI: 10.1371/journal.pone.0242358] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 10/30/2020] [Indexed: 12/11/2022] Open
Abstract
Pituitary stalk interruption syndrome is a rare disorder characterized by an absent or ectopic posterior pituitary, interrupted pituitary stalk and anterior pituitary hypoplasia, as well as in some cases, a range of heterogeneous somatic anomalies. A genetic cause is identified in only around 5% of all cases. Here, we define the genetic variants associated with PSIS followed by the same pediatric endocrinologist. Exome sequencing was performed in 52 (33 boys and 19 girls), including 2 familial cases single center pediatric cases, among them associated 36 (69.2%) had associated symptoms or syndromes. We identified rare and novel variants in genes (37 families with 39 individuals) known to be involved in one or more of the following-midline development and/or pituitary development or function (BMP4, CDON, GLI2, GLI3, HESX1, KIAA0556, LHX9, NKX2-1, PROP1, PTCH1, SHH, TBX19, TGIF1), syndromic and non-syndromic forms of hypogonadotropic hypogonadism (CCDC141, CHD7, FANCA, FANCC, FANCD2, FANCE, FANCG, IL17RD, KISS1R, NSMF, PMM2, SEMA3E, WDR11), syndromic forms of short stature (FGFR3, NBAS, PRMT7, RAF1, SLX4, SMARCA2, SOX11), cerebellum atrophy with optic anomalies (DNMT1, NBAS), axonal migration (ROBO1, SLIT2), and agenesis of the corpus callosum (ARID1B, CC2D2A, CEP120, CSPP1, DHCR7, INPP5E, VPS13B, ZNF423). Pituitary stalk interruption syndrome is characterized by a complex genetic heterogeneity, that reflects a complex phenotypic heterogeneity. Seizures, intellectual disability, micropenis or cryptorchidism, seen at presentation are usually considered as secondary to the pituitary deficiencies. However, this study shows that they are due to specific gene mutations. PSIS should therefore be considered as part of the phenotypic spectrum of other known genetic syndromes rather than as specific clinical entity.
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Affiliation(s)
- Raja Brauner
- Fondation Ophtalmologique Adolphe de Rothschild and Université Paris Descartes, Paris, France
| | | | - Anu Bashamboo
- Human Developmental Genetics Unit, Institute Pasteur, Paris, France
| | - Ken McElreavey
- Human Developmental Genetics Unit, Institute Pasteur, Paris, France
- * E-mail:
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33
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Tsang SM, Oliemuller E, Howard BA. Regulatory roles for SOX11 in development, stem cells and cancer. Semin Cancer Biol 2020; 67:3-11. [DOI: 10.1016/j.semcancer.2020.06.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 05/29/2020] [Accepted: 06/12/2020] [Indexed: 12/17/2022]
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34
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Jia S, Wu X, Wu Y, Cui X, Tao B, Zhu Z, Hu W. Multiple Developmental Defects in sox11a Mutant Zebrafish with Features of Coffin-Siris Syndrome. Int J Biol Sci 2020; 16:3039-3049. [PMID: 33061816 PMCID: PMC7545714 DOI: 10.7150/ijbs.47510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/16/2020] [Indexed: 12/14/2022] Open
Abstract
A previous study suggested that human Coffin-Siris syndrome is related to the mutation of SOX11. Since the homozygous SOX11 mutant mice died soon after birth, no suitable model was available for the study of the pathogenic mechanism of Coffin-Siris syndrome. To solve this problem, we generated two viable homozygous zebrafish mutants, sox11am/m and sox11bm/m. We found that the sox11am/m mutant possessed Coffin-Siris syndrome features. The sox11am/m mutants exhibited growth deficiency from 3.3 hpf embryos to adulthood. Furthermore, the sox11am/m mutant also displayed microcephaly, narrow pupillary distance, achondroplasia, and bone deformity in adults. Growth deficiency could be rescued by the injection of sox11a mRNA at the one-cell stage. In addition, the expression levels of genes related to cartilage and bone were downregulated in the sox11am/m mutant, indicating that sox11a mainly affected the growth and development of zebrafish by regulating the expression of genes related to skeletal development. Our results indicate that sox11am/m mutant zebrafish offered a potential model system to help with the search for pathogenic mechanisms of human Coffin-Siris syndrome.
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Affiliation(s)
- Shaoting Jia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xingxing Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunya Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuefan Cui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binbin Tao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wei Hu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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35
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Tolchin D, Yeager JP, Prasad P, Dorrani N, Russi AS, Martinez-Agosto JA, Haseeb A, Angelozzi M, Santen G, Ruivenkamp C, Mercimek-Andrews S, Depienne C, Kuechler A, Mikat B, Ludecke HJ, Bilan F, Le Guyader G, Gilbert-Dussardier B, Keren B, Heide S, Haye D, Van Esch H, Keldermans L, Ortiz D, Lancaster E, Krantz ID, Krock BL, Pechter KB, Arkader A, Medne L, DeChene ET, Calpena E, Melistaccio G, Wilkie AO, Suri M, Foulds N, Begtrup A, Henderson LB, Forster C, Reed P, McDonald MT, McConkie-Rosell A, Thevenon J, Le Tanno P, Coutton C, Tsai AC, Stewart S, Maver A, Gorazd R, Pichon O, Nizon M, Cogné B, Isidor B, Martin-Coignard D, Stoeva R, Lefebvre V, Le Caignec C, Ambrose J, Bleda M, Boardman-Pretty F, Boissiere J, Boustred C, Caulfield M, Chan G, Craig C, Daugherty L, de Burca A, Devereau A, Elgar G, Foulger R, Fowler T, Furió-Tarí P, Hackett J, Halai D, Holman J, Hubbard T, Kasperaviciute D, Kayikci M, Lahnstein L, Lawson K, Leigh S, Leong I, Lopez F, Maleady-Crowe F, Mason J, McDonagh E, Moutsianas L, Mueller M, Need A, Odhams C, Patch C, Perez-Gil D, Polychronopoulos D, Pullinger J, Rahim T, Rendon A, Rogers T, Ryten M, Savage K, Scott R, Siddiq A, Sieghart A, Smedley D, Smith K, Sosinsky A, Spooner W, Stevens H, Stuckey A, Thomas E, Thompson S, Tregidgo C, Tucci A, Walsh E, Watters S, Welland M, Williams E, Witkowska K, Wood S, Zarowiecki M. De Novo SOX6 Variants Cause a Neurodevelopmental Syndrome Associated with ADHD, Craniosynostosis, and Osteochondromas. Am J Hum Genet 2020; 106:830-845. [PMID: 32442410 DOI: 10.1016/j.ajhg.2020.04.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 04/24/2020] [Indexed: 12/21/2022] Open
Abstract
SOX6 belongs to a family of 20 SRY-related HMG-box-containing (SOX) genes that encode transcription factors controlling cell fate and differentiation in many developmental and adult processes. For SOX6, these processes include, but are not limited to, neurogenesis and skeletogenesis. Variants in half of the SOX genes have been shown to cause severe developmental and adult syndromes, referred to as SOXopathies. We here provide evidence that SOX6 variants also cause a SOXopathy. Using clinical and genetic data, we identify 19 individuals harboring various types of SOX6 alterations and exhibiting developmental delay and/or intellectual disability; the individuals are from 17 unrelated families. Additional, inconstant features include attention-deficit/hyperactivity disorder (ADHD), autism, mild facial dysmorphism, craniosynostosis, and multiple osteochondromas. All variants are heterozygous. Fourteen are de novo, one is inherited from a mosaic father, and four offspring from two families have a paternally inherited variant. Intragenic microdeletions, balanced structural rearrangements, frameshifts, and nonsense variants are predicted to inactivate the SOX6 variant allele. Four missense variants occur in residues and protein regions highly conserved evolutionarily. These variants are not detected in the gnomAD control cohort, and the amino acid substitutions are predicted to be damaging. Two of these variants are located in the HMG domain and abolish SOX6 transcriptional activity in vitro. No clear genotype-phenotype correlations are found. Taken together, these findings concur that SOX6 haploinsufficiency leads to a neurodevelopmental SOXopathy that often includes ADHD and abnormal skeletal and other features.
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36
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Sarogni P, Pallotta MM, Musio A. Cornelia de Lange syndrome: from molecular diagnosis to therapeutic approach. J Med Genet 2020; 57:289-295. [PMID: 31704779 PMCID: PMC7231464 DOI: 10.1136/jmedgenet-2019-106277] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/08/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022]
Abstract
Cornelia de Lange syndrome (CdLS) is a severe genetic disorder characterised by multisystemic malformations. CdLS is due to pathogenetic variants in NIPBL, SMC1A, SMC3, RAD21 and HDAC8 genes which belong to the cohesin pathway. Cohesin plays a pivotal role in chromatid cohesion, gene expression, and DNA repair. In this review, we will discuss how perturbations in those biological processes contribute to CdLS phenotype and will emphasise the state-of-art of CdLS therapeutic approaches.
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Affiliation(s)
- Patrizia Sarogni
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Maria M Pallotta
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Antonio Musio
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
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37
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Grönroos T, Mäkinen A, Laukkanen S, Mehtonen J, Nikkilä A, Oksa L, Rounioja S, Marincevic-Zuniga Y, Nordlund J, Pohjolainen V, Paavonen T, Heinäniemi M, Lohi O. Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia. Sci Rep 2020; 10:2043. [PMID: 32029838 PMCID: PMC7005266 DOI: 10.1038/s41598-020-58970-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
Acute lymphoblastic leukemia is marked by aberrant transcriptional features that alter cell differentiation, self-renewal, and proliferative features. We sought to identify the transcription factors exhibiting altered and subtype-specific expression patterns in B-ALL and report here that SOX11, a developmental and neuronal transcription factor, is aberrantly expressed in the ETV6-RUNX1 and TCF3-PBX1 subtypes of acute B-cell leukemias. We show that a high expression of SOX11 leads to alterations of gene expression that are typically associated with cell adhesion, migration, and differentiation. A high expression is associated with DNA hypomethylation at the SOX11 locus and a favorable outcome. The results indicate that SOX11 expression marks a group of patients with good outcomes and thereby prompts further study of its use as a biomarker.
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Affiliation(s)
- Toni Grönroos
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Artturi Mäkinen
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Saara Laukkanen
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Juha Mehtonen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Atte Nikkilä
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Laura Oksa
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Samuli Rounioja
- Fimlab Laboratories, Department of Hematology, Tampere University Hospital, Tampere, Finland
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Virva Pohjolainen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Timo Paavonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland.,Department of Pathology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Olli Lohi
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Department of Pediatrics, Tampere University Hospital, Tampere, Finland
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38
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Gao F, Elliott NJ, Ho J, Sharp A, Shokhirev MN, Hargreaves DC. Heterozygous Mutations in SMARCA2 Reprogram the Enhancer Landscape by Global Retargeting of SMARCA4. Mol Cell 2019; 75:891-904.e7. [PMID: 31375262 PMCID: PMC7291823 DOI: 10.1016/j.molcel.2019.06.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 04/24/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022]
Abstract
Mammalian SWI/SNF complexes are multi-subunit chromatin remodeling complexes associated with an ATPase (either SMARCA4 or SMARCA2). Heterozygous mutations in the SMARCA2 ATPase cause Nicolaides-Baraitser syndrome (NCBRS), an intellectual disability syndrome associated with delayed speech onset. We engineered human embryonic stem cells (hESCs) to carry NCBRS-associated heterozygous SMARCA2 K755R or R1159Q mutations. While SMARCA2 mutant hESCs were phenotypically normal, differentiation to neural progenitors cells (NPCs) was severely impaired. We find that SMARCA2 mutations cause enhancer reorganization with loss of SOX3-dependent neural enhancers and prominent emergence of astrocyte-specific de novo enhancers. Changes in chromatin accessibility at enhancers were associated with an increase in SMARCA2 binding and retargeting of SMARCA4. We show that the AP-1 family member FRA2 is aberrantly overexpressed in SMARCA2 mutant NPCs, where it functions as a pioneer factor at de novo enhancers. Together, our results demonstrate that SMARCA2 mutations cause impaired differentiation through enhancer reprogramming via inappropriate targeting of SMARCA4.
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Affiliation(s)
- Fangjian Gao
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Nicholas J Elliott
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Josephine Ho
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Alexzander Sharp
- Biological Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Diana C Hargreaves
- Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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39
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Angelozzi M, Lefebvre V. SOXopathies: Growing Family of Developmental Disorders Due to SOX Mutations. Trends Genet 2019; 35:658-671. [PMID: 31288943 DOI: 10.1016/j.tig.2019.06.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/15/2022]
Abstract
The SRY-related (SOX) transcription factor family pivotally contributes to determining cell fate and identity in many lineages. Since the original discovery that SRY deletions cause sex reversal, mutations in half of the 20 human SOX genes have been associated with rare congenital disorders, henceforward called SOXopathies. Mutations are generally de novo, heterozygous, and inactivating, revealing gene haploinsufficiency, but other types, including duplications, have been reported too. Missense variants primarily target the HMG domain, the SOX hallmark that mediates DNA binding and bending, nuclear trafficking, and protein-protein interactions. We here review key clinical and molecular features of SOXopathies and discuss the prospect that the disease family likely involves more SOX genes and larger clinical and genetic spectrums than currently appreciated.
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Affiliation(s)
- Marco Angelozzi
- Department of Surgery/Division of Orthopaedic Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Véronique Lefebvre
- Department of Surgery/Division of Orthopaedic Surgery, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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40
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McNeill A. Movement Disorders in Adults with 22q11 Deletion Syndrome. Mov Disord Clin Pract 2019; 6:339. [PMID: 31061849 DOI: 10.1002/mdc3.12752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 02/24/2019] [Indexed: 01/19/2023] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience The University of Sheffield Sheffield United Kingdom
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41
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McNeill A. Editorial for Brain Sciences Special Issue: "Diagnosis of Neurogenetic Disorders: Contribution of Next-Generation Sequencing and Deep Phenotyping". Brain Sci 2019; 9:brainsci9030072. [PMID: 30917557 PMCID: PMC6468541 DOI: 10.3390/brainsci9030072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 03/19/2019] [Indexed: 11/16/2022] Open
Abstract
In this Special Issue we bring together papers demonstrating the need for both detailed genomic and phenotypic studies to aid our scientific and clinical understanding of neurogenetic disorders [...].
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Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, University of Sheffield, 385a Glossop Road, Sheffield S10 2HQ, UK.
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42
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Abstract
SOX transcription factors participate in the specification, differentiation and activities of many cell types in development and beyond. The 20 mammalian family members are distributed into eight groups based on sequence identity, and while co-expressed same-group proteins often have redundant functions, different-group proteins typically have distinct functions. More than a handful of SOX proteins have pivotal roles in skeletogenesis. Heterozygous mutations in their genes cause human diseases, in which skeletal dysmorphism is a major feature, such as campomelic dysplasia (SOX9), or a minor feature, such as LAMSHF syndrome (SOX5) and Coffin-Siris-like syndromes (SOX4 and SOX11). Loss- and gain-of-function experiments in animal models have revealed that SOX4 and SOX11 (SOXC group) promote skeletal progenitor survival and control skeleton patterning and growth; SOX8 (SOXE group) delays the differentiation of osteoblast progenitors; SOX9 (SOXE group) is essential for chondrocyte fate maintenance and differentiation, and works in cooperation with SOX5 and SOX6 (SOXD group) and other types of transcription factors. These and other SOX proteins have also been proposed, mainly through in vitro experiments, to have key roles in other aspects of skeletogenesis, such as SOX2 in osteoblast stem cell self-renewal. We here review current knowledge of well-established and proposed skeletogenic roles of SOX proteins, their transcriptional and non-transcriptional actions, and their modes of regulation at the gene, RNA and protein levels. We also discuss gaps in knowledge and directions for future research to further decipher mechanisms underlying skeletogenesis in health and diseases and identify treatment options for skeletal malformation and degeneration diseases.
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Affiliation(s)
- Véronique Lefebvre
- The Children's Hospital of Philadelphia, Philadelphia, PA, United States.
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43
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De Novo SOX4 Variants Cause a Neurodevelopmental Disease Associated with Mild Dysmorphism. Am J Hum Genet 2019; 104:246-259. [PMID: 30661772 DOI: 10.1016/j.ajhg.2018.12.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/14/2018] [Indexed: 01/05/2023] Open
Abstract
SOX4, together with SOX11 and SOX12, forms group C of SRY-related (SOX) transcription factors. They play key roles, often in redundancy, in multiple developmental pathways, including neurogenesis and skeletogenesis. De novo SOX11 heterozygous mutations have been shown to cause intellectual disability, growth deficiency, and dysmorphic features compatible with mild Coffin-Siris syndrome. Using trio-based exome sequencing, we here identify de novo SOX4 heterozygous missense variants in four children who share developmental delay, intellectual disability, and mild facial and digital morphological abnormalities. SOX4 is highly expressed in areas of active neurogenesis in human fetuses, and sox4 knockdown in Xenopus embryos diminishes brain and whole-body size. The SOX4 variants cluster in the highly conserved, SOX family-specific HMG domain, but each alters a different residue. In silico tools predict that each variant affects a distinct structural feature of this DNA-binding domain, and functional assays demonstrate that these SOX4 proteins carrying these variants are unable to bind DNA in vitro and transactivate SOX reporter genes in cultured cells. These variants are not found in the gnomAD database of individuals with presumably normal development, but 12 other SOX4 HMG-domain missense variants are recorded and all demonstrate partial to full activity in the reporter assay. Taken together, these findings point to specific SOX4 HMG-domain missense variants as the cause of a characteristic human neurodevelopmental disorder associated with mild facial and digital dysmorphism.
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Machol K, Rousseau J, Ehresmann S, Garcia T, Nguyen TTM, Spillmann RC, Sullivan JA, Shashi V, Jiang YH, Stong N, Fiala E, Willing M, Pfundt R, Kleefstra T, Cho MT, McLaughlin H, Rosello Piera M, Orellana C, Martínez F, Caro-Llopis A, Monfort S, Roscioli T, Nixon CY, Buckley MF, Turner A, Jones WD, van Hasselt PM, Hofstede FC, van Gassen KL, Brooks AS, van Slegtenhorst MA, Lachlan K, Sebastian J, Madan-Khetarpal S, Sonal D, Sakkubai N, Thevenon J, Faivre L, Maurel A, Petrovski S, Krantz ID, Tarpinian JM, Rosenfeld JA, Lee BH, Campeau PM, Adams DR, Alejandro ME, Allard P, Azamian MS, Bacino CA, Balasubramanyam A, Barseghyan H, Batzli GF, Beggs AH, Behnam B, Bican A, Bick DP, Birch CL, Bonner D, Boone BE, Bostwick BL, Briere LC, Brown DM, Brush M, Burke EA, Burrage LC, Chen S, Clark GD, Coakley TR, Cogan JD, Cooper CM, Cope H, Craigen WJ, D’Souza P, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dillon A, Dipple KM, Donnell-Fink LA, Dorrani N, Dorset DC, Douine ED, Draper DD, Eckstein DJ, Emrick LT, Eng CM, Eskin A, Esteves C, Estwick T, Ferreira C, Fogel BL, Friedman ND, Gahl WA, Glanton E, Godfrey RA, Goldstein DB, Gould SE, Gourdine JPF, Groden CA, Gropman AL, Haendel M, Hamid R, Hanchard NA, Handley LH, Herzog MR, Holm IA, Hom J, Howerton EM, Huang Y, Jacob HJ, Jain M, Jiang YH, Johnston JM, Jones AL, Kohane IS, Krasnewich DM, Krieg EL, Krier JB, Lalani SR, Lau CC, Lazar J, Lee BH, Lee H, Levy SE, Lewis RA, Lincoln SA, Lipson A, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Markello TC, Marom R, Martínez-Agosto JA, Marwaha S, May T, McConkie-Rosell A, McCormack CE, McCray AT, Might M, Moretti PM, Morimoto M, Mulvihill JJ, Murphy JL, Muzny DM, Nehrebecky ME, Nelson SF, Newberry JS, Newman JH, Nicholas SK, Novacic D, Orange JS, Pallais JC, Palmer CG, Papp JC, Parker NH, Pena LD, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Reuter CM, Robertson AK, Rodan LH, Rosenfeld JA, Sampson JB, Samson SL, Schoch K, Schroeder MC, Scott DA, Sharma P, Shashi V, Signer R, Silverman EK, Sinsheimer JS, Smith KS, Spillmann RC, Splinter K, Stoler JM, Stong N, Sullivan JA, Sweetser DA, Tifft CJ, Toro C, Tran AA, Urv TK, Valivullah ZM, Vilain E, Vogel TP, Wahl CE, Walley NM, Walsh CA, Ward PA, Waters KM, Westerfield M, Wise AL, Wolfe LA, Worthey EA, Yamamoto S, Yang Y, Yu G, Zastrow DB, Zheng A. Expanding the Spectrum of BAF-Related Disorders: De Novo Variants in SMARCC2 Cause a Syndrome with Intellectual Disability and Developmental Delay. Am J Hum Genet 2019; 104:164-178. [PMID: 30580808 DOI: 10.1016/j.ajhg.2018.11.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/14/2018] [Indexed: 12/22/2022] Open
Abstract
SMARCC2 (BAF170) is one of the invariable core subunits of the ATP-dependent chromatin remodeling BAF (BRG1-associated factor) complex and plays a crucial role in embryogenesis and corticogenesis. Pathogenic variants in genes encoding other components of the BAF complex have been associated with intellectual disability syndromes. Despite its significant biological role, variants in SMARCC2 have not been directly associated with human disease previously. Using whole-exome sequencing and a web-based gene-matching program, we identified 15 individuals with variable degrees of neurodevelopmental delay and growth retardation harboring one of 13 heterozygous variants in SMARCC2, most of them novel and proven de novo. The clinical presentation overlaps with intellectual disability syndromes associated with other BAF subunits, such as Coffin-Siris and Nicolaides-Baraitser syndromes and includes prominent speech impairment, hypotonia, feeding difficulties, behavioral abnormalities, and dysmorphic features such as hypertrichosis, thick eyebrows, thin upper lip vermilion, and upturned nose. Nine out of the fifteen individuals harbor variants in the highly conserved SMARCC2 DNA-interacting domains (SANT and SWIRM) and present with a more severe phenotype. Two of these individuals present cardiac abnormalities. Transcriptomic analysis of fibroblasts from affected individuals highlights a group of differentially expressed genes with possible roles in regulation of neuronal development and function, namely H19, SCRG1, RELN, and CACNB4. Our findings suggest a novel SMARCC2-related syndrome that overlaps with neurodevelopmental disorders associated with variants in BAF-complex subunits.
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45
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Gazdagh G, Blyth M, Scurr I, Turnpenny PD, Mehta SG, Armstrong R, McEntagart M, Newbury-Ecob R, Tobias ES, Joss S. Extending the clinical and genetic spectrum of ARID2 related intellectual disability. A case series of 7 patients. Eur J Med Genet 2019; 62:27-34. [DOI: 10.1016/j.ejmg.2018.04.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 04/10/2018] [Accepted: 04/22/2018] [Indexed: 02/01/2023]
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46
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Balta EA, Schäffner I, Wittmann MT, Sock E, von Zweydorf F, von Wittgenstein J, Steib K, Heim B, Kremmer E, Häberle BM, Ueffing M, Lie DC, Gloeckner CJ. Phosphorylation of the neurogenic transcription factor SOX11 on serine 133 modulates neuronal morphogenesis. Sci Rep 2018; 8:16196. [PMID: 30385877 PMCID: PMC6212486 DOI: 10.1038/s41598-018-34480-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/25/2018] [Indexed: 02/07/2023] Open
Abstract
The intellectual disability gene, Sox11, encodes for a critical neurodevelopmental transcription factor with functions in precursor survival, neuronal fate determination, migration and morphogenesis. The mechanisms regulating SOX11’s activity remain largely unknown. Mass spectrometric analysis uncovered that SOX11 can be post-translationally modified by phosphorylation. Here, we report that phosphorylatable serines surrounding the high-mobility group box modulate SOX11’s transcriptional activity. Through Mass Spectrometry (MS), co-immunoprecipitation assays and in vitro phosphorylation assays followed by MS we verified that protein kinase A (PKA) interacts with SOX11 and phosphorylates it on S133. In vivo replacement of SoxC factors in developing adult-generated hippocampal neurons with SOX11 S133 phospho-mutants indicated that phosphorylation on S133 modulates dendrite development of adult-born dentate granule neurons, while reporter assays suggested that S133 phosphorylation fine-tunes the activation of select target genes. These data provide novel insight into the control of the critical neurodevelopmental regulator SOX11 and imply SOX11 as a mediator of PKA-regulated neuronal development.
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Affiliation(s)
- Elli-Anna Balta
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Iris Schäffner
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Marie-Theres Wittmann
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Elisabeth Sock
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Felix von Zweydorf
- DZNE-German Center for Neurodegenerative Diseases, 72076, Tübingen, Germany
| | - Julia von Wittgenstein
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Kathrin Steib
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Birgit Heim
- University of Tübingen, Institute for Ophthalmic Research, Center for Ophthalmology, 72076, Tübingen, Germany
| | - Elisabeth Kremmer
- Monoclonal Antibody Core Facility, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Benjamin Martin Häberle
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Marius Ueffing
- University of Tübingen, Institute for Ophthalmic Research, Center for Ophthalmology, 72076, Tübingen, Germany
| | - Dieter Chichung Lie
- Institute of Biochemistry, Friedrich-Alexander Universität Erlangen-Nürnberg, 91054, Erlangen, Germany.
| | - Christian Johannes Gloeckner
- DZNE-German Center for Neurodegenerative Diseases, 72076, Tübingen, Germany. .,University of Tübingen, Institute for Ophthalmic Research, Center for Ophthalmology, 72076, Tübingen, Germany.
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47
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Mannino EA, Miyawaki H, Santen G, Schrier Vergano SA. First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations. Am J Med Genet A 2018; 176:2250-2258. [PMID: 30276971 DOI: 10.1002/ajmg.a.40471] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 05/25/2018] [Accepted: 06/21/2018] [Indexed: 11/05/2022]
Abstract
Coffin-Siris syndrome (CSS; MIM 135900) is a multisystem congenital anomaly syndrome caused by mutations in the genes in the Brg-1 associated factors (BAF) complex. Classically, individuals with CSS have been described with hypo- or aplasia of the fifth digit nails or phalanges (hence the term "fifth digit syndrome"). Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities. Varying degrees of developmental and intellectual delay are universal. To date, approximately 200 individuals have been described in the literature. With the advent of large-scale genetic testing such as whole-exome sequencing is becoming more available, more individuals are being found to have mutations in this pathway, and the phenotypic spectrum appears to be broadening. We report here a large cohort of 81 individuals with the diagnosis of CSS from the first parent-reported CSS/BAF complex registry in an effort to describe this variation among individuals, the natural history of the syndrome, and draw some gene-phenotype correlations. We propose that changes in the BAF complex may represent a spectrum of disorders, including both ARID1B-related nonsyndromic intellectual disability (ARID1B-ID) and CSS with classic physical features. In addition, we offer surveillance and management recommendations based on the medical issues encountered in this cohort to help guide physicians and patients' families.
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Affiliation(s)
- Elizabeth A Mannino
- Doctor of Medicine Program, Eastern Virginia Medical School, Norfolk, Virginia
| | - Hanae Miyawaki
- Master of Public Health Program, Eastern Virginia Medical School, Old Dominion University, Norfolk, Virginia
| | - Gijs Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Samantha A Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia.,Department of Pediatrics, Eastern Virginia Medical School, Norfolk, Virginia
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48
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McNeill A. Are congenital anomalies of the kidney and urinary tract part of the SOX11 syndrome? Kidney Int 2018; 94:826-827. [PMID: 30243316 DOI: 10.1016/j.kint.2018.06.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 06/07/2018] [Indexed: 10/28/2022]
Affiliation(s)
- Alisdair McNeill
- University of Sheffield, The Sheffield Institute for Translational Neuroscience, Sheffield, South Yorkshire, UK.
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49
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Burnside RD, Molinari S, Botti C, Brooks SS, Chung WK, Mehta L, Schwartz S, Papenhausen P. Features of Feingold syndrome 1 dominate in subjects with 2p deletions including
MYCN. Am J Med Genet A 2018; 176:1956-1963. [DOI: 10.1002/ajmg.a.40355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 04/14/2018] [Accepted: 04/17/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Rachel D. Burnside
- Laboratory Corporation of America HoldingsCenter for Molecular Biology and Pathology, Research Triangle Park North Carolina
| | - Sharon Molinari
- Laboratory Corporation of America HoldingsCenter for Molecular Biology and Pathology, Research Triangle Park North Carolina
| | - Christina Botti
- Division of Medical Genetics, Department of PediatricsRutgers‐Robert Wood Johnson Medical School New Brunswick New Jersey
| | - Susan Sklower Brooks
- Division of Medical Genetics, Department of PediatricsRutgers‐Robert Wood Johnson Medical School New Brunswick New Jersey
| | - Wendy K. Chung
- Department of PediatricsColumbia University New York New York
- Department of MedicineColumbia University New York New York
| | - Lakshmi Mehta
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount Sinai New York New York
| | - Stuart Schwartz
- Laboratory Corporation of America HoldingsCenter for Molecular Biology and Pathology, Research Triangle Park North Carolina
| | - Peter Papenhausen
- Laboratory Corporation of America HoldingsCenter for Molecular Biology and Pathology, Research Triangle Park North Carolina
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50
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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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