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Zarate YA, Bosanko K, Derar N, Fish JL. Abnormalities in pharyngeal arch-derived structures in SATB2-associated syndrome. Clin Genet 2024; 106:209-213. [PMID: 38693682 PMCID: PMC11216868 DOI: 10.1111/cge.14540] [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: 02/06/2024] [Revised: 04/01/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
SATB2-associated syndrome (SAS, glass syndrome, OMIM#612313) is a neurodevelopmental autosomal dominant disorder with frequent craniofacial abnormalities including palatal and dental anomalies. To assess the role of Satb2 in craniofacial development, we analyzed mutant mice at different stages of development. Here, we show that Satb2 is broadly expressed in early embryonic mouse development including the mesenchyme of the second and third arches. Satb2-/- mutant mice exhibit microglossia, a shortened lower jaw, smaller trigeminal ganglia, and larger thyroids. We correlate these findings with the detailed clinical phenotype of four individuals with SAS and remarkable craniofacial phenotypes with one requiring mandibular distraction in childhood. We conclude that the mouse and patient data presented support less well-described phenotypic aspects of SAS including mandibular morphology and thyroid anatomical/functional issues.
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Affiliation(s)
- Yuri A Zarate
- Division of Genetics and Metabolism, University of Kentucky, Lexington, Kentucky, USA
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Katherine Bosanko
- Department of Pediatrics, Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Nada Derar
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
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2
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Shen JJ, Chen QC, Huang YL, Wu K, Yang LC, Wang SS. Facial recognition models for identifying genetic syndromes associated with pulmonary stenosis in children. Postgrad Med J 2024:qgae095. [PMID: 39075977 DOI: 10.1093/postmj/qgae095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/26/2024] [Accepted: 07/10/2024] [Indexed: 07/31/2024]
Abstract
BACKGROUND Williams-Beuren syndrome, Noonan syndrome, and Alagille syndrome are common types of genetic syndromes (GSs) characterized by distinct facial features, pulmonary stenosis, and delayed growth. In clinical practice, differentiating these three GSs remains a challenge. Facial gestalts serve as a diagnostic tool for recognizing Williams-Beuren syndrome, Noonan syndrome, and Alagille syndrome. Pretrained foundation models (PFMs) can be considered the foundation for small-scale tasks. By pretraining with a foundation model, we propose facial recognition models for identifying these syndromes. METHODS A total of 3297 (n = 1666) facial photos were obtained from children diagnosed with Williams-Beuren syndrome (n = 174), Noonan syndrome (n = 235), and Alagille syndrome (n = 51), and from children without GSs (n = 1206). The photos were randomly divided into five subsets, with each syndrome and non-GS equally and randomly distributed in each subset. The proportion of the training set and the test set was 4:1. The ResNet-100 architecture was employed as the backbone model. By pretraining with a foundation model, we constructed two face recognition models: one utilizing the ArcFace loss function, and the other employing the CosFace loss function. Additionally, we developed two models using the same architecture and loss function but without pretraining. The accuracy, precision, recall, and F1 score of each model were evaluated. Finally, we compared the performance of the facial recognition models to that of five pediatricians. RESULTS Among the four models, ResNet-100 with a PFM and CosFace loss function achieved the best accuracy (84.8%). Of the same loss function, the performance of the PFMs significantly improved (from 78.5% to 84.5% for the ArcFace loss function, and from 79.8% to 84.8% for the CosFace loss function). With and without the PFM, the performance of the CosFace loss function models was similar to that of the ArcFace loss function models (79.8% vs 78.5% without PFM; 84.8% vs 84.5% with PFM). Among the five pediatricians, the highest accuracy (0.700) was achieved by the senior-most pediatrician with genetics training. The accuracy and F1 scores of the pediatricians were generally lower than those of the models. CONCLUSIONS A facial recognition-based model has the potential to improve the identification of three common GSs with pulmonary stenosis. PFMs might be valuable for building screening models for facial recognition. Key messages What is already known on this topic: Early identification of genetic syndromes (GSs) is crucial for the management and prognosis of children with pulmonary stenosis (PS). Facial phenotyping with convolutional neural networks (CNNs) often requires large-scale training data, limiting its usefulness for GSs. What this study adds: We successfully built multi-classification models based on face recognition using a CNN to accurately identify three common PS-associated GSs. ResNet-100 with a pretrained foundation model (PFM) and CosFace loss function achieved the best accuracy (84.8%). Pretrained with the foundation model, the performance of the models significantly improved, although the impact of the type of loss function appeared to be minimal. How this study might affect research, practice, or policy: A facial recognition-based model has the potential to improve the identification of GSs in children with PS. The PFM might be valuable for building identification models for facial detection.
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Affiliation(s)
- Jun-Jun Shen
- Department of Pediatric Surgery, Zhujiang Hospital, Southern Medical University, No. 253, Industrial Avenue Middle, Guangzhou 510282, Guangdong, China
- Department of Pediatric Cardiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, No. 106, Zhongshan 2nd Road, Guangzhou 510000, China
| | - Qin-Chang Chen
- Department of Pediatric Cardiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, No. 106, Zhongshan 2nd Road, Guangzhou 510000, China
| | - Yu-Lu Huang
- Department of Pediatric Cardiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, No. 106, Zhongshan 2nd Road, Guangzhou 510000, China
| | - Kai Wu
- Department of Pediatric Surgery, Zhujiang Hospital, Southern Medical University, No. 253, Industrial Avenue Middle, Guangzhou 510282, Guangdong, China
| | - Liu-Cheng Yang
- Department of Pediatric Surgery, Zhujiang Hospital, Southern Medical University, No. 253, Industrial Avenue Middle, Guangzhou 510282, Guangdong, China
| | - Shu-Shui Wang
- Department of Pediatric Cardiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, No. 106, Zhongshan 2nd Road, Guangzhou 510000, China
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3
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Pagnamenta AT, Yu J, Walker S, Noble AJ, Lord J, Dutta P, Hashim M, Camps C, Green H, Devaiah S, Nashef L, Parr J, Fratter C, Ibnouf Hussein R, Lindsay SJ, Lalloo F, Banos-Pinero B, Evans D, Mallin L, Waite A, Evans J, Newman A, Allen Z, Perez-Becerril C, Ryan G, Hart R, Taylor J, Bedenham T, Clement E, Blair E, Hay E, Forzano F, Higgs J, Canham N, Majumdar A, McEntagart M, Lahiri N, Stewart H, Smithson S, Calpena E, Jackson A, Banka S, Titheradge H, McGowan R, Rankin J, Shaw-Smith C, Evans DG, Burghel GJ, Smith MJ, Anderson E, Madhu R, Firth H, Ellard S, Brennan P, Anderson C, Taupin D, Rogers MT, Cook JA, Durkie M, East JE, Fowler D, Wilson L, Igbokwe R, Gardham A, Tomlinson I, Baralle D, Uhlig HH, Taylor JC. The impact of inversions across 33,924 families with rare disease from a national genome sequencing project. Am J Hum Genet 2024; 111:1140-1164. [PMID: 38776926 PMCID: PMC11179413 DOI: 10.1016/j.ajhg.2024.04.018] [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: 11/12/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Detection of structural variants (SVs) is currently biased toward those that alter copy number. The relative contribution of inversions toward genetic disease is unclear. In this study, we analyzed genome sequencing data for 33,924 families with rare disease from the 100,000 Genomes Project. From a database hosting >500 million SVs, we focused on 351 genes where haploinsufficiency is a confirmed disease mechanism and identified 47 ultra-rare rearrangements that included an inversion (24 bp to 36.4 Mb, 20/47 de novo). Validation utilized a number of orthogonal approaches, including retrospective exome analysis. RNA-seq data supported the respective diagnoses for six participants. Phenotypic blending was apparent in four probands. Diagnostic odysseys were a common theme (>50 years for one individual), and targeted analysis for the specific gene had already been performed for 30% of these individuals but with no findings. We provide formal confirmation of a European founder origin for an intragenic MSH2 inversion. For two individuals with complex SVs involving the MECP2 mutational hotspot, ambiguous SV structures were resolved using long-read sequencing, influencing clinical interpretation. A de novo inversion of HOXD11-13 was uncovered in a family with Kantaputra-type mesomelic dysplasia. Lastly, a complex translocation disrupting APC and involving nine rearranged segments confirmed a clinical diagnosis for three family members and resolved a conundrum for a sibling with a single polyp. Overall, inversions play a small but notable role in rare disease, likely explaining the etiology in around 1/750 families across heterogeneous clinical cohorts.
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Affiliation(s)
- Alistair T Pagnamenta
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Jing Yu
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK; Novo Nordisk Oxford Research Centre, Oxford, UK
| | | | - Alexandra J Noble
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Jenny Lord
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK; Sheffield Institute for Translational Neuroscience, The University of Sheffield, Sheffield, UK
| | - Prasun Dutta
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Mona Hashim
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Carme Camps
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hannah Green
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Smrithi Devaiah
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Lina Nashef
- Department of Neurology, King's College Hospital, London, UK
| | - Jason Parr
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Carl Fratter
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Rana Ibnouf Hussein
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Sarah J Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Benito Banos-Pinero
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - David Evans
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Lucy Mallin
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Adrian Waite
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Julie Evans
- Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Andrew Newman
- The All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Zoe Allen
- North Thames Rare and Inherited Disease Laboratory, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Cristina Perez-Becerril
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham, UK
| | - Rachel Hart
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - John Taylor
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Tina Bedenham
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Emma Clement
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ed Blair
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Eleanor Hay
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Francesca Forzano
- Clinical Genetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Jenny Higgs
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Anirban Majumdar
- Department of Paediatric Neurology, Bristol Children's Hospital, Bristol, UK
| | - Meriel McEntagart
- SW Thames Centre for Genomic Medicine, University of London & St George's University Hospitals NHS Foundation Trust, St George's, London, UK
| | - Nayana Lahiri
- SW Thames Centre for Genomic Medicine, University of London & St George's University Hospitals NHS Foundation Trust, St George's, London, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Smithson
- Department of Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, UK
| | - Eduardo Calpena
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK; Grupo de Investigación en Biomedicina Molecular, Celular y Genómica, Unidad CIBERER (CB06/07/1030), Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Adam Jackson
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Hannah Titheradge
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Ruth McGowan
- West of Scotland Centre for Genomic Medicine, Glasgow, UK
| | - Julia Rankin
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - Charles Shaw-Smith
- Department of Clinical Genetics, Royal Devon University Healthcare NHS Trust, Exeter, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Miriam J Smith
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Emily Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women's NHS Foundation Trust, Liverpool, UK
| | - Rajesh Madhu
- Paediatric Neurosciences Department, Alder Hey Children's Hospital NHS Foundation Trust, Liverpool, UK
| | - Helen Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sian Ellard
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Paul Brennan
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle University, Newcastle, UK
| | - Claire Anderson
- Canberra Clinical Genomics, Canberra Health Services and The Australian National University, Canberra, ACT, Australia
| | - Doug Taupin
- Cancer Research, Canberra Hospital, Canberra, ACT, Australia
| | - Mark T Rogers
- The All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Jackie A Cook
- Department of Clinical Genetics, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Miranda Durkie
- Sheffield Diagnostic Genetics Service, Sheffield Children's NHS Foundation Trust, North East and Yorkshire Genomic Laboratory Hub, Sheffield, UK
| | - James E East
- Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Darren Fowler
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Louise Wilson
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Rebecca Igbokwe
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Alice Gardham
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford, UK
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Holm H Uhlig
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, John Radcliffe Hospital, Oxford, UK
| | - Jenny C Taylor
- Oxford Biomedical Research Centre, Centre for Human Genetics, University of Oxford, Oxford, UK.
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Wahl N, Espeso-Gil S, Chietera P, Nagel A, Laighneach A, Morris DW, Rajarajan P, Akbarian S, Dechant G, Apostolova G. SATB2 organizes the 3D genome architecture of cognition in cortical neurons. Mol Cell 2024; 84:621-639.e9. [PMID: 38244545 PMCID: PMC10923151 DOI: 10.1016/j.molcel.2023.12.024] [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: 01/27/2023] [Revised: 10/02/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on the three-dimensional (3D) epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal-activity-regulated genes, thus influencing their expression. It also alters A/B compartments, topologically associating domains, and frequently interacting regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with a SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence, and schizophrenia. Our data establish SATB2 as a cell-type-specific 3D genome modulator, which operates both independently and in cooperation with CCCTC-binding factor (CTCF) to set up the chromatin landscape of pyramidal neurons for cognitive processes.
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Affiliation(s)
- Nico Wahl
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Sergio Espeso-Gil
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria; Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paola Chietera
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Amelie Nagel
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Derek W Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Prashanth Rajarajan
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georg Dechant
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
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5
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Wang N, Wan R, Tang K. Transcriptional regulation in the development and dysfunction of neocortical projection neurons. Neural Regen Res 2024; 19:246-254. [PMID: 37488873 PMCID: PMC10503610 DOI: 10.4103/1673-5374.379039] [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: 01/29/2023] [Revised: 04/10/2023] [Accepted: 05/17/2023] [Indexed: 07/26/2023] Open
Abstract
Glutamatergic projection neurons generate sophisticated excitatory circuits to integrate and transmit information among different cortical areas, and between the neocortex and other regions of the brain and spinal cord. Appropriate development of cortical projection neurons is regulated by certain essential events such as neural fate determination, proliferation, specification, differentiation, migration, survival, axonogenesis, and synaptogenesis. These processes are precisely regulated in a tempo-spatial manner by intrinsic factors, extrinsic signals, and neural activities. The generation of correct subtypes and precise connections of projection neurons is imperative not only to support the basic cortical functions (such as sensory information integration, motor coordination, and cognition) but also to prevent the onset and progression of neurodevelopmental disorders (such as intellectual disability, autism spectrum disorders, anxiety, and depression). This review mainly focuses on the recent progress of transcriptional regulations on the development and diversity of neocortical projection neurons and the clinical relevance of the failure of transcriptional modulations.
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Affiliation(s)
- Ningxin Wang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong Province, China
| | - Rong Wan
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong Province, China
| | - Ke Tang
- Precise Genome Engineering Center, School of Life Sciences, Guangzhou University, Guangzhou, Guangdong Province, China
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6
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Ma Y, Liu H, Shi L. Progress of epigenetic modification of SATB2 gene in the pathogenesis of non-syndromic cleft lip and palate. Asian J Surg 2024; 47:72-76. [PMID: 37852859 DOI: 10.1016/j.asjsur.2023.09.113] [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: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 10/20/2023] Open
Abstract
Non-syndromic Cleft Lip and Palate (NSCLP) is one of the most common congenital craniofacial malformations. However, there is no enough knowledge about its mechanism, even through many relevant studies verify that cleft lip and palate is caused by interactions between environmental and genetic factors. SATB2 gene is one of the most common candidate genes of NSCLP, and the development of epigenetics provides a new direction on pathogenesis of cleft lip and palate. This review summarizes SATB2 gene in the pathogenesis of non-syndromic cleft lip and palate, expecting to provide strategies to prevent and treat cleft and palate in the future.
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Affiliation(s)
- Yang Ma
- Department of Plastic Surgery, Meizhou Clinical Institute of Shantou University Medical College, No 63 Huangtang Road, Meizhou, 514031, Guangdong, China
| | - Hangyu Liu
- Department of Plastic Surgery and Burn Center, The Second Affiliated Hospital of Shantou University Medical College, North Dongxia Road, Shantou, 515041, Guangdong, China
| | - Lungang Shi
- Department of Plastic Surgery, Meizhou Clinical Institute of Shantou University Medical College, No 63 Huangtang Road, Meizhou, 514031, Guangdong, China; Department of Plastic Surgery and Burn Center, The Second Affiliated Hospital of Shantou University Medical College, North Dongxia Road, Shantou, 515041, Guangdong, China.
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7
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Alexander KD, Ramachandran S, Biswas K, Lambert CM, Russell J, Oliver DB, Armstrong W, Rettler M, Liu S, Doitsidou M, Bénard C, Walker AK, Francis MM. The homeodomain transcriptional regulator DVE-1 directs a program for synapse elimination during circuit remodeling. Nat Commun 2023; 14:7520. [PMID: 37980357 PMCID: PMC10657367 DOI: 10.1038/s41467-023-43281-4] [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] [Accepted: 11/02/2023] [Indexed: 11/20/2023] Open
Abstract
The elimination of synapses during circuit remodeling is critical for brain maturation; however, the molecular mechanisms directing synapse elimination and its timing remain elusive. We show that the transcriptional regulator DVE-1, which shares homology with special AT-rich sequence-binding (SATB) family members previously implicated in human neurodevelopmental disorders, directs the elimination of juvenile synaptic inputs onto remodeling C. elegans GABAergic neurons. Juvenile acetylcholine receptor clusters and apposing presynaptic sites are eliminated during the maturation of wild-type GABAergic neurons but persist into adulthood in dve-1 mutants, producing heightened motor connectivity. DVE-1 localization to GABAergic nuclei is required for synapse elimination, consistent with DVE-1 regulation of transcription. Pathway analysis of putative DVE-1 target genes, proteasome inhibitor, and genetic experiments implicate the ubiquitin-proteasome system in synapse elimination. Together, our findings define a previously unappreciated role for a SATB family member in directing synapse elimination during circuit remodeling, likely through transcriptional regulation of protein degradation processes.
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Affiliation(s)
- Kellianne D Alexander
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Shankar Ramachandran
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Kasturi Biswas
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Christopher M Lambert
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Julia Russell
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Devyn B Oliver
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - William Armstrong
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Monika Rettler
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Samuel Liu
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Maria Doitsidou
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, Scotland
| | - Claire Bénard
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Department of Biological Sciences, Université du Québec à Montréal, Quebec, Canada
| | - Amy K Walker
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Michael M Francis
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, MA, USA.
- Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, MA, USA.
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8
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Perry JL, Williams JL, Snodgrass TD, Sitzman TJ. VPI Management in SATB2 Syndrome: Use of MRI to Evaluate Anatomy and Physiology in Non-Cleft VPI. Cleft Palate Craniofac J 2023; 60:1499-1504. [PMID: 35695193 PMCID: PMC10183239 DOI: 10.1177/10556656221106888] [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] [Indexed: 11/15/2022] Open
Abstract
This clinical case study describes the velopharyngeal anatomy and physiology in a patient who presented with SATB2-associated syndrome (SAS) and velopharyngeal insufficiency (VPI) in the absence of an overt cleft palate. The clinical presentation, treatment, outcome, and the contribution of anatomical findings from MRI to surgical treatment planning for this rare genetic disorder, SAS, are described. This case study contributes to our current understanding of the anatomy and physiology of the velopharyngeal mechanism in an individual born with SAS and non-cleft VPI. It also details the changes following bilateral buccal myomucosal flaps in this patient.
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Affiliation(s)
- Jamie L Perry
- Department of Communication Sciences and Disorders, East Carolina University, Greenville, NC, USA
| | - Jessica L Williams
- Barrow Cleft and Craniofacial Center, Phoenix, AZ, USA
- Department of Speech and Hearing Science, Arizona State University, Tempe, AZ, USA
| | - Taylor D Snodgrass
- Department of Communication Sciences and Disorders, East Carolina University, Greenville, NC, USA
| | - Thomas J Sitzman
- Barrow Cleft and Craniofacial Center, Phoenix, AZ, USA
- Division of Plastic Surgery, Phoenix Children's Hospital, Phoenix, AZ, USA
- Division of Plastic Surgery, Mayo Clinic Arizona, Scottsdale, AZ, USA
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9
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Liu Q, Feng NN, Chen LJ. Genetic analysis of a child with SATB2‑associated syndrome and literature study. Exp Ther Med 2023; 26:372. [PMID: 37415841 PMCID: PMC10320656 DOI: 10.3892/etm.2023.12071] [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: 07/02/2022] [Accepted: 02/23/2023] [Indexed: 07/08/2023] Open
Abstract
The present study aimed to investigate clinical phenotype and genotype characteristics of a male child with SATB2-associated syndrome (SAS) and analyzed the relationship between these characteristics and the possible underlying genetic mechanism. His clinical phenotype was analyzed. Using a high-throughput sequencing platform, his DNA samples were subjected to medical exome sequencing, screened for suspected variant loci and analyzed for chromosomal copy number variations. The suspected pathogenic loci were verified by Sanger sequencing. He presented with phenotypic anomalies of delayed growth, delayed speech and mental development, facial dysmorphism showing the typical manifestation of SAS and motor retardation symptoms. Gene sequencing result analyses revealed a de novo heterozygous repeat insertion shift mutation in the SATB2 gene (NM_015265.3) c.771dupT (p.Met258Tyrfs*46), resulting in a frameshift mutation from methionine to tyrosine at the amino acid site 258 and a truncated protein with 46 amino acids missing. The parents showed no mutation at this locus. This mutation was identified as the nosogenesis of this syndrome in children. To the best of the authors' knowledge, this is the first report on this mutation. The clinical manifestations and gene variation characteristics of 39 previously reported SAS cases were analyzed together with this case. The findings of the present study suggested severely impaired language development, facial dysmorphism and varying degrees of delayed intellectual development as the characteristic clinical manifestations of SAS.
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Affiliation(s)
- Qian Liu
- Center for Reproductive Medicine, Center for Prenatal Genetics, First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Nan-Nan Feng
- Center for Reproductive Medicine, Center for Prenatal Genetics, First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Lin-Jiao Chen
- Center for Reproductive Medicine, Center for Prenatal Genetics, First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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10
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Kurosaka H, Yamamoto S, Hirasawa K, Yanagishita T, Fujioka K, Yagasaki H, Nagata M, Ishihara Y, Yonei A, Asano Y, Nagata N, Tsujimoto T, Inubushi T, Yamamoto T, Sakai N, Yamashiro T. Craniofacial and dental characteristics of three Japanese individuals with genetically diagnosed SATB2-associated syndrome. Am J Med Genet A 2023. [PMID: 37141439 DOI: 10.1002/ajmg.a.63225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/06/2023]
Abstract
Craniofacial defects are one of the most frequent phenotypes in syndromic diseases. More than 30% of syndromic diseases are associated with craniofacial defects, which are important for the precise diagnosis of systemic diseases. Special AT-rich sequence-binding protein 2 (SATB2)-associated syndrome (SAS) is a rare syndromic disease associated with a wide variety of phenotypes, including intellectual disability and craniofacial defects. Among them, dental anomalies are the most frequently observed phenotype and thus becomes an important diagnostic criterion for SAS. In this report, we demonstrate three Japanese cases of genetically diagnosed SAS with detailed craniofacial phenotypes. The cases showed multiple dental problems, which have been previously reported to be linked to SAS, including abnormal crown morphologies and pulp stones. One case showed a characteristic enamel pearl at the root furcation. These phenotypes add new insights for differentiating SAS from other disorders.
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Affiliation(s)
- Hiroshi Kurosaka
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Sayuri Yamamoto
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Kyoko Hirasawa
- Department of Pediatrics, Tokyo Women's Medical University, Tokyo, Japan
| | - Tomoe Yanagishita
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Kaoru Fujioka
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Hideaki Yagasaki
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Miho Nagata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yasuki Ishihara
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Ayumi Yonei
- Department of Genetic Counseling Osaka University Hospital, Osaka, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Namiki Nagata
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Takayuki Tsujimoto
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Toshihiro Inubushi
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Toshiyuki Yamamoto
- Institute of Medical Genetics, Tokyo Women's Medical University, Tokyo, Japan
| | - Norio Sakai
- Department of Genetic Counseling Osaka University Hospital, Osaka, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Health Science, Child Healthcare and Genetic Science, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takashi Yamashiro
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
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11
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Copelli MDM, Pairet E, Atique-Tacla M, Vieira TP, Appenzeller S, Helaers R, Vikkula M, Gil-da-Silva-Lopes VL. SATB2-Associated Syndrome Due to a c.715C>T:p(Arg239*) Variant in Adulthood: Natural History and Literature Review. Genes (Basel) 2023; 14:genes14040882. [PMID: 37107640 PMCID: PMC10137462 DOI: 10.3390/genes14040882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/03/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
SATB2-associated syndrome (SAS) is a rare condition, and it is characterized by severe developmental delay/intellectual disability, especially severe speech delay/or absence, craniofacial abnormalities, and behavioral problems. Most of the published reports are limited to children, with little information about the natural history of the disease and the possible novel signs and symptoms or behavioral changes in adulthood. We describe the management and follow-up of a 25-year-old male with SAS due to a de novo heterozygous nonsense variant SATB2:c.715C>T:p.(Arg239*) identified by whole-exome sequencing and review the literature. The case herein described contributes to a better characterization of the natural history of this genetic condition and in addition to the genotype-phenotype correlation of the SATB2:c.715C>T:p.(Arg239*) variant in SAS, highlights some particularities of its management.
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Affiliation(s)
- Matheus de Mello Copelli
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas CEP 13083-887, SP, Brazil
| | - Eleonore Pairet
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Milena Atique-Tacla
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas CEP 13083-887, SP, Brazil
| | - Társis Paiva Vieira
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas CEP 13083-887, SP, Brazil
| | - Simone Appenzeller
- Department of Orthopedics, Rheumatology and Traumatology, School of Medical Science, University of Campinas (UNICAMP), Campinas CEP 13083-887, SP, Brazil
| | - Raphaël Helaers
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Miikka Vikkula
- Human Molecular Genetics, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Vera Lúcia Gil-da-Silva-Lopes
- Department of Translational Medicine, Area of Medical Genetics and Genomic Medicine, University of Campinas (UNICAMP), Campinas CEP 13083-887, SP, Brazil
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12
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Li X, Ye X, Su J. The dental phenotype of primary dentition in SATB2-associated syndrome: a report of three cases and literature review. BMC Oral Health 2022; 22:522. [PMID: 36457071 PMCID: PMC9717407 DOI: 10.1186/s12903-022-02594-4] [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: 05/30/2022] [Accepted: 11/13/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND SATB2-associated syndrome (SAS; OMIM: 612,313) is an autosomal dominant inherited multisystemic disorder caused by several variants of the SATB2 gene. SAS is characterized by intellectual disability, developmental delay, severe speech anomalies, craniofacial anomalies, and dental abnormalities. Here, we report the dental phenotype of primary dentition of three Chinese children with SAS. CASE PRESENTATION All three cases with SAS showed intellectual disability, speech and language anomalies, and palate anomalies. For the dental phenotype, all three cases showed macrodontia, crowded dentition, extensive caries, periapical abscesses and fistulas. Radiographs showed the wide-open root apex of deciduous teeth, loss of mandibular second bicuspids, delayed root formation of permanent teeth, rotated teeth, and taurodontism. Sanger sequencing of case 1 showed that there was a heterozygous code shift variation, c1985delT (p.F662Sfs*9) in the SATB2 gene, which has not been reported in literature. Root canal therapy, carious restoration, and teeth extraction were managed promptly, while preventive dental care was given regularly. CONCLUSIONS The dental phenotype of primary dentition in SAS may show macrodontia, crowded dentition, severe caries, wide-open root apex of deciduous teeth, loss of mandibular second bicuspids, delayed root formation of permanent teeth, rotated teeth, and taurodontism. Regular oral hygiene instructions and preventive dental care are both required.
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Affiliation(s)
- Xiaojing Li
- grid.13402.340000 0004 1759 700XDepartment of Stomatology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052 Zhejiang China
| | - Xiaowei Ye
- grid.13402.340000 0004 1759 700XDepartment of Stomatology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052 Zhejiang China
| | - Jimei Su
- grid.13402.340000 0004 1759 700XDepartment of Stomatology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052 Zhejiang China
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13
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Yan F, Simon L, Suzuki A, Iwaya C, Jia P, Iwata J, Zhao Z. Spatiotemporal MicroRNA-Gene Expression Network Related to Orofacial Clefts. J Dent Res 2022; 101:1398-1407. [PMID: 35774010 PMCID: PMC9516630 DOI: 10.1177/00220345221105816] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Craniofacial structures change dynamically in morphology during development through the coordinated regulation of various cellular molecules. However, it remains unclear how these complex mechanisms are regulated in a spatiotemporal manner. Here we applied natural cubic splines to model gene and microRNA (miRNA) expression from embryonic day (E) 10.5 to E14.5 in the proximal and distal regions of the maxillary processes to identify spatiotemporal patterns of gene and miRNA expression, followed by constructing corresponding regulatory networks. Three major groups of differentially expressed genes (DEGs) were identified, including 3,927 temporal, 314 spatial, and 494 spatiotemporal DEGs. Unsupervised clustering further resolved these spatiotemporal DEGs into 8 clusters with distinct expression patterns. Interestingly, we found 2 clusters of differentially expressed miRNAs: 1 had 80 miRNAs monotonically decreasing and the other had 97 increasing across developmental stages. To evaluate the phenotypic relevance of these DEGs during craniofacial development, we integrated data from the CleftGeneDB database and constructed the regulatory networks of genes related to orofacial clefts. Our analysis revealed 2 hub miRNAs, mmu-miR-325-3p and mmu-miR-384-5p, that repressed cleft-related genes Adamts3, Runx2, Fgfr2, Acvr1, and Edn2, while their expression increased over time. On the contrary, 2 hub miRNAs, mmu-miR-218-5p and mmu-miR-338-5p, repressed cleft-related genes Pbx2, Ermp1, Snai1, Tbx2, and Bmi1, while their expression decreased over time. Our experiments indicated that these miRNA mimics significantly inhibited cell proliferation in mouse embryonic palatal mesenchymal (MEPM) cells and O9-1 cells through the regulation of genes associated with cleft palate and validated the role of our regulatory networks in orofacial clefts. To facilitate interactive exploration of these data, we developed a user-friendly web tool to visualize the gene and miRNA expression patterns across developmental stages, as well as the regulatory networks (https://fyan.shinyapps.io/facebase_shiny/). Taken together, our results provide a valuable resource that serves as a reference map for future research in craniofacial development.
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Affiliation(s)
- F. Yan
- Center for Precision Health, School of
Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston,
TX, USA
| | - L.M. Simon
- Therapeutic Innovation Center, Baylor College
of Medicine, Houston, TX, USA
| | - A. Suzuki
- Department of Diagnostic and Biomedical
Sciences, School of Dentistry, The University of Texas Health Science Center at Houston,
Houston, TX, USA
- Center for Craniofacial Research, The
University of Texas Health Science Center at Houston, Houston, TX, USA
| | - C. Iwaya
- Department of Diagnostic and Biomedical
Sciences, School of Dentistry, The University of Texas Health Science Center at Houston,
Houston, TX, USA
- Center for Craniofacial Research, The
University of Texas Health Science Center at Houston, Houston, TX, USA
| | - P. Jia
- Center for Precision Health, School of
Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston,
TX, USA
| | - J. Iwata
- Department of Diagnostic and Biomedical
Sciences, School of Dentistry, The University of Texas Health Science Center at Houston,
Houston, TX, USA
- Center for Craniofacial Research, The
University of Texas Health Science Center at Houston, Houston, TX, USA
- MD Anderson Cancer Center UTHealth Graduate
School of Biomedical Sciences, Houston, TX, USA
| | - Z. Zhao
- Center for Precision Health, School of
Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston,
TX, USA
- MD Anderson Cancer Center UTHealth Graduate
School of Biomedical Sciences, Houston, TX, USA
- Human Genetics Center, School of Public
Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
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14
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Zarate YA, Kannan A, Bosanko KA, Caffrey AR. Growth in individuals with SATB2-associated syndrome. Am J Med Genet A 2022; 188:2952-2957. [PMID: 35838081 DOI: 10.1002/ajmg.a.62896] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/16/2022] [Accepted: 06/24/2022] [Indexed: 01/31/2023]
Abstract
SATB2-associated syndrome (SAS) is an autosomal dominant multisystemic disorder caused by alterations in the SATB2 gene. In addition to a predominant neurodevelopmental phenotype, individuals with SAS often present with feeding difficulties and growth retardation that persist past infancy. In this study, we present growth and measurement data from 211 individuals (53.6% male, 46.4% female) with SAS due to different molecular mechanisms. To delineate growth in this population, we constructed SAS-specific growth charts by sex from birth to 10 years of age. Smoothed SAS percentiles were superimposed with normative percentiles from WHO (birth to <24 months) and CDC (24 months to 10 years) growth charts. Individuals with SAS tend to display slower postnatal growth with 22.2% (32/144), 19.0% (26/137), and 21.6% having at least one weight, height, or weight-for-length /body mass index (BMI) measurement below -2 standard deviations, respectively. The SAS 50th centile BMI was consistently below the normative data 50th centile and negative mean Z-scores were seen across almost all age groups analyzed for both genders. Individuals with chromosomal abnormalities displayed significantly lower weight for age Z-score, height for age Z-scores, occipitofrontal head circumference for age Z-scores, and BMI for age Z-scores compared to either missense or null variants.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Amrit Kannan
- University of Arkansas for Medical Sciences School of Medicine, Little Rock, Arkansas, USA
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Aisling R Caffrey
- Health Outcomes, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
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15
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Bissell S, Oliver C, Moss J, Heald M, Waite J, Crawford H, Kothari V, Rumbellow L, Walters G, Richards C. The behavioural phenotype of SATB2-associated syndrome: a within-group and cross-syndrome analysis. J Neurodev Disord 2022; 14:25. [PMID: 35350986 PMCID: PMC8966214 DOI: 10.1186/s11689-022-09426-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 02/14/2022] [Indexed: 11/10/2022] Open
Abstract
Background SATB2-associated syndrome (SAS) is a multisystem neurodevelopmental disorder characterised by intellectual disability, speech delay, and craniofacial anomalies. Although the clinical presentation of SAS is well-delineated, behaviours associated with SAS are less well-defined. Given the varied social profile reported in SAS of a ‘jovial’ predisposition and autistic behaviours, there may be phenotypic overlap with both Angelman syndrome (AS) and non-syndromal autism. This study aimed to describe behaviours in SAS in relation to chronological age and level of ability and contrast aspects of the behavioural phenotype with AS and non-syndromal autism. Methods Informant report questionnaire measures of behaviour, emotion, and autism characteristics were completed for 81 individuals with SAS (aged 1–36 years; 43 male). Within-group associations were analysed, and categorical data were compared between pre-school (1–5 years), school-age (6–15 years), and adolescent and adult SAS sub-groups (16 years and over). Cross-syndrome subscale and item-level analyses were conducted for 63 individuals with SAS (aged 1–27 years; 31 male), who were matched according to age and level of ability to 63 individuals with AS (aged 2–25 years; 32 male) and 63 individuals with non-syndromal autism (aged 3–26 years; 53 male). Results In SAS, higher rates of overactivity were moderately associated with lower self-help ability, and higher general anxiety scores were reported for males compared with females. Cross-syndrome subscale analyses uncovered several significant differences (p < .01), with comparatively low rates of stereotyped behaviour, overactivity, insistence on sameness and positive affect, and comparatively greater interest and pleasure and compulsive behaviour in individuals with SAS. Item-level analyses revealed a distinct profile of repetitive and autistic behaviours. Limitations Developmental analysis was based on a cross-sectional rather than a longitudinal research design, the contribution of pain and sleep to behaviour was not explored, and molecular genetic testing to determine genotype–phenotype behavioural relationships was not possible. Conclusions This study highlights the importance of behavioural comparisons to well-delineated groups and the utility of fine-grained item-level analyses to elucidate aspects of behaviour that might be syndrome related or shared across neurodevelopmental disorders. Future research is needed to further describe the distinctive repetitive and autistic behavioural phenotype in SAS. Supplementary Information The online version contains supplementary material available at 10.1186/s11689-022-09426-0.
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Affiliation(s)
- Stacey Bissell
- School of Psychology, University of Birmingham, Edgbaston, Birmingham, UK.
| | - Chris Oliver
- School of Psychology, University of Birmingham, Edgbaston, Birmingham, UK
| | - Joanna Moss
- School of Psychology, University of Surrey, Guildford, Surrey, UK
| | - Mary Heald
- Blackpool Teaching Hospitals NHS Foundation Trust, Blackpool, Lancashire, UK
| | - Jane Waite
- School of Health and Life Sciences, Aston University, Birmingham, UK
| | - Hayley Crawford
- Mental Health and Wellbeing Unit, Warwick Medical School, University of Warwick, Coventry, UK
| | - Vishakha Kothari
- School of Psychology, University of Birmingham, Edgbaston, Birmingham, UK
| | - Lauren Rumbellow
- School of Psychology, University of Birmingham, Edgbaston, Birmingham, UK
| | - Grace Walters
- School of Psychology, University of Birmingham, Edgbaston, Birmingham, UK
| | - Caroline Richards
- School of Psychology, University of Birmingham, Edgbaston, Birmingham, UK
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16
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Lo H, Ng W, Fong N, Lui CD, Lam C. Novel finding of lissencephaly and severe osteopenia in a Chinese patient with
SATB2
‐associated syndrome and a brief review of literature. Am J Med Genet A 2022; 188:2168-2172. [DOI: 10.1002/ajmg.a.62732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Hui‐Yin Lo
- Department of Pathology Princess Margaret Hospital Kowloon Hong Kong
| | - Wai‐Fu Ng
- Department of Pathology Hong Kong Children's Hospital Kowloon Hong Kong
| | - Nai‐Chung Fong
- Department of Paediatrics and Adolescent Medicine Princess Margaret Hospital Kowloon Hong Kong
| | - Choi‐Yu Dilys Lui
- Department of Radiology Princess Margaret Hospital Kowloon Hong Kong
| | - Ching‐Wan Lam
- Department of Pathology The University of Hong Kong, Queen Mary Hospital Pok Fu Lam Hong Kong
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17
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Mouillé M, Rio M, Breton S, Piketty ML, Afenjar A, Amiel J, Capri Y, Goldenberg A, Francannet C, Michot C, Mignot C, Perrin L, Quelin C, Van Gils J, Barcia G, Pingault V, Maruani G, Koumakis E, Cormier-Daire V. SATB2-associated syndrome: characterization of skeletal features and of bone fragility in a prospective cohort of 19 patients. Orphanet J Rare Dis 2022; 17:100. [PMID: 35241104 PMCID: PMC8895909 DOI: 10.1186/s13023-022-02229-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/06/2022] [Indexed: 11/10/2022] Open
Abstract
Background Individuals with pathogenic variants in SATB2 display intellectual disability, speech and behavioral disorders, dental abnormalities and often features of Pierre Robin sequence. SATB2 encodes a transcription factor thought to play a role in bone remodeling. The primary aim of our study was to systematically review the skeletal manifestations of SATB2-associated syndrome. For this purpose, we performed a non-interventional, multicenter cohort study, from 2017 to 2018. We included 19 patients, 9 females and 10 males ranging in age from 2 to 19 years-old. The following data were collected prospectively for each patient: clinical data, bone markers and calcium and phosphate metabolism parameters, skeletal X-rays and bone mineral density. Results Digitiform impressions were present in 8/14 patients (57%). Vertebral compression fractures affected 6/17 patients (35%). Skeletal demineralization (16/17, 94%) and cortical thinning of vertebrae (15/17) were the most frequent radiological features at the spine. Long bones were generally demineralized (18/19). The distal phalanges were short, thick and abnormally shaped. C-telopeptide (CTX) and Alkaline phosphatase levels were in the upper normal values and osteocalcin and serum procollagen type 1 amino-terminal propeptide (P1NP) were both increased. Vitamin D insufficiency was frequent (66.7%). Conclusion We conclude that SATB2 pathogenic variants are responsible for skeletal demineralization and osteoporosis. We found increased levels of bone formation markers, supporting the key role of SATB2 in osteoblast differentiation. These results support the need for bone evaluation in children and adult patients with SATB2-associated syndrome (SAS). Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02229-5.
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Affiliation(s)
- M Mouillé
- Clinical Genetics, Necker Enfants Malades Hospital, APHP, 149 rue de Sevres, Paris, 75015, France.,Department of Neonatal Medicine, Cochin-Port Royal Hospital, APHP, Paris, France
| | - M Rio
- Clinical Genetics, Necker Enfants Malades Hospital, APHP, 149 rue de Sevres, Paris, 75015, France
| | - S Breton
- Department of Pediatric Radiology, Necker Enfants Malades Hospital, APHP, Paris, France
| | - M L Piketty
- Functional Exploration Laboratory, Necker Enfants Malades Hospital, APHP, Paris, France
| | - A Afenjar
- Sorbonne University, Reference Center for Intellectual Disabilities, Department of Genetics and Medical Embryology, Armand-Trousseau Hospital, APHP, Paris, France
| | - J Amiel
- Clinical Genetics, Necker Enfants Malades Hospital, APHP, 149 rue de Sevres, Paris, 75015, France
| | - Y Capri
- Clinical Genetics Functional Unit, Robert Debré Hospital, APHP, Paris, France
| | | | - C Francannet
- Clinical Genetics, Clermont-Ferrand CHU, Clermont-Ferrand, France
| | - C Michot
- Clinical Genetics, Necker Enfants Malades Hospital, APHP, 149 rue de Sevres, Paris, 75015, France.,Paris Cité University, Reference Center for Constitutional Bone Diseases, INSERM UMR1163, Imagine Institute, Paris, France
| | - C Mignot
- Sorbonne University, Reference Center for Intellectual Disabilities, Department of Genetics and Medical Embryology, Armand-Trousseau Hospital, APHP, Paris, France.,Clinical Genetics, La Pitié Salpétrière Hospital, APHP, Paris, France
| | - L Perrin
- Clinical Genetics Functional Unit, Robert Debré Hospital, APHP, Paris, France
| | - C Quelin
- Clinical Genetics, Hospital Sud, Rennes, France
| | - J Van Gils
- Clinical Genetics, Hospital Pellegrin, Bordeaux, France
| | - G Barcia
- Molecular Genetics, Necker Enfants Malades Hospital, APHP, Paris, France
| | - V Pingault
- Molecular Genetics, Necker Enfants Malades Hospital, APHP, Paris, France
| | - G Maruani
- Department of Physiology, Hôpital Necker Enfants Malades and Hôpital Européen Georges Pompidou, AP-HP, Paris, France
| | - E Koumakis
- Paris Cité University, Reference Center for Constitutional Bone Diseases, INSERM UMR1163, Imagine Institute, Paris, France.,Reference Center for Skeletal Dysplasia, Cochin Hospital, APHP, Paris, France
| | - V Cormier-Daire
- Clinical Genetics, Necker Enfants Malades Hospital, APHP, 149 rue de Sevres, Paris, 75015, France. .,Paris Cité University, Reference Center for Constitutional Bone Diseases, INSERM UMR1163, Imagine Institute, Paris, France.
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18
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Xin T, Li Q, Bai R, Zhang T, Zhou Y, Zhang Y, Han B, Yang R. A novel mutation of SATB2 inhibits odontogenesis of human dental pulp stem cells through Wnt/β-catenin signaling pathway. Stem Cell Res Ther 2021; 12:595. [PMID: 34863303 PMCID: PMC8642962 DOI: 10.1186/s13287-021-02660-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/23/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND SATB2-associated syndrome (SAS) is a multisystem disorder caused by mutation of human SATB2 gene. Tooth agenesis is one of the most common phenotypes observed in SAS. Our study aimed at identifying novel variant of SATB2 in a patient with SAS, and to investigate the cellular and molecular mechanism of tooth agenesis caused by SATB2 mutation. METHODS We applied whole exome sequencing (WES) to identify the novel mutation of SATB2 in a Chinese patient with SAS. Construction and overexpression of wild-type and the mutant vector was performed, followed by functional analysis including flow cytometry assay, fluorescent immunocytochemistry, western blot, quantitative real-time PCR and Alizarin Red S staining to investigate its impact on hDPSCs and the underlying mechanisms. RESULTS As a result, we identified a novel frameshift mutation of SATB2 (c. 376_378delinsTT) in a patient with SAS exhibiting tooth agenesis. Human DPSCs transfected with mutant SATB2 showed decreased cell proliferation and odontogenic differentiation capacity compared with hDPSCs transfected with wild-type SATB2 plasmid. Mechanistically, mutant SATB2 failed to translocate into nucleus and distributed in the cytoplasm, failing to activate Wnt/β-catenin signaling pathway, whereas the wild-type SATB2 translocated into the nucleus and upregulated the expression of active β-catenin. When we used Wnt inhibitor XAV939 to treat hDPSCs transfected with wild-type SATB2 plasmid, the increased odontogenic differentiation capacity was attenuated. Furthermore, we found that SATB2 mutation resulted in the upregulation of DKK1 and histone demethylase JHDM1D to inhibit Wnt/β-catenin signaling pathway. CONCLUSION We identified a novel frameshift mutation of SATB2 (c.376_378delinsTT, p.Leu126SerfsX6) in a Chinese patient with SATB2-associated syndrome (SAS) exhibiting tooth agenesis. Mechanistically, SATB2 regulated osteo/odontogenesis of human dental pulp stem cells through Wnt/β-catenin signaling pathway by regulating DKK1 and histone demethylase JHDM1D.
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Affiliation(s)
- Tianyi Xin
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, No. 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, People's Republic of China
| | - Qian Li
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, No. 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, People's Republic of China
| | - Rushui Bai
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, No. 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, People's Republic of China
| | - Ting Zhang
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, No. 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, People's Republic of China
| | - Yanheng Zhou
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, No. 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, People's Republic of China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, 100034, People's Republic of China
| | - Bing Han
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, No. 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, People's Republic of China.
| | - Ruili Yang
- Department of Orthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Laboratory for Digital and Material Technology of Stomatology & Beijing Key Laboratory of Digital Stomatology & Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health & NMPA Key Laboratory for Dental Materials, No. 22 Zhongguancun South Avenue, Haidian District, Beijing, 100081, People's Republic of China.
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19
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Aguilera C, Gabau E, Ramirez-Mallafré A, Brun-Gasca C, Dominguez-Carral J, Delgadillo V, Laurie S, Derdak S, Padilla N, de la Cruz X, Capdevila N, Spataro N, Baena N, Guitart M, Ruiz A. New genes involved in Angelman syndrome-like: Expanding the genetic spectrum. PLoS One 2021; 16:e0258766. [PMID: 34653234 PMCID: PMC8519432 DOI: 10.1371/journal.pone.0258766] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Angelman syndrome (AS) is a neurogenetic disorder characterized by severe developmental delay with absence of speech, happy disposition, frequent laughter, hyperactivity, stereotypies, ataxia and seizures with specific EEG abnormalities. There is a 10–15% of patients with an AS phenotype whose genetic cause remains unknown (Angelman-like syndrome, AS-like). Whole-exome sequencing (WES) was performed on a cohort of 14 patients with clinical features of AS and no molecular diagnosis. As a result, we identified 10 de novo and 1 X-linked pathogenic/likely pathogenic variants in 10 neurodevelopmental genes (SYNGAP1, VAMP2, TBL1XR1, ASXL3, SATB2, SMARCE1, SPTAN1, KCNQ3, SLC6A1 and LAS1L) and one deleterious de novo variant in a candidate gene (HSF2). Our results highlight the wide genetic heterogeneity in AS-like patients and expands the differential diagnosis.
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Affiliation(s)
- Cinthia Aguilera
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Elisabeth Gabau
- Paediatric Unit, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Ariadna Ramirez-Mallafré
- Paediatric Unit, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Carme Brun-Gasca
- Paediatric Unit, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
- Department of Clinical Psychology and Health Psychology, Universitat Autònoma de Barcelona, Bellatera, Barcelona, Spain
| | - Jana Dominguez-Carral
- Paediatric Unit, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Veronica Delgadillo
- Paediatric Unit, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Steve Laurie
- CNAG‐CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sophia Derdak
- CNAG‐CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Natàlia Padilla
- Neurosciences Area, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier de la Cruz
- Neurosciences Area, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Núria Capdevila
- Paediatric Unit, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Nino Spataro
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Neus Baena
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Miriam Guitart
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
- * E-mail: (AR); (MG)
| | - Anna Ruiz
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d’Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
- * E-mail: (AR); (MG)
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20
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Zhu YY, Sun GL, Yang ZL. SATB2-associated syndrome caused by a novel SATB2 mutation in a Chinese boy: A case report and literature review. World J Clin Cases 2021; 9:6081-6090. [PMID: 34368330 PMCID: PMC8316932 DOI: 10.12998/wjcc.v9.i21.6081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/04/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Special AT-rich sequence binding protein 2 (SATB2)-associated syndrome (SAS; OMIM 612313) is an autosomal dominant disorder. Alterations in the SATB2 gene have been identified as causative.
CASE SUMMARY We report a case of a 13-year-old Chinese boy with lifelong global developmental delay, speech and language delay, and intellectual disabilities. He had short stature and irregular dentition, but no other abnormal clinical findings. A de novo heterozygous nonsense point mutation was detected by genetic analysis in exon 6 of SATB2, c.687C>A (p.Y229X) (NCBI reference sequence: NM_001172509.2), and neither of his parents had the mutation. This mutation is the first reported and was evaluated as pathogenic according to the guidelines from the American College of Medical Genetics and Genomics. SAS was diagnosed, and special education performed. Our report of a SAS case in China caused by a SATB2 mutation expanded the genotype options for the disease. The heterogeneous manifestations can be induced by complicated pathogenic involvements and functions of SATB2 from reviewed literatures: (1) SATB2 haploinsufficiency; (2) the interference of truncated SATB2 protein to wild-type SATB2; and (3) different numerous genes regulated by SATB2 in brain and skeletal development in different developmental stages.
CONCLUSION Global developmental delays are usually the initial presentations, and the diagnosis was challenging before other presentations occurred. Regular follow-up and genetic analysis can help to diagnose SAS early. Verification for genes affected by SATB2 mutations for heterogeneous manifestations may help to clarify the possible pathogenesis of SAS in the future.
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Affiliation(s)
- Yan-Yan Zhu
- Department of Pediatrics, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| | - Gui-Lian Sun
- Department of Pediatrics, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
| | - Zhi-Liang Yang
- Department of Pediatrics, The First Hospital of China Medical University, Shenyang 110001, Liaoning Province, China
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21
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Blok LS, Goosen YM, van Haaften L, van Hulst K, Fisher SE, Brunner HG, Egger JIM, Kleefstra T. Speech-language profiles in the context of cognitive and adaptive functioning in SATB2-associated syndrome. GENES BRAIN AND BEHAVIOR 2021; 20:e12761. [PMID: 34241948 PMCID: PMC9285502 DOI: 10.1111/gbb.12761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 07/03/2021] [Accepted: 07/07/2021] [Indexed: 11/28/2022]
Abstract
SATB2‐associated syndrome (SAS) is a neurodevelopmental disorder caused by heterozygous pathogenic variants in the SATB2 gene, and is typically characterized by intellectual disability and severely impaired communication skills. The goal of this study was to contribute to the understanding of speech and language impairments in SAS, in the context of general developmental skills and cognitive and adaptive functioning. We performed detailed oral motor, speech and language profiling in combination with neuropsychological assessments in 23 individuals with a molecularly confirmed SAS diagnosis: 11 primarily verbal individuals and 12 primarily nonverbal individuals, independent of their ages. All individuals had severe receptive language delays. For all verbal individuals, we were able to define underlying speech conditions. While childhood apraxia of speech was most prevalent, oral motor problems appeared frequent as well and were more present in the nonverbal group than in the verbal group. For seven individuals, age‐appropriate Wechsler indices could be derived, showing that the level of intellectual functioning of these individuals varied from moderate–mild ID to mild ID‐borderline intellectual functioning. Assessments of adaptive functioning with the Vineland Screener showed relatively high scores on the domain “daily functioning” and relatively low scores on the domain “communication” in most individuals. Altogether, this study provides a detailed delineation of oral motor, speech and language skills and neuropsychological functioning in individuals with SAS, and can provide families and caregivers with information to guide diagnosis, management and treatment approaches.
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Affiliation(s)
- L Snijders Blok
- Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition & Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Y M Goosen
- Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands
| | - L van Haaften
- Donders Institute for Brain, Cognition & Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Rehabilitation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - K van Hulst
- Donders Institute for Brain, Cognition & Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Rehabilitation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - S E Fisher
- Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition & Behaviour, Centre for Neuroscience, Radboud University, Nijmegen, the Netherlands
| | - H G Brunner
- Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition & Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Clinical Genetics, MHeNS School of Neuroscience, and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - J I M Egger
- Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands.,Stevig Specialized and Forensic Care for People with Intellectual Disabilities, Dichterbij, Oostrum, The Netherlands.,Donders Institute for Brain, Cognition & Behaviour, Centre for Cognition, Radboud University, Nijmegen, the Netherlands
| | - T Kleefstra
- Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition & Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands
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22
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Zarate YA, Vernon HJ, Bosanko KA, Ramani PK, Gokden M, Writzl K, Meznaric M, Vipotnik Vesnaver T, Ramakrishnaiah R, Osredkar D. Case Report: SATB2-Associated Syndrome Overlapping With Clinical Mitochondrial Disease Presentation: Report of Two Cases. Front Genet 2021; 12:692087. [PMID: 34234817 PMCID: PMC8257052 DOI: 10.3389/fgene.2021.692087] [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: 04/07/2021] [Accepted: 05/14/2021] [Indexed: 11/13/2022] Open
Abstract
SATB2-associated syndrome (SAS) is an autosomal dominant neurogenetic multisystemic disorder. We describe two individuals with global developmental delay and hypotonia who underwent an extensive evaluation to rule out an underlying mitochondrial disorder before their eventual diagnosis of SAS. Although the strict application of the clinical mitochondrial disease score only led to the designation of "possible" mitochondrial disorder for these two individuals, other documented abnormalities included nonspecific neuroimaging findings on magnetic resonance imaging and magnetic resonance spectroscopy, decreased complex I activity on muscle biopsy for patient 2, and variation in the size and relative proportion of types of muscle fibers in the muscle biopsies that were aligned with mitochondrial diseases. SAS should be in the differential diagnoses of mitochondrial disorders, and broad-spectrum diagnostic tests such as exome sequencing need to be considered early in the evaluation process of undiagnosed neurodevelopmental disorders.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Hilary J Vernon
- Department of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Praveen K Ramani
- Department of Pediatric Neurology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Karin Writzl
- Clinical Institute of Medical Genetics, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Marija Meznaric
- Faculty of Medicine, Institute of Anatomy, University of Ljubljana, Ljubljana, Slovenia
| | | | - Raghu Ramakrishnaiah
- Division of Neuroradiology and Pediatric Radiology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Damjan Osredkar
- Department of Pediatric Neurology, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, Slovenia
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23
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Zarate YA, Örsell JL, Bosanko K, Srikanth S, Cascio L, Pauly R, Boccuto L. Individuals with SATB2-associated syndrome with and without autism have a recognizable metabolic profile and distinctive cellular energy metabolism alterations. Metab Brain Dis 2021; 36:1049-1056. [PMID: 33661512 DOI: 10.1007/s11011-021-00706-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/23/2021] [Indexed: 12/25/2022]
Abstract
SATB2-associated syndrome (SAS) is a multisystemic disorder characterized by developmental delay often with concurrent autistic tendencies. This study aimed to characterize cellular metabolic pathways and energy metabolism from cells derived from individuals with SAS. The cellular production of NADH (nicotinamide adenine dinucleotide, reduced form) as determined by the Phenotype Mammalian MicroArrays was measured in lymphoblastoid cell lines derived from 11 subjects with a molecularly confirmed diagnosis of SAS and compared to a control population of 50 age-matched typically developing individuals. All patients were evaluated clinically by a multidisciplinary team. Eleven individuals (five in a screening cohort and six in the validation cohort, mean age 6.1 years) were recruited to the study. All individuals had developmental delay and the diagnosis of autism was previously established in five of them. Key metabolic findings included reduced NADH production in the presence of phosphorylated carbohydrates (with corresponding increased production in the presence of alternative carbon-based energy sources), increased response to certain hormones (β-estradiol in particular), and significantly reduced levels of NADH in wells containing tryptophan. The individual analysis revealed no particular differences among the SAS subjects based on molecular findings or phenotypic features. In conclusion, individuals with SAS have a common and recognizable metabolic profile. A lower capacity to utilize glucose as an energy substrate could be contributing to the neurodevelopment phenotype of SAS. The identified abnormalities offer previously unexplored insight into the potential pathophysiology of common SAS phenotypic features.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Hospital, 1 Children's Way; Slot 512-22, Little Rock, AR, 72202, USA.
| | - Jenny-Li Örsell
- Division of Psychology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Katherine Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | | | - Rini Pauly
- Greenwood Genetic Center, Greenwood, SC, USA
| | - Luigi Boccuto
- Greenwood Genetic Center, Greenwood, SC, USA
- School of Nursing, College of Behavioral, Social and Health Sciences, Clemson University, Clemson, SC, USA
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24
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Zarate YA, Bosanko KA, Caffrey AR. SATB2-associated syndrome in adolescents and adults. Am J Med Genet A 2021; 185:2391-2398. [PMID: 33969926 DOI: 10.1002/ajmg.a.62258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 12/20/2022]
Abstract
The goal of this study was to investigate the medical, communication, activities of daily living (ADLs), and mental health concerns affecting adolescents and adults with SATB2-associated syndrome (SAS). A comprehensive questionnaire was administered to the caregivers of 49 individuals 12 years or older with SAS (mean age was 19.4 years, range 12-37 years). For all individuals, medical records, including laboratory results, were reviewed. Most individuals required some degree of assistance for ADLs and none of the adults were able to live independently. Health status was qualified as excellent or very good in 61% of individuals. The most common medical problems were dental anomalies, with a significantly higher frequency of hypotonia and gastroesophageal reflux in younger individuals. Medical and surgical interventions were often required. Sixty-nine percent (n = 33) of individuals spoke 10 or fewer words. Autism (41%), anxiety (37%), and attention deficit disorder (37%) were common with one third of individuals receiving medical treatments for these diagnoses. While medical and developmental problems in individuals with SAS were similar to those previously reported, many of these are persistent into adolescence and adulthood. This study provides better guidance for the challenges facing adults with SAS and their families.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Aisling R Caffrey
- Health Outcomes, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
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25
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Abe‐Hatano C, Iida A, Kosugi S, Momozawa Y, Terao C, Ishikawa K, Okubo M, Hachiya Y, Nishida H, Nakamura K, Miyata R, Murakami C, Takahashi K, Hoshino K, Sakamoto H, Ohta S, Kubota M, Takeshita E, Ishiyama A, Nakagawa E, Sasaki M, Kato M, Matsumoto N, Kamatani Y, Kubo M, Takahashi Y, Natsume J, Inoue K, Goto Y. Whole genome sequencing of 45 Japanese patients with intellectual disability. Am J Med Genet A 2021; 185:1468-1480. [PMID: 33624935 PMCID: PMC8247954 DOI: 10.1002/ajmg.a.62138] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/23/2020] [Accepted: 02/06/2021] [Indexed: 02/06/2023]
Abstract
Intellectual disability (ID) is characterized by significant limitations in both intellectual functioning and adaptive behaviors, originating before the age of 18 years. However, the genetic etiologies of ID are still incompletely elucidated due to the wide range of clinical and genetic heterogeneity. Whole genome sequencing (WGS) has been applied as a single-step clinical diagnostic tool for ID because it detects genetic variations with a wide range of resolution from single nucleotide variants (SNVs) to structural variants (SVs). To explore the causative genes for ID, we employed WGS in 45 patients from 44 unrelated Japanese families and performed a stepwise screening approach focusing on the coding variants in the genes. Here, we report 12 pathogenic and likely pathogenic variants: seven heterozygous variants of ADNP, SATB2, ANKRD11, PTEN, TCF4, SPAST, and KCNA2, three hemizygous variants of SMS, SLC6A8, and IQSEC2, and one homozygous variant in AGTPBP1. Of these, four were considered novel. Furthermore, a novel 76 kb deletion containing exons 1 and 2 in DYRK1A was identified. We confirmed the clinical and genetic heterogeneity and high frequency of de novo causative variants (8/12, 66.7%). This is the first report of WGS analysis in Japanese patients with ID. Our results would provide insight into the correlation between novel variants and expanded phenotypes of the disease.
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Affiliation(s)
- Chihiro Abe‐Hatano
- Department of Mental Retardation and Birth Defect ResearchNational Institute of Neuroscience, National Center of Neurology and PsychiatryTokyoJapan
- Department of PediatricsNagoya University Graduate School of MedicineAichiJapan
| | - Aritoshi Iida
- Medical Genome CenterNational Center of Neurology and PsychiatryTokyoJapan
| | - Shunichi Kosugi
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical SciencesKanagawaJapan
| | - Yukihide Momozawa
- Laboratory for Genotyping DevelopmentRIKEN Center for Integrative Medical SciencesKanagawaJapan
| | - Chikashi Terao
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical SciencesKanagawaJapan
- Clinical Research CenterShizuoka General HospitalShizuokaJapan
- The Department of Applied GeneticsThe School of Pharmaceutical Sciences, University of ShizuokaShizuokaJapan
| | - Keiko Ishikawa
- Medical Genome CenterNational Center of Neurology and PsychiatryTokyoJapan
| | - Mariko Okubo
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Yasuo Hachiya
- Department of NeuropediatricsTokyo Metropolitan Neurological HospitalTokyoJapan
| | - Hiroya Nishida
- Department of NeuropediatricsTokyo Metropolitan Neurological HospitalTokyoJapan
| | - Kazuyuki Nakamura
- Department of PediatricsYamagata University Faculty of MedicineYamagataJapan
| | - Rie Miyata
- Department of PediatricsTokyo‐Kita Medical CenterTokyoJapan
| | - Chie Murakami
- Department of PediatricsKitakyusyu Children's Rehabilitation CenterFukuokaJapan
| | - Kan Takahashi
- Department of PediatricsOme Municipal General HospitalTokyoJapan
| | - Kyoko Hoshino
- Department of PediatricsMinami Wakayama Medical CenterWakayamaJapan
| | - Haruko Sakamoto
- Department of NeonatologyJapanese Red Cross Osaka HospitalOsakaJapan
| | - Sayaka Ohta
- Division of NeurologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Masaya Kubota
- Division of NeurologyNational Center for Child Health and DevelopmentTokyoJapan
| | - Eri Takeshita
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Akihiko Ishiyama
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Eiji Nakagawa
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Masayuki Sasaki
- Department of Child NeurologyNational Center Hospital, National Center of Neurology and PsychiatryTokyoJapan
| | - Mitsuhiro Kato
- Department of PediatricsYamagata University Faculty of MedicineYamagataJapan
- Department of PediatricsShowa University School of MedicineTokyoJapan
| | - Naomichi Matsumoto
- Department of Human GeneticsYokohama City University Graduate School of MedicineKanagawaJapan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational GeneticsRIKEN Center for Integrative Medical SciencesKanagawaJapan
- Department of Computational Biology and Medical SciencesGraduate School of Frontier Sciences, The University of TokyoTokyoJapan
| | - Michiaki Kubo
- Laboratory for Genotyping DevelopmentRIKEN Center for Integrative Medical SciencesKanagawaJapan
| | - Yoshiyuki Takahashi
- Department of PediatricsNagoya University Graduate School of MedicineAichiJapan
| | - Jun Natsume
- Department of PediatricsNagoya University Graduate School of MedicineAichiJapan
| | - Ken Inoue
- Department of Mental Retardation and Birth Defect ResearchNational Institute of Neuroscience, National Center of Neurology and PsychiatryTokyoJapan
| | - Yu‐Ichi Goto
- Department of Mental Retardation and Birth Defect ResearchNational Institute of Neuroscience, National Center of Neurology and PsychiatryTokyoJapan
- Medical Genome CenterNational Center of Neurology and PsychiatryTokyoJapan
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26
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Zarate YA, Bosanko KA, Thomas MA, Miller DT, Cusmano-Ozog K, Martinez-Monseny A, Curry CJ, Graham JM, Velsher L, Bekheirnia MR, Seidel V, Dedousis D, Mitchell AL, DiMarino AM, Riess A, Balasubramanian M, Fish JL, Caffrey AR, Fleischer N, Pierson TM, Lacro RV. Growth, development, and phenotypic spectrum of individuals with deletions of 2q33.1 involving SATB2. Clin Genet 2021; 99:547-557. [PMID: 33381861 DOI: 10.1111/cge.13912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/18/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023]
Abstract
SATB2-Associated syndrome (SAS) is an autosomal dominant, multisystemic, neurodevelopmental disorder due to alterations in SATB2 at 2q33.1. A limited number of individuals with 2q33.1 contiguous deletions encompassing SATB2 (ΔSAS) have been described in the literature. We describe 17 additional individuals with ΔSAS, review the phenotype of 33 previously published individuals with 2q33.1 deletions (n = 50, mean age = 8.5 ± 7.8 years), and provide a comprehensive comparison to individuals with other molecular mechanisms that result in SAS (non-ΔSAS). Individuals in the ΔSAS group were often underweight for age (20/41 = 49%) with a progressive decline in weight (95% CI = -2.3 to -1.1, p < 0.0001) and height (95% CI = -2.3 to -1.0, p < 0.0001) Z-score means from birth to last available measurement. ΔSAS individuals were often noted to have a broad spectrum of facial dysmorphism. A composite image of ΔSAS individuals generated by automated image analysis was distinct as compared to matched controls and non-ΔSAS individuals. We also present additional genotype-phenotype correlations for individuals in the ΔSAS group such as an increased risk for aortic root/ascending aorta dilation and primary pulmonary hypertension for those individuals with contiguous gene deletions that include COL3A1/COL5A2 and BMPR2, respectively. Based on these findings, we provide additional care recommendations for individuals with ΔSAS variants.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Mary Ann Thomas
- Departments of Medical Genetics and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Kristina Cusmano-Ozog
- Department of Pathology, Stanford University Medical Center, Stanford, California, USA
| | - Antonio Martinez-Monseny
- Department of Clinical Genetics and Rare Disease Paediatric Unit, Hospital Sant Joan de Déu, University of Barcelona, Barcelona, Spain
| | - Cynthia J Curry
- Genetic Medicine, Department of Pediatrics, University of California, San Francisco/Fresno, Fresno, California, USA
| | - John M Graham
- Medical Genetics, Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lea Velsher
- Genetics Division, North York General, Toronto, Ontario, Canada
| | - Mir Reza Bekheirnia
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Veronica Seidel
- Clinical Genetics, Department of Pediatrics, HGU Gregorio Marañón, Madrid, Spain
| | - Demitrios Dedousis
- Department of Genetics and Genome Sciences, University Hospitals Center for Human Genetics, Cleveland, Ohio, USA
| | - Anna L Mitchell
- Department of Genetics and Genome Sciences, University Hospitals Center for Human Genetics, Cleveland, Ohio, USA
| | - Amy M DiMarino
- Division of Pediatric Pulmonology, UH Rainbow Babies and Children's Hospital, Cleveland, Ohio, USA
| | - Angelika Riess
- Institute of Medical Genetics and Applied Genomics, Medical faculty, University of Tuebingen, Tuebingen, Germany
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, United States
| | - Aisling R Caffrey
- Health Outcomes, College of Pharmacy, University of Rhode Island, Kingston, Rhode Island, USA
| | | | - Tyler Mark Pierson
- Departments of Pediatrics and Neurology, The Board of Governors Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, California, USA
| | - Ronald V Lacro
- Department of Cardiology, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
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27
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Feurle P, Abentung A, Cera I, Wahl N, Ablinger C, Bucher M, Stefan E, Sprenger S, Teis D, Fischer A, Laighneach A, Whitton L, Morris DW, Apostolova G, Dechant G. SATB2-LEMD2 interaction links nuclear shape plasticity to regulation of cognition-related genes. EMBO J 2021; 40:e103701. [PMID: 33319920 PMCID: PMC7849313 DOI: 10.15252/embj.2019103701] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/22/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023] Open
Abstract
SATB2 is a schizophrenia risk gene and is genetically associated with human intelligence. How it affects cognition at molecular level is currently unknown. Here, we show that interactions between SATB2, a chromosomal scaffolding protein, and the inner nuclear membrane protein LEMD2 orchestrate the response of pyramidal neurons to neuronal activation. Exposure to novel environment in vivo causes changes in nuclear shape of CA1 hippocampal neurons via a SATB2-dependent mechanism. The activity-driven plasticity of the nuclear envelope requires not only SATB2, but also its protein interactor LEMD2 and the ESCRT-III/VPS4 membrane-remodeling complex. Furthermore, LEMD2 depletion in cortical neurons, similar to SATB2 ablation, affects neuronal activity-dependent regulation of multiple rapid and delayed primary response genes. In human genetic data, LEMD2-regulated genes are enriched for de novo mutations reported in intellectual disability and schizophrenia and are, like SATB2-regulated genes, enriched for common variants associated with schizophrenia and cognitive function. Hence, interactions between SATB2 and the inner nuclear membrane protein LEMD2 influence gene expression programs in pyramidal neurons that are linked to cognitive ability and psychiatric disorder etiology.
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Affiliation(s)
- Patrick Feurle
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Andreas Abentung
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Isabella Cera
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Nico Wahl
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Cornelia Ablinger
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Michael Bucher
- Institute of Biochemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Simon Sprenger
- Institute for Cell BiologyMedical University of InnsbruckInnsbruckAustria
| | - David Teis
- Institute for Cell BiologyMedical University of InnsbruckInnsbruckAustria
| | - Andre Fischer
- Department of Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GoettingenGermany
- Department of Psychiatry and PsychotherapyUniversity Medical CenterGoettingenGermany
| | - Aodán Laighneach
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Laura Whitton
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Derek W Morris
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Galina Apostolova
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Georg Dechant
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
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28
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Sobering AK, Li D, Beighley JS, Carey JC, Donald T, Elsea SH, Figueroa KP, Gerdts J, Hamlet A, Mirzaa GM, Nelson B, Pulst SM, Smith JL, Tassone F, Toriello HV, Walker RH, Yearwood KR, Bhoj EJ. Experiences with offering pro bono medical genetics services in the West Indies: Benefits to patients, physicians, and the community. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:1030-1041. [PMID: 33274544 DOI: 10.1002/ajmg.c.31871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/21/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022]
Abstract
We describe our experiences with organizing pro bono medical genetics and neurology outreach programs on several different resource-limited islands in the West Indies. Due to geographic isolation, small population sizes, and socioeconomic disparities, most Caribbean islands lack medical services for managing, diagnosing, and counseling individuals with genetic disorders. From 2015 to 2019, we organized 2-3 clinics per year on various islands in the Caribbean. We also organized a week-long clinic to provide evaluations for children suspected of having autism spectrum disorder. Consultations for over 100 different individuals with suspected genetic disorders were performed in clinics or during home visits following referral by locally registered physicians. When possible, follow-up visits were attempted. When available and appropriate, clinical samples were shipped to collaborating laboratories for molecular analysis. Laboratory tests included karyotyping, cytogenomic microarray analysis, exome sequencing, triplet repeat expansion testing, blood amino acid level determination, biochemical assaying, and metabolomic profiling. We believe that significant contributions to healthcare by genetics professionals can be made even if availability is limited. Visiting geneticists may help by providing continuing medical education seminars. Clinical teaching rounds help to inform local physicians regarding the management of genetic disorders with the aim of generating awareness of genetic conditions. Even when only periodically available, a visiting geneticist may benefit affected individuals, their families, their local physicians, and the community at large.
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Affiliation(s)
- Andrew K Sobering
- Department of Biochemistry, St. George's University School of Medicine, St. George's, Grenada.,Windward Islands Research and Education Foundation, True Blue, St. George's, Grenada
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jennifer S Beighley
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - John C Carey
- Department of Pediatrics, University of Utah Health, Salt Lake City, Utah, USA
| | - Tyhiesia Donald
- Grenada General Hospital, Pediatrics Ward, St. George's, Grenada.,Clinical Teaching Unit, St. George's University School of Medicine, St. George's, Grenada
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Karla P Figueroa
- Department of Neurology, University of Utah, Salt Lake City, Utah, USA
| | - Jennifer Gerdts
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Andre Hamlet
- Grenada General Hospital, Pediatrics Ward, St. George's, Grenada.,Clinical Teaching Unit, St. George's University School of Medicine, St. George's, Grenada
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Beverly Nelson
- Clinical Teaching Unit, St. George's University School of Medicine, St. George's, Grenada
| | - Stefan M Pulst
- Department of Neurology, University of Utah, Salt Lake City, Utah, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Flora Tassone
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, California, USA.,MIND Institute, University of California Davis Medical Center, Sacramento, California, USA
| | - Helga V Toriello
- Department of Pediatrics/Human Development College of Human Medicine, Michigan State University, Grand Rapids, Michigan, USA
| | - Ruth H Walker
- Department of Neurology, James J. Peters Veterans Affairs Medical Center, Bronx, New York, USA.,Department of Neurology, Mount Sinai School of Medicine, New York City, New York, USA
| | | | - Elizabeth J Bhoj
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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29
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Lewis H, Samanta D, Örsell JL, Bosanko KA, Rowell A, Jones M, Dale RC, Taravath S, Hahn CD, Krishnakumar D, Chagnon S, Keller S, Hagebeuk E, Pathak S, Bebin EM, Arndt DH, Alexander JJ, Mainali G, Coppola G, Maclean J, Sparagana S, McNamara N, Smith DM, Raggio V, Cruz M, Fernández-Jaén A, Kava MP, Emrick L, Fish JL, Vanderver A, Helman G, Pierson TM, Zarate YA. Epilepsy and Electroencephalographic Abnormalities in SATB2-Associated Syndrome. Pediatr Neurol 2020; 112:94-100. [PMID: 32446642 DOI: 10.1016/j.pediatrneurol.2020.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 11/20/2022]
Abstract
BACKGROUND Seizures are an under-reported feature of the SATB2-associated syndrome phenotype. We describe the electroencephalographic findings and seizure semiology and treatment in a population of individuals with SATB2-associated syndrome. METHODS We performed a retrospective review of 101 individuals with SATB2-associated syndrome who were reported to have had a previous electroencephalographic study to identify those who had at least one reported abnormal result. For completeness, a supplemental survey was distributed to the caregivers and input from the treating neurologist was obtained whenever possible. RESULTS Forty-one subjects were identified as having at least one prior abnormal electroencephalography. Thirty-eight individuals (93%) had epileptiform discharges, 28 (74%) with central localization. Sleep stages were included as part of the electroencephalographies performed in 31 individuals (76%), and epileptiform activity was recorded during sleep in all instances (100%). Definite clinical seizures were diagnosed in 17 individuals (42%) with a mean age of onset of 3.2 years (four months to six years), and focal seizures were the most common type of seizure observed (42%). Six subjects with definite clinical seizures needed polytherapy (35%). Delayed myelination and/or abnormal white matter hyperintensities were seen on neuroimaging in 19 individuals (61%). CONCLUSIONS Epileptiform abnormalities are commonly seen in individuals with SATB2-associated syndrome. A baseline electroencephalography that preferably includes sleep stages is recommended during the initial evaluation of all individuals with SATB2-associated syndrome, regardless of clinical suspicion of epilepsy.
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Affiliation(s)
- Hannah Lewis
- University of Arkansas for Medical Sciences School of Medicine, Little Rock, Arkansas
| | - Debopam Samanta
- Section of Child Neurology, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jenny-Li Örsell
- Division of Psychology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Katherine A Bosanko
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Amy Rowell
- Department of Radiology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Russell C Dale
- Kids Neuroscience Centre, Children's Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Australia
| | - Sasidharan Taravath
- Department of Pediatric Neurology, Coastal Childrens service, Wilmington, North Carolina
| | - Cecil D Hahn
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | - Deepa Krishnakumar
- Department of Paediatric Neurology, Addenbrooke's Hospital, Cambridge, UK
| | - Sarah Chagnon
- Division of Child and Adolescent Neurology, Children's Hospital of the Kings Daughters, Norfolk, Virginia
| | - Stephanie Keller
- Division of Pediatric Neurology, Department of Pediatrics, Emory University, Atlanta, Georgia
| | - Eveline Hagebeuk
- Stichting Epilepsie Instellingen Nederland (SEIN) Zwolle, the Netherlands
| | - Sheel Pathak
- Division of Pediatric and Developmental Neurology, Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
| | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Daniel H Arndt
- Division of Pediatric Neurology, Department of Pediatrics, Beaumont Children's, Oakland University William Beaumont School of Medicine, Royal Oak, Michigan
| | - John J Alexander
- Division of Neurology, Seattle Children's Hospital, Seattle, Washington
| | - Gayatra Mainali
- Division of Pediatric Neurology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Giangennaro Coppola
- Department of Medicine, Surgery and Dentistry, Child and Adolescent Neuropsychiatry, University of Salerno, Italy
| | - Jane Maclean
- Pediatric Neurology, Palo Alto medical foundation, San Jose, California
| | - Steven Sparagana
- Department of Neurology, Texas Scottish Rite Hospital for Children and University of Texas Southwestern Medical Center, Dallas, Texas
| | - Nancy McNamara
- Division of Child Neurology, Department of Pediatrics, Mott Children's Hospital, University of Michigan, Ann Arbor, Michigan
| | | | - Víctor Raggio
- Departamento de Genética, Facultad de Medicina, Udelar, Uruguay
| | - Marcos Cruz
- HighPoint Neurology Associates, Hendersonville, Tennessee
| | - Alberto Fernández-Jaén
- Department of Pediatric Neurology, Hospital Universitario Quirónsalud and Universidad Europea de Madrid, Madrid, Spain
| | - Maina P Kava
- Department of Neurology, Perth Children's Hospital, Western Australia, Australia; School of Paediatrics and Child Health, University of Western Australia, Australia
| | - Lisa Emrick
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, and Department of Molecular and Human Genetics, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Guy Helman
- Murdoch Children's Research Institute, The Royal Children's Hospital, Victoria, Australia; Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Tyler M Pierson
- Departments of Pediatrics and Neurology & The Board of Governors Regenerative Medicine Institute, Cedars Sinai Medical Center, Los Angeles, California
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas.
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30
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Pantel JT, Hajjir N, Danyel M, Elsner J, Abad-Perez AT, Hansen P, Mundlos S, Spielmann M, Horn D, Ott CE, Mensah MA. Efficiency of Computer-Aided Facial Phenotyping (DeepGestalt) in Individuals With and Without a Genetic Syndrome: Diagnostic Accuracy Study. J Med Internet Res 2020; 22:e19263. [PMID: 33090109 PMCID: PMC7644377 DOI: 10.2196/19263] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/26/2020] [Accepted: 07/26/2020] [Indexed: 12/11/2022] Open
Abstract
Background Collectively, an estimated 5% of the population have a genetic disease. Many of them feature characteristics that can be detected by facial phenotyping. Face2Gene CLINIC is an online app for facial phenotyping of patients with genetic syndromes. DeepGestalt, the neural network driving Face2Gene, automatically prioritizes syndrome suggestions based on ordinary patient photographs, potentially improving the diagnostic process. Hitherto, studies on DeepGestalt’s quality highlighted its sensitivity in syndromic patients. However, determining the accuracy of a diagnostic methodology also requires testing of negative controls. Objective The aim of this study was to evaluate DeepGestalt's accuracy with photos of individuals with and without a genetic syndrome. Moreover, we aimed to propose a machine learning–based framework for the automated differentiation of DeepGestalt’s output on such images. Methods Frontal facial images of individuals with a diagnosis of a genetic syndrome (established clinically or molecularly) from a convenience sample were reanalyzed. Each photo was matched by age, sex, and ethnicity to a picture featuring an individual without a genetic syndrome. Absence of a facial gestalt suggestive of a genetic syndrome was determined by physicians working in medical genetics. Photos were selected from online reports or were taken by us for the purpose of this study. Facial phenotype was analyzed by DeepGestalt version 19.1.7, accessed via Face2Gene CLINIC. Furthermore, we designed linear support vector machines (SVMs) using Python 3.7 to automatically differentiate between the 2 classes of photographs based on DeepGestalt's result lists. Results We included photos of 323 patients diagnosed with 17 different genetic syndromes and matched those with an equal number of facial images without a genetic syndrome, analyzing a total of 646 pictures. We confirm DeepGestalt’s high sensitivity (top 10 sensitivity: 295/323, 91%). DeepGestalt’s syndrome suggestions in individuals without a craniofacially dysmorphic syndrome followed a nonrandom distribution. A total of 17 syndromes appeared in the top 30 suggestions of more than 50% of nondysmorphic images. DeepGestalt’s top scores differed between the syndromic and control images (area under the receiver operating characteristic [AUROC] curve 0.72, 95% CI 0.68-0.76; P<.001). A linear SVM running on DeepGestalt’s result vectors showed stronger differences (AUROC 0.89, 95% CI 0.87-0.92; P<.001). Conclusions DeepGestalt fairly separates images of individuals with and without a genetic syndrome. This separation can be significantly improved by SVMs running on top of DeepGestalt, thus supporting the diagnostic process of patients with a genetic syndrome. Our findings facilitate the critical interpretation of DeepGestalt’s results and may help enhance it and similar computer-aided facial phenotyping tools.
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Affiliation(s)
- Jean Tori Pantel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Nurulhuda Hajjir
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Klinik für Pädiatrie mit Schwerpunkt Gastroenterologie, Nephrologie und Stoffwechselmedizin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Magdalena Danyel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Berlin Center for Rare Diseases, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Jonas Elsner
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Angela Teresa Abad-Perez
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Peter Hansen
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Malte Spielmann
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Denise Horn
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Claus-Eric Ott
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Martin Atta Mensah
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
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31
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Cotton AP, Gokarakonda S, Caffrey AR, Zarate YA, Kumar N. Behavioral phenotype and sleep problems in SATB2-associated syndrome. Dev Med Child Neurol 2020; 62:827-832. [PMID: 31420882 DOI: 10.1111/dmcn.14330] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/01/2019] [Indexed: 01/01/2023]
Abstract
AIM To determine the nature and frequency of behavioral phenotypes and sleep disturbances in individuals with SATB2-associated syndrome (SAS). METHOD The Strengths and Difficulties Questionnaire (SDQ) and an age-appropriate sleep questionnaire were distributed to the parents of individuals with SAS. All scores were compared to available normative data. RESULTS Thirty-one individuals completed the assessment (18 females, 13 males; mean age 7y 4mo [SD 4y 1mo], range 2-16y). Individuals with SAS had significantly higher Total Difficulty scores than the normative sample (14.9 [SD 5.8] vs 7.1 [SD 5.7], p<0.001). A high frequency of emotional problems (22.6% vs 8%, p=0.01), peer problems (48.4% vs 10%, p<0.001), hyperactivity (48.4% vs 9%, p<0.001), and low prosocial behaviors (45.2% vs 9%, p<0.001) contribute to the behavioral profile in SAS. Concurrent sleeping difficulties were also frequently identified. Ten individuals in the 5 to 15 years age range had at least one sleep disorder (mean Sleep Disturbance Scale for Children total score 40.9 [SD 8.4] vs 35.1 [SD 7.7], p<0.001). INTERPRETATION With previous limited available objective neurobehavioral data on the SAS population, we reported evidence of high-risk for a broad spectrum of burdensome behavioral phenotype and concurrent sleeping difficulties, the latter being particularly prevalent during early childhood. Routine assessment and treatment for behavioral issues and sleep problems is recommended. WHAT THIS PAPER ADDS Emotional and peer problems, hyperactivity, and low prosocial behavior are common in SATB2-associated syndrome. The Strength and Difficulties Questionnaire Total Difficulty scores are atypical in nearly half of individuals. Behavioral difficulties are perceived as burdensome to over half of the parents. Nearly half of individuals have at least one sleep disorder. Sleep-wake transition disorders were most common.
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Affiliation(s)
- Allison Pierce Cotton
- Department of Child and Adolescent Psychiatry, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Srinivasa Gokarakonda
- Department of Child and Adolescent Psychiatry, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Aisling R Caffrey
- Health Outcomes, College of Pharmacy, University of Rhode Island, Kingston, RI, USA
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Nihit Kumar
- Department of Child and Adolescent Psychiatry, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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SATB2-associated syndrome: first report of a gonadal and somatic mosaicism for an intragenic copy number variation. Clin Dysmorphol 2020; 28:205-210. [PMID: 31425298 DOI: 10.1097/mcd.0000000000000293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gonadal mosaicism has been reported in a variety of dominant or X-linked conditions and should be considered in all cases of apparent de-novo variation. Recently, some cases of supposed parental germline mosaicism have been shown to result from low-level somatic mosaicism. In most of the cases, mosaicism has been reported for pathogenic single nucleotide variants with only a few cases of copy number variation mosaicism described so far. Herein, we present the first case of parental somatic and gonadal copy number variation mosaicism in the SATB2 gene. We report three brothers presenting with the SATB2-associated syndrome. They all carry the same 121-kb heterozygous intragenic deletion of SATB2. Parental somatic mosaicism was detected by array-comparative genomic hybridization on a maternal blood sample and confirmed by Fluorescence in situ hybridization analysis on blood and buccal cells. This clinical report highlights the importance of investigating for parental somatic mosaicism to estimate the proper recurrence risk for subsequent pregnancy.
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Helman G, Lajoie BR, Crawford J, Takanohashi A, Walkiewicz M, Dolzhenko E, Gross AM, Gainullin VG, Bent SJ, Jenkinson EM, Ferdinandusse S, Waterham HR, Dorboz I, Bertini E, Miyake N, Wolf NI, Abbink TEM, Kirwin SM, Tan CM, Hobson GM, Guo L, Ikegawa S, Pizzino A, Schmidt JL, Bernard G, Schiffmann R, van der Knaap MS, Simons C, Taft RJ, Vanderver A. Genome sequencing in persistently unsolved white matter disorders. Ann Clin Transl Neurol 2020; 7:144-152. [PMID: 31912665 PMCID: PMC6952322 DOI: 10.1002/acn3.50957] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 01/01/2023] Open
Abstract
Genetic white matter disorders have heterogeneous etiologies and overlapping clinical presentations. We performed a study of the diagnostic efficacy of genome sequencing in 41 unsolved cases with prior exome sequencing, resolving an additional 14 from an historical cohort (n = 191). Reanalysis in the context of novel disease-associated genes and improved variant curation and annotation resolved 64% of cases. The remaining diagnoses were directly attributable to genome sequencing, including cases with small and large copy number variants (CNVs) and variants in deep intronic and technically difficult regions. Genome sequencing, in combination with other methodologies, achieved a diagnostic yield of 85% in this retrospective cohort.
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Affiliation(s)
- Guy Helman
- Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | | | - Joanna Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Asako Takanohashi
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Marzena Walkiewicz
- Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, Australia
| | | | | | | | - Stephen J Bent
- Data61, Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia
| | - Emma M Jenkinson
- Faculty of Biology, Medicine and Health, School of Biological Sciences, Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Imen Dorboz
- INSERM UMR 1141, DHU PROTECT, Université Paris Diderot- Sorbonne, Paris Cité, France
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesu' Children's Hospital, Rome, Italy.,Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, 00146, Rome, Italy
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Nicole I Wolf
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Truus E M Abbink
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Susan M Kirwin
- Molecular Diagnostics Laboratory, Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Christina M Tan
- Molecular Diagnostics Laboratory, Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Grace M Hobson
- Molecular Diagnostics Laboratory, Nemours Biomedical Research, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Long Guo
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Amy Pizzino
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Johanna L Schmidt
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Genevieve Bernard
- Departments of Neurology and Neurosurgery, Pediatrics, and Human Genetics, McGill University, Montreal, Canada.,Division of Medical Genetics, Montreal Children's Hospital, McGill University Health Center, Montreal, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, Texas
| | - Marjo S van der Knaap
- Department of Child Neurology, Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience, Amsterdam, The Netherlands.,Department of Functional Genomics, Amsterdam Neuroscience, VU University, Amsterdam, the Netherlands
| | - Cas Simons
- Murdoch Children's Research Institute, The Royal Children's Hospital Melbourne, Parkville, Melbourne, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | | | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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Brasil S, Pascoal C, Francisco R, dos Reis Ferreira V, A. Videira P, Valadão G. Artificial Intelligence (AI) in Rare Diseases: Is the Future Brighter? Genes (Basel) 2019; 10:genes10120978. [PMID: 31783696 PMCID: PMC6947640 DOI: 10.3390/genes10120978] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/06/2023] Open
Abstract
The amount of data collected and managed in (bio)medicine is ever-increasing. Thus, there is a need to rapidly and efficiently collect, analyze, and characterize all this information. Artificial intelligence (AI), with an emphasis on deep learning, holds great promise in this area and is already being successfully applied to basic research, diagnosis, drug discovery, and clinical trials. Rare diseases (RDs), which are severely underrepresented in basic and clinical research, can particularly benefit from AI technologies. Of the more than 7000 RDs described worldwide, only 5% have a treatment. The ability of AI technologies to integrate and analyze data from different sources (e.g., multi-omics, patient registries, and so on) can be used to overcome RDs’ challenges (e.g., low diagnostic rates, reduced number of patients, geographical dispersion, and so on). Ultimately, RDs’ AI-mediated knowledge could significantly boost therapy development. Presently, there are AI approaches being used in RDs and this review aims to collect and summarize these advances. A section dedicated to congenital disorders of glycosylation (CDG), a particular group of orphan RDs that can serve as a potential study model for other common diseases and RDs, has also been included.
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Affiliation(s)
- Sandra Brasil
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Carlota Pascoal
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Rita Francisco
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Vanessa dos Reis Ferreira
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- Correspondence:
| | - Paula A. Videira
- Portuguese Association for CDG, 2820-381 Lisboa, Portugal; (S.B.); (C.P.); (R.F.); (P.A.V.)
- CDG & Allies—Professionals and Patient Associations International Network (CDG & Allies—PPAIN), Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
- UCIBIO, Departamento Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Lisboa, Portugal
| | - Gonçalo Valadão
- Instituto de Telecomunicações, 1049-001 Lisboa, Portugal;
- Departamento de Ciências e Tecnologias, Autónoma Techlab–Universidade Autónoma de Lisboa, 1169-023 Lisboa, Portugal
- Electronics, Telecommunications and Computers Engineering Department, Instituto Superior de Engenharia de Lisboa, 1959-007 Lisboa, Portugal
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35
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Dowrey T, Schwager EE, Duong J, Merkuri F, Zarate YA, Fish JL. Satb2 regulates proliferation and nuclear integrity of pre-osteoblasts. Bone 2019; 127:488-498. [PMID: 31325654 PMCID: PMC6708767 DOI: 10.1016/j.bone.2019.07.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/08/2019] [Accepted: 07/14/2019] [Indexed: 12/25/2022]
Abstract
Special AT-rich sequence binding protein 2 (Satb2) is a matrix attachment region (MAR) binding protein. Satb2 impacts skeletal development by regulating gene transcription required for osteogenic differentiation. Although its role as a high-order transcription factor is well supported, other roles for Satb2 in skeletal development remain unclear. In particular, the impact of dosage sensitivity (heterozygous mutations) and variance on phenotypic severity is still not well understood. To further investigate molecular and cellular mechanisms of Satb2-mediated skeletal defects, we used the CRISPR/Cas9 system to generate Satb2 mutations in MC3T3-E1 cells. Our data suggest that, in addition to its role in differentiation, Satb2 regulates progenitor proliferation. We also find that mutations in Satb2 cause chromatin defects including nuclear blebbing and donut-shaped nuclei. These defects may contribute to a slight increase in apoptosis in mutant cells, but apoptosis is insufficient to explain the proliferation defects. Satb2 expression exhibits population-level variation and is most highly expressed from late G1 to late G2. Based on these data, we hypothesize that Satb2 may regulate proliferation through two separate mechanisms. First, Satb2 may regulate the expression of genes necessary for cell cycle progression in pre-osteoblasts. Second, similar to other MAR-binding proteins, Satb2 may participate in DNA replication. We also hypothesize that variation in the severity or penetrance of Satb2-mediated proliferation defects is due to stochastic variation in Satb2 binding to DNA, which may be buffered in some genetic backgrounds. Further elucidation of the role of Satb2 in proliferation has potential impacts on our understanding of both skeletal defects and cancer.
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Affiliation(s)
- Todd Dowrey
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States of America
| | - Evelyn E Schwager
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States of America
| | - Julieann Duong
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States of America
| | - Fjodor Merkuri
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States of America
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, United States of America
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, United States of America.
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36
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Using facial analysis technology in a typical genetic clinic: experience from 30 individuals from a single institution. J Hum Genet 2019; 64:1243-1245. [PMID: 31551534 DOI: 10.1038/s10038-019-0673-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/15/2019] [Accepted: 09/08/2019] [Indexed: 12/13/2022]
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37
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Thomason A, Pankey E, Nutt B, Caffrey AR, Zarate YA. Speech, language, and feeding phenotypes of
SATB2
‐associated syndrome. Clin Genet 2019; 96:485-492. [DOI: 10.1111/cge.13619] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/24/2019] [Accepted: 08/01/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Ashlen Thomason
- Audiology/Speech Pathology DepartmentArkansas Children's Hospital Little Rock Arkansas
| | - Emily Pankey
- Audiology/Speech Pathology DepartmentArkansas Children's Hospital Little Rock Arkansas
| | - Beth Nutt
- Audiology/Speech Pathology DepartmentArkansas Children's Hospital Little Rock Arkansas
| | - Aisling R. Caffrey
- Health Outcomes Department, College of PharmacyUniversity of Rhode Island Kingston Rhode Island
| | - Yuri A. Zarate
- Section of Genetics and MetabolismUniversity of Arkansas for Medical Sciences Little Rock Arkansas
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38
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Nellåker C, Alkuraya FS, Baynam G, Bernier RA, Bernier FP, Boulanger V, Brudno M, Brunner HG, Clayton-Smith J, Cogné B, Dawkins HJ, deVries BB, Douzgou S, Dudding-Byth T, Eichler EE, Ferlaino M, Fieggen K, Firth HV, FitzPatrick DR, Gration D, Groza T, Haendel M, Hallowell N, Hamosh A, Hehir-Kwa J, Hitz MP, Hughes M, Kini U, Kleefstra T, Kooy RF, Krawitz P, Küry S, Lees M, Lyon GJ, Lyonnet S, Marcadier JL, Meyn S, Moslerová V, Politei JM, Poulton CC, Raymond FL, Reijnders MR, Robinson PN, Romano C, Rose CM, Sainsbury DC, Schofield L, Sutton VR, Turnovec M, Van Dijck A, Van Esch H, Wilkie AO. Enabling Global Clinical Collaborations on Identifiable Patient Data: The Minerva Initiative. Front Genet 2019; 10:611. [PMID: 31417602 PMCID: PMC6681681 DOI: 10.3389/fgene.2019.00611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/12/2019] [Indexed: 01/25/2023] Open
Abstract
The clinical utility of computational phenotyping for both genetic and rare diseases is increasingly appreciated; however, its true potential is yet to be fully realized. Alongside the growing clinical and research availability of sequencing technologies, precise deep and scalable phenotyping is required to serve unmet need in genetic and rare diseases. To improve the lives of individuals affected with rare diseases through deep phenotyping, global big data interrogation is necessary to aid our understanding of disease biology, assist diagnosis, and develop targeted treatment strategies. This includes the application of cutting-edge machine learning methods to image data. As with most digital tools employed in health care, there are ethical and data governance challenges associated with using identifiable personal image data. There are also risks with failing to deliver on the patient benefits of these new technologies, the biggest of which is posed by data siloing. The Minerva Initiative has been designed to enable the public good of deep phenotyping while mitigating these ethical risks. Its open structure, enabling collaboration and data sharing between individuals, clinicians, researchers and private enterprise, is key for delivering precision public health.
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Affiliation(s)
- Christoffer Nellåker
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Institute for Biomedical Engineering, University of Oxford, Oxford, United Kingdom
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Gareth Baynam
- Western Australian Register of Developmental Anomalies, and Genetic Services of Western Australia, King Edward Memorial, Subiaco, WA, Australia
- Telethon Kids Institute and School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
- Spatial Sciences, Science and Engineering, Curtin University, Perth, WA, Australia
| | - Raphael A. Bernier
- Department of Psychiatry & Behavioral Science, University of Washington School of Medicine, Seattle, WA, United States
| | | | - Vanessa Boulanger
- National Organization for Rare Disorders, Danbury, CT, United States
| | - Michael Brudno
- Department of Computer Science, University of Toronto and the Hospital for Sick Children, Toronto, Canada
| | - Han G. Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jill Clayton-Smith
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary’s Hospital, Manchester, United Kingdom
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Hugh J.S. Dawkins
- Office of Population Health Genomics, Public and Aboriginal Health Division, Department of Health Government of Western Australia, Perth, WA, Australia
- Sir Walter Murdoch School of Policy and International Affairs, Murdoch University
- Centre for Population Health Research, Curtin University of Technology, Perth, WA, Australia
| | - Bert B.A. deVries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Sofia Douzgou
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Saint Mary’s Hospital, Manchester, United Kingdom
| | | | - Evan E. Eichler
- Department of Genome Science, University of Washington School of Medicine, Seattle, WA, United States
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, United States
| | - Michael Ferlaino
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Karen Fieggen
- Division of Human Genetics, Level 3, Wernher and Beit North, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Observatory, South Africa
| | - Helen V. Firth
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - David R. FitzPatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Dylan Gration
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Tudor Groza
- The Garvan Institute, Sydney, NSW, Australia
| | - Melissa Haendel
- Oregon Health & Science University, Portland, OR, United States
| | - Nina Hallowell
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Ethics and Humanities, University of Oxford, Oxford, United Kingdom
- Ethox Centre, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Ada Hamosh
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Jayne Hehir-Kwa
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Marc-Phillip Hitz
- Department of Congenital Heart Disease and Pediatric Cardiology, University Hospital of Schleswig-Holstein–Campus Kiel, Kiel, Germany
| | - Mark Hughes
- Department of Clinical Neurosciences, Western General Hospital, Edinburgh, United Kingdom
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford, United Kingdom
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Peter Krawitz
- Institut für Genomische Statistik und Bioinformatik, Universitätsklinikum Bonn, Rheinische-Friedrich-Wilhelms-Universität, Bonn, Germany
| | - Sébastien Küry
- CHU Nantes, Service de Génétique Médicale, Nantes, France
| | - Melissa Lees
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Gholson J. Lyon
- George A. Jervis Clinic and Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, United States
| | | | | | - Stephen Meyn
- Department of Computer Science, University of Toronto and the Hospital for Sick Children, Toronto, Canada
| | - Veronika Moslerová
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital, Prague, Czechia
| | - Juan M. Politei
- Laboratorio Chamoles, Errores Congénitos del Metabolismo, Buenos Aires, Argentina
| | - Cathryn C. Poulton
- Department of Paediatrics and Neonates, Fiona Stanley Hospital, Perth, WA, Australia
| | - F Lucy Raymond
- CIMR (Wellcome Trust/MRC Building), Cambridge, United Kingdom
| | - Margot R.F. Reijnders
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | | | | | - Catherine M. Rose
- Victorian Clinical Genetics Service and Murdoch Childrens Research Institute, The Royal Children’s Hospital, Parkville, VIC, Australia
| | - David C.G. Sainsbury
- Northern & Yorkshire Cleft Lip and Palate Service, Royal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Lyn Schofield
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Vernon R. Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Marek Turnovec
- Department of Biology and Medical Genetics, 2nd Faculty of Medicine, Charles University and University Hospital, Prague, Czechia
| | - Anke Van Dijck
- Department of Medical Genetics, University and University Hospital Antwerp, Antwerp, Belgium
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, University of Leuven, Leuven, Belgium
| | - Andrew O.M. Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford, United Kingdom
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39
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Differentiation of MISSLA and Fanconi anaemia by computer-aided image analysis and presentation of two novel MISSLA siblings. Eur J Hum Genet 2019; 27:1827-1835. [PMID: 31320746 DOI: 10.1038/s41431-019-0469-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 06/07/2019] [Accepted: 06/25/2019] [Indexed: 01/15/2023] Open
Abstract
Variants in DONSON were recently identified as the cause of microcephaly, short stature, and limb abnormalities syndrome (MISSLA). The clinical spectra of MISSLA and Fanconi anaemia (FA) strongly overlap. For that reason, some MISSLA patients have been clinically diagnosed with FA. Here, we present the clinical data of siblings with MISSLA featuring a novel DONSON variant and summarize the current literature on MISSLA. Additionally, we perform computer-aided image analysis using the DeepGestalt technology to test how distinct the facial features of MISSLA and FA patients are. We show that MISSLA has a specific facial gestalt. Notably, we find that also FA patients feature facial characteristics recognizable by computer-aided image analysis. We conclude that computer-assisted image analysis improves diagnostic precision in both MISSLA and FA.
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40
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Qian Y, Liu J, Yang Y, Chen M, Jin C, Chen P, Lei Y, Pan H, Dong M. Paternal Low-Level Mosaicism-Caused SATB2-Associated Syndrome. Front Genet 2019; 10:630. [PMID: 31333717 PMCID: PMC6614923 DOI: 10.3389/fgene.2019.00630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 06/17/2019] [Indexed: 12/27/2022] Open
Abstract
Mutations of SATB2 (OMIM#608148) gene at 2q33.1 have been associated with the autosomal dominant SATB2-associated syndrome (SAS), which is still short of comprehensive diagnosis technologies for small deletions and low-level mosaicism. In this Chinese Han family, single nucleotide polymorphism array identified a 4.9-kb deletion in the SATB2 gene in two consecutive siblings exhibiting obvious developmental delay and dental abnormalities but failed to find so in their parents. Prenatal diagnosis revealed that their third child carried the same deletion in SATB2 and the pregnancy was terminated. To determine the genetic causes behind the inheritance of SATB2 deletion, gap-PCR was performed on peripheral blood-derived genomic DNA of the family and semen-derived DNA from the father. Gap-PCR that revealed the deletions in the two affected siblings were inherited from the father, while the less intense mutant band indicated the mosaicism of this mutation in the father. The deletion was 3,013 bp in size, spanning from chr2: 200,191,313-200,194,324 (hg19), and covering the entire exon 9 and part of intron 8 and 9 sequences. Droplet digital PCR demonstrated mosaicism percentage of 13.2% and 16.7% in peripheral blood-derived genomic DNA and semen-derived DNA of the father, respectively. Hereby, we describe a family of special AT-rich sequence-binding protein 2-associated syndrome caused by paternal low-level mosaicism and provide effective diagnostic technologies for intragenic deletions.
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Affiliation(s)
- Yeqing Qian
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Jiao Liu
- Prenatal Diagnosis Center, Lishui Maternity and Child Health Care Hospital, Lishui, China
| | - Yanmei Yang
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Min Chen
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Chunlei Jin
- Prenatal Diagnosis Center, Lishui Maternity and Child Health Care Hospital, Lishui, China
| | - Penglong Chen
- Prenatal Diagnosis Center, Lishui Maternity and Child Health Care Hospital, Lishui, China
| | - Yongliang Lei
- Prenatal Diagnosis Center, Lishui Maternity and Child Health Care Hospital, Lishui, China
| | - Hangyi Pan
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Minyue Dong
- Women's Hospital, School of Medicine Zhejiang University, Hangzhou, China.,Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
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41
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Abstract
Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype-to-phenotype theory embraces the view that the encoded protein shape together with gene expression level largely determines the resulting phenotypic trait. Here, we point out that the molecular biology revolution at the turn of the century explained that the gene encodes not one but ensembles of conformations, which in turn spell all possible gene-associated phenotypes. The significance of a dynamic ensemble view is in understanding the linkage between genetic change and the gained observable physical or biochemical characteristics. Thus, despite the transformative shift in our understanding of the basis of protein structure and function, the literature still commonly relates to the classical genotype-phenotype paradigm. This is important because an ensemble view clarifies how even seemingly small genetic alterations can lead to pleiotropic traits in adaptive evolution and in disease, why cellular pathways can be modified in monogenic and polygenic traits, and how the environment may tweak protein function.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
- Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, Maryland, United States of America
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42
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Mishima H, Suzuki H, Doi M, Miyazaki M, Watanabe S, Matsumoto T, Morifuji K, Moriuchi H, Yoshiura KI, Kondoh T, Kosaki K. Evaluation of Face2Gene using facial images of patients with congenital dysmorphic syndromes recruited in Japan. J Hum Genet 2019; 64:789-794. [PMID: 31138847 DOI: 10.1038/s10038-019-0619-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 11/09/2022]
Abstract
An increasing number of genetic syndromes present a challenge to clinical geneticists. A deep learning-based diagnosis assistance system, Face2Gene, utilizes the aggregation of "gestalt," comprising data summarizing features of patients' facial images, to suggest candidate syndromes. Because Face2Gene's results may be affected by ethnicity and age at which training facial images were taken, the system performance for patients in Japan is still unclear. Here, we present an evaluation of Face2Gene using the following two patient groups recruited in Japan: Group 1 consisting of 74 patients with 47 congenital dysmorphic syndromes, and Group 2 consisting of 34 patients with Down syndrome. In Group 1, facial recognition failed for 4 of 74 patients, while 13-21 of 70 patients had a diagnosis for which Face2Gene had not been trained. Omitting these 21 patients, for 85.7% (42/49) of the remainder, the correct syndrome was identified within the top 10 suggested list. In Group 2, for the youngest facial images taken for each of the 34 patients, Down syndrome was successfully identified as the highest-ranking condition using images taken from newborns to those aged 25 years. For the oldest facial images taken at ≥20 years in each of 17 applicable patients, Down syndrome was successfully identified as the highest- and second-highest-ranking condition in 82.2% (14/17) and 100% (17/17) of the patients using images taken from 20 to 40 years. These results suggest that Face2Gene in its current format is already useful in suggesting candidate syndromes to clinical geneticists, using patients with congenital dysmorphic syndromes in Japan.
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Affiliation(s)
- Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Michiko Doi
- Department of Pediatrics, Nagasaki University Hospital, Nagasaki, Japan
| | - Mutsuko Miyazaki
- Department of Pediatrics, Nagasaki Prefectural Children Medical Welfare Center, Isahaya, Japan
| | - Satoshi Watanabe
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tadashi Matsumoto
- Division of Developmental Disabilities, Misakaenosono Mutsumi Developmental, Medical and Welfare Center, Isahaya, Japan
| | - Kanako Morifuji
- Department of Nursing, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroyuki Moriuchi
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tatsuro Kondoh
- Division of Developmental Disabilities, Misakaenosono Mutsumi Developmental, Medical and Welfare Center, Isahaya, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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43
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Pascolini G, Fleischer N, Ferraris A, Majore S, Grammatico P. The facial dysmorphology analysis technology in intellectual disability syndromes related to defects in the histones modifiers. J Hum Genet 2019; 64:721-728. [PMID: 31086247 DOI: 10.1038/s10038-019-0598-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022]
Abstract
Genetic syndromes are frequently associated with Intellectual Disability (ID), as well as craniofacial dysmorphisms. A group of ID syndromes with typical abnormal face related to chromatin remodeling defects, have been recognized, coining the term chromatinopathies. This is a molecular heterogeneous subset of congenital disorders caused by mutations of the various components of the Chromatin-Marking System (CMS), including modifiers of DNA and chromatin remodelers. We performed a phenotypic study on a sample of 120 individuals harboring variants in genes codifying for the histones enzymes, using the DeepGestalt technology. Three experiments (two multiclass comparison experiments and a frontal face-crop analysis) were conducted, analyzing respectively a total of 181 pediatric images in the first comparison experiment and 180 in the second, all individuals belonging predominantly to Caucasian population. The classification results were expressed in terms of the area under the curve (AUC) of the receiver-operating-characteristic curve (ROC). Significant values of AUC and low p-values were registered for all syndromes in the three experiments, in comparison with each other, with other ID syndromes characterized by recognizable craniofacial dysmorphisms and with unaffected controls. Final findings indicated that this group of diseases is characterized by distinctive dysmorphisms, which result pathognomonic. A correct interrogation and use of adequate informatics aids, could become a valid support for clinicians.
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Affiliation(s)
- Giulia Pascolini
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy.
| | | | - Alessandro Ferraris
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Silvia Majore
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
| | - Paola Grammatico
- Medical Genetics Laboratory, Department of Molecular Medicine, Sapienza University, San Camillo-Forlanini Hospital, Rome, Italy
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44
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Yamada M, Uehara T, Suzuki H, Takenouchi T, Yoshihashi H, Suzumura H, Mizuno S, Kosaki K. SATB2-associated syndrome in patients from Japan: Linguistic profiles. Am J Med Genet A 2019; 179:896-899. [PMID: 30848049 DOI: 10.1002/ajmg.a.61114] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 11/30/2018] [Accepted: 11/30/2018] [Indexed: 11/06/2022]
Abstract
Cleft palate can be classified as either syndromic or nonsyndromic. SATB2-associated syndrome is one example of a syndromic cleft palate that is accompanied by intellectual disability, and various dental anomalies. SATB2-associated syndrome can be caused by several different molecular mechanisms including intragenic mutations and deletions of SATB2. Here, we report two patients with SATB2 truncating mutations (p.Arg239* and p.Asp702Thrfs*38) and one with a 4.4 megabase deletion including the SATB2 locus. All three patients had cleft palate and other dysmorphic features including macrodontia wide diastema. None of the three patients had acquired any meaningful words at the age of 5 years. In a review of the linguistic natural history of presently reported three patients and 30 previously reported patients, only two patients had attained verbal skills beyond speaking a few words. This degree of delayed speech contrasts with that observed in the prototypic form of syndromic cleft palate, 22q11.2 deletion syndrome. The recognition of SATB2-associated syndrome prior to palatoplasty would be important for plastic surgeons and the families of patients because precise diagnosis should provide predictive information regarding the future linguistic and intellectual abilities of the patients. Macrodontia with a wide diastema and cleft palate is a helpful and highly suggestive sign for the diagnosis of SATB2-associated syndrome.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.,Health Center, Keio University, Tokyo, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Hiroshi Yoshihashi
- Department of Medical Genetics, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Hiroshi Suzumura
- Department of Pediatrics, Dokkyo Medical University, Tochigi, Japan
| | - Seiji Mizuno
- Department of Pediatrics, Central Hospital, Aichi Human Service Center, Kasugai, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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45
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Zhang Q, Huang Y, Zhang L, Ding YQ, Song NN. Loss of Satb2 in the Cortex and Hippocampus Leads to Abnormal Behaviors in Mice. Front Mol Neurosci 2019; 12:33. [PMID: 30809123 PMCID: PMC6380165 DOI: 10.3389/fnmol.2019.00033] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 01/25/2019] [Indexed: 01/05/2023] Open
Abstract
Satb2-associated syndrome (SAS) is a genetic disorder that results from the deletion or mutation of one allele within the Satb2 locus. Patients with SAS show behavioral abnormalities, including developmental delay/intellectual disability, hyperactivity, and symptoms of autism. To address the role of Satb2 in SAS-related behaviors and generate an SAS mouse model, Satb2 was deleted in the cortex and hippocampus of Emx1-Cre; Satb2flox/flox [Satb2 conditional knockout (CKO)] mice. Satb2 CKO mice showed hyperactivity, increased impulsivity, abnormal social novelty, and impaired spatial learning and memory. Furthermore, we also found that the development of neurons in cortical layer IV was defective in Satb2 CKO mice, as shown by the loss of layer-specific gene expression and abnormal thalamocortical projections. In summary, the abnormal behaviors revealed in Satb2 CKO mice may reflect the SAS symptoms associated with Satb2 mutation in human patients, possibly due to defective development of cortical neurons in multiple layers including alterations of their inputs/outputs.
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Affiliation(s)
- Qiong Zhang
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Anatomy and Neurobiology, Tongji University School of Medicine, Shanghai, China
| | - Ying Huang
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Anatomy and Neurobiology, Tongji University School of Medicine, Shanghai, China
| | - Lei Zhang
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Anatomy and Neurobiology, Tongji University School of Medicine, Shanghai, China
| | - Yu-Qiang Ding
- Key Laboratory of Arrhythmias, Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Anatomy and Neurobiology, Tongji University School of Medicine, Shanghai, China.,State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China.,Department of Laboratory Animal Science, Fudan University, Shanghai, China
| | - Ning-Ning Song
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
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46
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Cera I, Whitton L, Donohoe G, Morris DW, Dechant G, Apostolova G. Genes encoding SATB2-interacting proteins in adult cerebral cortex contribute to human cognitive ability. PLoS Genet 2019; 15:e1007890. [PMID: 30726206 PMCID: PMC6364870 DOI: 10.1371/journal.pgen.1007890] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 12/12/2018] [Indexed: 12/16/2022] Open
Abstract
During CNS development, the nuclear protein SATB2 is expressed in superficial cortical layers and determines projection neuron identity. In the adult CNS, SATB2 is expressed in pyramidal neurons of all cortical layers and is a regulator of synaptic plasticity and long-term memory. Common variation in SATB2 locus confers risk of schizophrenia, whereas rare, de novo structural and single nucleotide variants cause severe intellectual disability and absent or limited speech. To characterize differences in SATB2 molecular function in developing vs adult neocortex, we isolated SATB2 protein interactomes at the two ontogenetic stages and identified multiple novel SATB2 interactors. SATB2 interactomes are highly enriched for proteins that stabilize de novo chromatin loops. The comparison between the neonatal and adult SATB2 protein complexes indicates a developmental shift in SATB2 molecular function, from transcriptional repression towards organization of chromosomal superstructure. Accordingly, gene sets regulated by SATB2 in the neocortex of neonatal and adult mice show limited overlap. Genes encoding SATB2 protein interactors were grouped for gene set analysis of human GWAS data. Common variants associated with human cognitive ability are enriched within the genes encoding adult but not neonatal SATB2 interactors. Our data support a shift in the function of SATB2 in cortex over lifetime and indicate that regulation of spatial chromatin architecture by the SATB2 interactome contributes to cognitive function in the general population.
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Affiliation(s)
- Isabella Cera
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
| | - Laura Whitton
- Cognitive Genetics and Cognitive Therapy Group, Neuroimaging, Cognition and Genomics (NICOG) Centre and NCBES Galway Neuroscience Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
| | - Gary Donohoe
- Cognitive Genetics and Cognitive Therapy Group, Neuroimaging, Cognition and Genomics (NICOG) Centre and NCBES Galway Neuroscience Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
| | - Derek W. Morris
- Cognitive Genetics and Cognitive Therapy Group, Neuroimaging, Cognition and Genomics (NICOG) Centre and NCBES Galway Neuroscience Centre, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
| | - Georg Dechant
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck, Austria
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47
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Identifying facial phenotypes of genetic disorders using deep learning. Nat Med 2019; 25:60-64. [PMID: 30617323 DOI: 10.1038/s41591-018-0279-0] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 10/29/2018] [Indexed: 01/18/2023]
Abstract
Syndromic genetic conditions, in aggregate, affect 8% of the population1. Many syndromes have recognizable facial features2 that are highly informative to clinical geneticists3-5. Recent studies show that facial analysis technologies measured up to the capabilities of expert clinicians in syndrome identification6-9. However, these technologies identified only a few disease phenotypes, limiting their role in clinical settings, where hundreds of diagnoses must be considered. Here we present a facial image analysis framework, DeepGestalt, using computer vision and deep-learning algorithms, that quantifies similarities to hundreds of syndromes. DeepGestalt outperformed clinicians in three initial experiments, two with the goal of distinguishing subjects with a target syndrome from other syndromes, and one of separating different genetic subtypes in Noonan syndrome. On the final experiment reflecting a real clinical setting problem, DeepGestalt achieved 91% top-10 accuracy in identifying the correct syndrome on 502 different images. The model was trained on a dataset of over 17,000 images representing more than 200 syndromes, curated through a community-driven phenotyping platform. DeepGestalt potentially adds considerable value to phenotypic evaluations in clinical genetics, genetic testing, research and precision medicine.
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48
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Kikuiri T, Mishima H, Imura H, Suzuki S, Matsuzawa Y, Nakamura T, Fukumoto S, Yoshimura Y, Watanabe S, Kinoshita A, Yamada T, Shindoh M, Sugita Y, Maeda H, Yawaka Y, Mikoya T, Natsume N, Yoshiura KI. Patients with SATB2-associated syndrome exhibiting multiple odontomas. Am J Med Genet A 2018; 176:2614-2622. [PMID: 30575289 DOI: 10.1002/ajmg.a.40670] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/28/2018] [Accepted: 10/02/2018] [Indexed: 01/09/2023]
Abstract
Special AT-rich sequence-binding protein 2 (SATB2)-associated syndrome (SAS) is characterized by alterations of SATB2. Its clinical features include intellectual disability and craniofacial abnormalities, such as cleft palate, dysmorphic features, and dental abnormalities. Here, we describe three previously undiagnosed, unrelated patients with SAS who exhibited dental abnormalities, including multiple odontomas. Although isolated odontomas are common, multiple odontomas are rare. Individuals in families 1 and 3 underwent whole-exome sequencing. Patient 2 and parents underwent targeted amplicon sequencing. On the basis of the hg19/GRCh37 reference and the RefSeq mRNA NM_001172517, respective heterozygous mutations were found and validated in Patients 1, 2, and 3: a splice-site mutation (chr2:g.200137396C > T, c.1741-1G > A), a nonsense mutation (chr2:g.200213750G > A, c.847C > T, p.R283*), and a frame-shift mutations (chr2:g.200188589_200188590del, c.1478_1479del, p.Q493Rfs*19). All mutations occurred de novo. The mutations in Patients 1 and 3 were novel; the mutation in Patient 2 has been described previously. Tooth mesenchymal cells derived from Patient 2 showed diminished SATB2 expression. Multiple odontomas were evident in the patients in this report; however, this has not been recognized previously as a SAS-associated phenotype. We propose that multiple odontomas be considered as an occasional manifestation of SAS.
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Affiliation(s)
- Takashi Kikuiri
- Department of Dentistry for Children and Disabled Persons, Hokkaido University Graduate School of Dental Medicine, Sapporo, Hokkaido, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hideto Imura
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Satoshi Suzuki
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Yusuke Matsuzawa
- Department of Oral and Maxillofacial Surgery, Keiyukai Sapporo Hospital, Sapporo, Japan
| | - Takashi Nakamura
- Division of Molecular Pharmacology & Cell Biophysics, Department of Oral Biology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Satoshi Fukumoto
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Yoshitaka Yoshimura
- Department of Molecular Cell Pharmacology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Satoshi Watanabe
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Akira Kinoshita
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takahiro Yamada
- Clinical Genetics Unit, Kyoto University Hospital, Kyoto, Japan
| | - Masanobu Shindoh
- Department of Oral Pathology and Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan.,Tenshi College School of Nursing and Nutrition, Sapporo, Japan
| | - Yoshihiko Sugita
- Department of Oral Pathology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Hatsuhiko Maeda
- Department of Oral Pathology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Yasutaka Yawaka
- Department of Dentistry for Children and Disabled Persons, Hokkaido University Graduate School of Dental Medicine, Sapporo, Hokkaido, Japan
| | - Tadashi Mikoya
- Center for Advanced Oral Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Nagato Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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49
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Scott J, Adams C, Simmons K, Feather A, Jones J, Hartzell L, Wesley L, Johnson A, Fish J, Bosanko K, Beetstra S, Zarate YA. Dental radiographic findings in 18 individuals with SATB2-associated syndrome. Clin Oral Investig 2018; 22:2947-2951. [PMID: 30315422 DOI: 10.1007/s00784-018-2702-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/02/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To characterize the radiographic dental phenotype of individuals with SATB2-associated syndrome (SAS). MATERIALS AND METHODS Participants were evaluated by a multidisciplinary team during a concurrent clinic conducted during the 1st international SAS family meeting held in 2017 at a single institution. Whenever possible, panoramic and/or periapical radiographs were obtained in clinic or previously obtained and provided by the caregiver. RESULTS Of the 37 individuals evaluated, 18 (12 males, median age 8.5 years) underwent radiographic examination. Dental radiographs revealed anomalies in all individuals starting at 2 years of age. The most consistent finding was delayed development of the mandibular second bicuspids (83%) with other common radiographic findings including delayed development of the roots of the permanent teeth (78%), severely rotated (56%) or malformed teeth (44%), and taurodontism (44%). CONCLUSIONS Dental anomalies are fully penetrant and can be documented radiographically in all individuals with SAS. CLINICAL RELEVANCE Dental radiographic findings of delayed second premolar development and delayed development of permanent root formation, especially concurrent with findings of taurodontism and malformed teeth, support a clinical suspicion for SAS and should help differentiate SAS from other neurodevelopmental syndromes.
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Affiliation(s)
- John Scott
- Center for Dental Education, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Chad Adams
- Center for Dental Education, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kirt Simmons
- Center for Dental Education, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Andrea Feather
- Center for Dental Education, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - John Jones
- Department of Surgery, Plastic and Reconstructive Surgery, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Otolaryngology, Head and Neck Surgery, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Larry Hartzell
- Department of Otolaryngology, Head and Neck Surgery, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Lucia Wesley
- Department of Otolaryngology, Head and Neck Surgery, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Adam Johnson
- Department of Otolaryngology, Head and Neck Surgery, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jennifer Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - Katherine Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stephen Beetstra
- Center for Dental Education, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
- Arkansas Children's Hospital, Little Rock, USA.
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50
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Vorravanpreecha N, Lertboonnum T, Rodjanadit R, Sriplienchan P, Rojnueangnit K. Studying Down syndrome recognition probabilities in Thai children with de‐identified computer‐aided facial analysis. Am J Med Genet A 2018; 176:1935-1940. [DOI: 10.1002/ajmg.a.40483] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 06/05/2018] [Accepted: 06/28/2018] [Indexed: 01/24/2023]
Affiliation(s)
| | | | | | | | - Kitiwan Rojnueangnit
- Pediatric Department, Faculty of MedicineThammasat University Pathumthani Thailand
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