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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [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: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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2
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Cleven AHG, Szuhai K, van IJzendoorn DGP, Groen E, Baelde H, Schreuder WH, Briaire-de Bruijn IH, van der Meeren SW, Kleijwegt MC, Furth WR, Kroon HM, Suurmeijer AJH, Savci-Heijink DC, Baumhoer D, Bovée JVMG. Psammomatoid Ossifying Fibroma Is Defined by SATB2 Rearrangement. Mod Pathol 2023; 36:100013. [PMID: 36788065 DOI: 10.1016/j.modpat.2022.100013] [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: 04/11/2022] [Revised: 09/12/2022] [Accepted: 09/16/2022] [Indexed: 01/19/2023]
Abstract
Psammomatoid ossifying fibroma (PsOF), also known as juvenile PsOF, is a benign fibro-osseous neoplasm predominantly affecting the extragnathic bones, particularly the frontal and ethmoid bones, with a preference for adolescents and young adults. The clinical and morphologic features of PsOF may overlap with those of other fibro-osseous lesions, and additional molecular markers would help increase diagnostic accuracy. Because identical chromosomal breakpoints at bands Xq26 and 2q33 have been described in 3 cases of PsOF located in the orbita, we aimed to identify the exact genes involved in these chromosomal breakpoints and determine their frequency in PsOF using transcriptome sequencing and fluorescence in situ hybridization (FISH). We performed whole RNA transcriptome sequencing on frozen tissue in 2 PsOF index cases and identified a fusion transcript involving SATB2, located on chromosome 2q33.1, and AL513487.1, located on chromosome Xq26, in one of the cases. The fusion was validated using reverse transcription (RT)-PCR and SATB2 FISH. The fusion lead to a truncated protein product losing most of the functional domains. Subsequently, we analyzed an additional 24 juvenile PsOFs, 8 juvenile trabecular ossifying fibromas (JTOFs), and 11 cemento-ossifying fibromas (COFs) for SATB2 using FISH and found evidence of SATB2 gene rearrangements in 58% (7 of 12) of the evaluable PsOF cases but not in any of the evaluable JTOF (n = 7) and COF (n = 7) cases. A combination of SATB2 immunofluorescence and a 2-color SATB2 FISH in our index case revealed that most tumor cells harboring the rearrangement lacked SATB2 expression. Using immunohistochemistry, 65% of PsOF, 100% of JTOF, and 100% of COF cases showed moderate or strong staining for SATB2. In these cases, we observed a mosaic pattern of expression with >25% of the spindle cells in between the bone matrix, with osteoblasts and osteocytes being positive for SATB2. Interestingly, 35% (8 of 23) of PsOFs, in contrast to JTOFs and COFs, showed SATB2 expression in <5% of cells. To our knowledge, this is the first report that shows the involvement of SATB2 in the development of a neoplastic lesion. In this study, we have showed that SATB2 rearrangement is a recurrent molecular alteration that appears to be highly specific for PsOF. Our findings support that PsOF is not only morphologically and clinically but also genetically distinct from JTOF and COF.
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Affiliation(s)
- Arjen H G Cleven
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands; Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands.
| | - Karoly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - David G P van IJzendoorn
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands; Department of Pathology, Stanford University, Stanford, California
| | - Eline Groen
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Hans Baelde
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Willem H Schreuder
- Department of Oral and Maxillofacial Surgery/Head and Neck Surgery, Amsterdam University Medical Center/Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | | | - Stijn W van der Meeren
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands; Department of Ophthalmology, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - Maarten C Kleijwegt
- Department Head and Neck Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Wouter R Furth
- Department of Neurosurgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Herman M Kroon
- Department of Radiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Albert J H Suurmeijer
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | | | - Daniel Baumhoer
- Bone Tumour Reference Centre, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
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3
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Bhatia S, Kleinjan DJ, Uttley K, Mann A, Dellepiane N, Bickmore WA. Quantitative spatial and temporal assessment of regulatory element activity in zebrafish. eLife 2021; 10:65601. [PMID: 34796872 PMCID: PMC8604437 DOI: 10.7554/elife.65601] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Mutations or genetic variation in noncoding regions of the genome harbouring cis-regulatory elements (CREs), or enhancers, have been widely implicated in human disease and disease risk. However, our ability to assay the impact of these DNA sequence changes on enhancer activity is currently very limited because of the need to assay these elements in an appropriate biological context. Here, we describe a method for simultaneous quantitative assessment of the spatial and temporal activity of wild-type and disease-associated mutant human CRE alleles using live imaging in zebrafish embryonic development. We generated transgenic lines harbouring a dual-CRE dual-reporter cassette in a pre-defined neutral docking site in the zebrafish genome. The activity of each CRE allele is reported via expression of a specific fluorescent reporter, allowing simultaneous visualisation of where and when in development the wild-type allele is active and how this activity is altered by mutation.
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Affiliation(s)
- Shipra Bhatia
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Dirk Jan Kleinjan
- Centre for Mammalian Synthetic Biology at the Institute of Quantitative Biology, Biochemistry, and Biotechnology, SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Kirsty Uttley
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Anita Mann
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Nefeli Dellepiane
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics & Cancer, University of Edinburgh, Edinburgh, United Kingdom
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4
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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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5
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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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6
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Chen Q, Zheng L, Zhang Y, Huang X, Wang F, Li S, Yang Z, Liang F, Hu J, Jiang Y, Li Y, Zhou P, Luo W, Zhang H. Special AT-rich sequence-binding protein 2 (Satb2) synergizes with Bmp9 and is essential for osteo/odontogenic differentiation of mouse incisor mesenchymal stem cells. Cell Prolif 2021; 54:e13016. [PMID: 33660290 PMCID: PMC8016638 DOI: 10.1111/cpr.13016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVES Mouse incisor mesenchymal stem cells (MSCs) have self-renewal ability and osteo/odontogenic differentiation potential. However, the mechanism controlling the continuous self-renewal and osteo/odontogenic differentiation of mouse incisor MSCs remains unclear. Special AT-rich sequence-binding protein 2 (SATB2) positively regulates craniofacial patterning, bone development and regeneration, whereas SATB2 deletion or mutation leads to craniomaxillofacial dysplasia and delayed tooth and root development, similar to bone morphogenetic protein (BMP) loss-of-function phenotypes. However, the detailed mechanism underlying the SATB2 role in odontogenic MSCs is poorly understood. The aim of this study was to investigate whether SATB2 can regulate self-renewal and osteo/odontogenic differentiation of odontogenic MSCs. MATERIALS AND METHODS Satb2 expression was detected in the rapidly renewing mouse incisor mesenchyme by immunofluorescence staining, quantitative RT-PCR and Western blot analysis. Ad-Satb2 and Ad-siSatb2 were constructed to evaluate the effect of Satb2 on odontogenic MSCs self-renewal and osteo/odontogenic differentiation properties and the potential role of Satb2 with the osteogenic factor bone morphogenetic protein 9 (Bmp9) in vitro and in vivo. RESULTS Satb2 was found to be expressed in mesenchymal cells and pre-odontoblasts/odontoblasts. We further discovered that Satb2 effectively enhances mouse incisor MSCs self-renewal. Satb2 acted synergistically with the potent osteogenic factor Bmp9 in inducing osteo/odontogenic differentiation of mouse incisor MSCs in vitro and in vivo. CONCLUSIONS Satb2 promotes self-renewal and osteo/odontogenic differentiation of mouse incisor MSCs. Thus, Satb2 can cooperate with Bmp9 as a new efficacious bio-factor for osteogenic regeneration and tooth engineering.
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Affiliation(s)
- Qiuman Chen
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Liwen Zheng
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Yuxin Zhang
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Xia Huang
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqingChina
| | - Feilong Wang
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Shuang Li
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Zhuohui Yang
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Fang Liang
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Jing Hu
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Yucan Jiang
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Yeming Li
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
| | - Pengfei Zhou
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqingChina
| | - Wenping Luo
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher EducationChongqingChina
| | - Hongmei Zhang
- Chongqing Key Laboratory for Oral Diseases and Biomedical SciencesThe Affiliated Hospital of Stomatology of Chongqing Medical UniversityChongqingChina
- Department of Pediatric DentistryThe Affiliated Stomatology Hospital, Chongqing Medical UniversityChongqingChina
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7
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Fazio M, van Rooijen E, Dang M, van de Hoek G, Ablain J, Mito JK, Yang S, Thomas A, Michael J, Fabo T, Modhurima R, Pessina P, Kaufman CK, Zhou Y, White RM, Zon LI. SATB2 induction of a neural crest mesenchyme-like program drives melanoma invasion and drug resistance. eLife 2021; 10:64370. [PMID: 33527896 PMCID: PMC7880683 DOI: 10.7554/elife.64370] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/01/2021] [Indexed: 12/14/2022] Open
Abstract
Recent genomic and scRNA-seq analyses of melanoma demonstrated a lack of recurrent genetic drivers of metastasis, while identifying common transcriptional states correlating with invasion or drug resistance. To test whether transcriptional adaptation can drive melanoma progression, we made use of a zebrafish mitfa:BRAFV600E;tp53-/- model, in which malignant progression is characterized by minimal genetic evolution. We undertook an overexpression-screen of 80 epigenetic/transcriptional regulators and found neural crest-mesenchyme developmental regulator SATB2 to accelerate aggressive melanoma development. Its overexpression induces invadopodia formation and invasion in zebrafish tumors and human melanoma cell lines. SATB2 binds and activates neural crest-regulators, including pdgfab and snai2. The transcriptional program induced by SATB2 overlaps with known MITFlowAXLhigh and AQP1+NGFR1high drug-resistant states and functionally drives enhanced tumor propagation and resistance to Vemurafenib in vivo. In summary, we show that melanoma transcriptional rewiring by SATB2 to a neural crest mesenchyme-like program can drive invasion and drug resistance in autochthonous tumors.
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Affiliation(s)
- Maurizio Fazio
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, United States
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, United States
| | - Michelle Dang
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, United States
| | - Glenn van de Hoek
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Julien Ablain
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, United States
| | - Jeffrey K Mito
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Brigham and Women's Hospital, Department of Pathology, Boston, United States
| | - Song Yang
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Andrew Thomas
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Jonathan Michael
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Tania Fabo
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, United States
| | - Rodsy Modhurima
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, United States
| | - Patrizia Pessina
- Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States
| | - Charles K Kaufman
- Division of Medical Oncology, Department of Medicine, Washington University in Saint Louis, Saint Louis, United States.,Department of Developmental Biology, Washington University in Saint Louis, St. Louis, United States
| | - Yi Zhou
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, United States
| | - Richard M White
- Memorial Sloan Kettering Cancer Center and Weill-Cornell Medical College, New York, United States
| | - Leonard I Zon
- Howard Hughes Medical Institute, Stem Cell Program and the Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States.,Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, United States
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8
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Tao W, Zhang A, Zhai K, Huang Z, Huang H, Zhou W, Huang Q, Fang X, Prager BC, Wang X, Wu Q, Sloan AE, Ahluwalia MS, Lathia JD, Yu JS, Rich JN, Bao S. SATB2 drives glioblastoma growth by recruiting CBP to promote FOXM1 expression in glioma stem cells. EMBO Mol Med 2020; 12:e12291. [PMID: 33124191 PMCID: PMC7721366 DOI: 10.15252/emmm.202012291] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 09/19/2020] [Accepted: 09/22/2020] [Indexed: 12/16/2022] Open
Abstract
Nuclear matrix-associated proteins (NMPs) play critical roles in regulating chromatin organization and gene transcription by binding to the matrix attachment regions (MARs) of DNA. However, the functional significance of NMPs in glioblastoma (GBM) progression remains unclear. Here, we show that the Special AT-rich Binding Protein-2 (SATB2), one of crucial NMPs, recruits histone acetyltransferase CBP to promote the FOXM1-mediated cell proliferation and tumor growth of GBM. SATB2 is preferentially expressed by glioma stem cells (GSCs) in GBM. Disrupting SATB2 markedly inhibited GSC proliferation and GBM malignant growth by down-regulating expression of key genes involved in cell proliferation program. SATB2 activates FOXM1 expression to promote GSC proliferation through binding to the MAR sequence of FOXM1 gene locus and recruiting CBP to the MAR. Importantly, pharmacological inhibition of SATB2/CBP transcriptional activity by the CBP inhibitor C646 suppressed GSC proliferation in vitro and GBM growth in vivo. Our study uncovers a crucial role of the SATB2/CBP-mediated transcriptional regulation in GBM growth, indicating that targeting SATB2/CBP may effectively improve GBM treatment.
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Affiliation(s)
- Weiwei Tao
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Aili Zhang
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Kui Zhai
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Zhi Huang
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Haidong Huang
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Wenchao Zhou
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Qian Huang
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Xiaoguang Fang
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Briana C Prager
- Division of Regenerative MedicineDepartment of MedicineUniversity of California, San DiegoSan DiegoCAUSA
- Department of PathologyCase Western Reserve University School of MedicineClevelandOHUSA
| | - Xiuxing Wang
- Division of Regenerative MedicineDepartment of MedicineUniversity of California, San DiegoSan DiegoCAUSA
| | - Qiulian Wu
- Division of Regenerative MedicineDepartment of MedicineUniversity of California, San DiegoSan DiegoCAUSA
| | - Andrew E Sloan
- Brain Tumor and Neuro‐Oncology Center & Center of Excellence for Translational Neuro‐OncologyUniversity Hospitals Seidman Cancer CenterCase Western Reserve UniversityClevelandOHUSA
- Case Comprehensive Cancer CenterCase Western Reserve University School of MedicineClevelandOHUSA
| | - Manmeet S Ahluwalia
- Brain Tumor and Neuro‐Oncology CenterTaussig Cancer InstituteCleveland ClinicClevelandOHUSA
| | - Justin D Lathia
- Case Comprehensive Cancer CenterCase Western Reserve University School of MedicineClevelandOHUSA
- Brain Tumor and Neuro‐Oncology CenterTaussig Cancer InstituteCleveland ClinicClevelandOHUSA
- Department of Cardiovascular and Metabolic SciencesCleveland ClinicClevelandOHUSA
| | - Jennifer S Yu
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
- Case Comprehensive Cancer CenterCase Western Reserve University School of MedicineClevelandOHUSA
- Center for Cancer Stem Cell ResearchLerner Research InstituteCleveland ClinicClevelandOHUSA
- Department of Radiation OncologyTaussig Cancer InstituteCleveland ClinicClevelandOHUSA
| | - Jeremy N Rich
- Division of Regenerative MedicineDepartment of MedicineUniversity of California, San DiegoSan DiegoCAUSA
| | - Shideng Bao
- Department of Cancer BiologyLerner Research InstituteCleveland ClinicClevelandOHUSA
- Case Comprehensive Cancer CenterCase Western Reserve University School of MedicineClevelandOHUSA
- Center for Cancer Stem Cell ResearchLerner Research InstituteCleveland ClinicClevelandOHUSA
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9
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Interpreting the impact of noncoding structural variation in neurodevelopmental disorders. Genet Med 2020; 23:34-46. [PMID: 32973355 PMCID: PMC7790743 DOI: 10.1038/s41436-020-00974-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/03/2020] [Accepted: 09/14/2020] [Indexed: 12/21/2022] Open
Abstract
The emergence of novel sequencing technologies has greatly improved the identification of structural variation, revealing that a human genome harbors tens of thousands of structural variants (SVs). Since these SVs primarily impact noncoding DNA sequences, the next challenge is one of interpretation, not least to improve our understanding of human disease etiology. However, this task is severely complicated by the intricacy of the gene regulatory landscapes embedded within these noncoding regions, their incomplete annotation, as well as their dependence on the three-dimensional (3D) conformation of the genome. Also in the context of neurodevelopmental disorders (NDDs), reports of putatively causal, noncoding SVs are accumulating and understanding their impact on transcriptional regulation is presenting itself as the next step toward improved genetic diagnosis.
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10
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Saleem K, Zaib T, Sun W, Fu S. Assessment of candidate genes and genetic heterogeneity in human non syndromic orofacial clefts specifically non syndromic cleft lip with or without palate. Heliyon 2019; 5:e03019. [PMID: 31886431 PMCID: PMC6921104 DOI: 10.1016/j.heliyon.2019.e03019] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 12/26/2022] Open
Abstract
Non syndromic orofacial clefts specifically non-syndromic cleft lip/palate are one of the most common craniofacial malformation among birth defects in human having multifactorial etiology with an incidence of 1:700/1000. On the basis of association with other congenital malformations or their presence as isolated anomaly, OFC can be classified as syndromic (30%) and nonsyndromic (70%) respectively. The major cause of disease demonstrates complex interplay between genetic and environmental factors. The pathogenic mechanism of underlying factors have been provided by different genetic studies on large-scale with significant recent advances in genotyping technologies usually based on linkage or genome wide association studies (GWAS). On the basis of recent studies, new tools to identify causative genes involved in NSCL/P reported approximately more than 30 genetic risk loci that are responsible for pathogenesis of facial deformation. Despite these findings, it is still uncertain that how much of variance in NSCL/P predisposing factors can be explain by identified risk loci, as they all together accounts for only 20%-25% of NSCL/P heritability. So there is need of further findings about the problem of rare low frequency coding variants and other missing responsive factors or genetic modifiers. This review will described those potential genes and loci reported in different studies whose involvement in pathogenesis of nonsyndromic OFC has wide scientific evidence.
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Affiliation(s)
- Komal Saleem
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
| | - Tahir Zaib
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, China.,Key Laboratory of Preservation of Human Genetics Resources and Disease Control in China (Harbin Medical University), Ministry of Education, China
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11
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Mann A, Bhatia S. Zebrafish: A Powerful Model for Understanding the Functional Relevance of Noncoding Region Mutations in Human Genetic Diseases. Biomedicines 2019; 7:E71. [PMID: 31527394 PMCID: PMC6784013 DOI: 10.3390/biomedicines7030071] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
Determining aetiology of genetic disorders caused by damaging mutations in protein-coding genes is well established. However, understanding how mutations in the vast stretches of the noncoding genome contribute to genetic abnormalities remains a huge challenge. Cis-regulatory elements (CREs) or enhancers are an important class of noncoding elements. CREs function as the primary determinants of precise spatial and temporal regulation of their target genes during development by serving as docking sites for tissue-specific transcription factors. Although a large number of potential disease-associated CRE mutations are being identified in patients, lack of robust methods for mechanistically linking these mutations to disease phenotype is currently hampering the understanding of their roles in disease aetiology. Here, we have described the various systems available for testing the CRE potential of stretches of noncoding regions harbouring mutations implicated in human disease. We highlight advances in the field leading to the establishment of zebrafish as a powerful system for robust and cost-effective functional assays of CRE activity, enabling rapid identification of causal variants in regulatory regions and the validation of their role in disruption of appropriate gene expression.
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Affiliation(s)
- Anita Mann
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Shipra Bhatia
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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12
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Seelan RS, Pisano M, Greene RM. Nucleic acid methylation and orofacial morphogenesis. Birth Defects Res 2019; 111:1593-1610. [PMID: 31385455 DOI: 10.1002/bdr2.1564] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022]
Abstract
In this review, we highlight the current state of knowledge of the diverse roles nucleic acid methylation plays in the embryonic development of the orofacial region and how aberrant methylation may contribute to orofacial clefts. We also consider the role of methylation in the regulation of neural crest cell function as it pertains to orofacial ontogeny. Changes in DNA methylation, as a consequence of environmental effects, have been observed in the regulatory regions of several genes, potentially identifying new candidate genes for orofacial clefting and opening promising new avenues for further research. While the focus of this review is primarily on the nonsyndromic forms of orofacial clefting, syndromic forms are briefly discussed in the context of aberrant nucleic acid methylation.
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Affiliation(s)
- Ratnam S Seelan
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Michele Pisano
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
| | - Robert M Greene
- Department of Oral Immunology and Infectious Diseases, Division of Craniofacial Development and Anomalies, University of Louisville School of Dentistry, Louisville, Kentucky
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13
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Arican P, Olgac Dundar N, Ozyilmaz B, Cavusoglu D, Gencpinar P, Erdogan KM, Saka Guvenc M. Chromosomal Microarray Analysis in Children with Unexplained Developmental Delay/Intellectual Disability. J Pediatr Genet 2019; 8:1-9. [PMID: 30775046 DOI: 10.1055/s-0038-1676583] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
Abstract
Chromosomal microarray (CMA) analysis for discovery of copy number variants (CNVs) is now recommended as a first-line diagnostic tool in patients with unexplained developmental delay/intellectual disability (DD/ID) and autism spectrum disorders. In this study, we present the results of CMA analysis in patients with DD/ID. Of 210 patients, pathogenic CNVs were detected in 26 (12%) and variants of uncertain clinical significance in 36 (17%) children. The diagnosis of well-recognized genetic syndromes was achieved in 12 patients. CMA analysis revealed pathogenic de novo CNVs, such as 11p13 duplication with new clinical features. Our results support the utility of CMA as a routine diagnostic test for unexplained DD/ID.
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Affiliation(s)
- Pinar Arican
- Department of Pediatric Neurology, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Nihal Olgac Dundar
- Department of Pediatric Neurology, Katip Celebi University, Izmir, Turkey
| | - Berk Ozyilmaz
- Department of Medical Genetics, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Dilek Cavusoglu
- Department of Pediatric Neurology, Katip Celebi University, Izmir, Turkey
| | - Pinar Gencpinar
- Department of Pediatric Neurology, Katip Celebi University, Izmir, Turkey
| | - Kadri Murat Erdogan
- Department of Medical Genetics, Tepecik Training and Research Hospital, Izmir, Turkey
| | - Merve Saka Guvenc
- Department of Medical Genetics, Tepecik Training and Research Hospital, Izmir, Turkey
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14
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Logjes RJH, Breugem CC, Van Haaften G, Paes EC, Sperber GH, van den Boogaard MJH, Farlie PG. The ontogeny of Robin sequence. Am J Med Genet A 2018; 176:1349-1368. [PMID: 29696787 DOI: 10.1002/ajmg.a.38718] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 12/17/2017] [Accepted: 03/23/2018] [Indexed: 02/06/2023]
Abstract
The triad of micrognathia, glossoptosis, and concomitant airway obstruction defined as "Robin sequence" (RS) is caused by oropharyngeal developmental events constrained by a reduced stomadeal space. This sequence of abnormal embryonic development also results in an anatomical configuration that might predispose the fetus to a cleft palate. RS is heterogeneous and many different etiologies have been described including syndromic, RS-plus, and isolated forms. For an optimal diagnosis, subsequent treatment and prognosis, a thorough understanding of the embryology and pathogenesis is necessary. This manuscript provides an update about our current understanding of the development of the mandible, tongue, and palate and possible mechanisms involved in the development of RS. Additionally, we provide the reader with an up-to-date summary of the different etiologies of this phenotype and link this to the embryologic, developmental, and genetic mechanisms.
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Affiliation(s)
- Robrecht J H Logjes
- Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Wilhelmina Children's Hospital Utrecht, Utrecht, The Netherlands
| | - Corstiaan C Breugem
- Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Wilhelmina Children's Hospital Utrecht, Utrecht, The Netherlands
| | - Gijs Van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emma C Paes
- Department of Plastic and Reconstructive Surgery, University Medical Center Utrecht, Wilhelmina Children's Hospital Utrecht, Utrecht, The Netherlands
| | - Geoffrey H Sperber
- Faculty of Medicine and Dentistry, University of Alberta, Alberta, Canada
| | | | - Peter G Farlie
- Royal Children's Hospital, Murdoch Children's Research Institute, Parkville, Australia
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15
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Zarate YA, Smith-Hicks CL, Greene C, Abbott MA, Siu VM, Calhoun ARUL, Pandya A, Li C, Sellars EA, Kaylor J, Bosanko K, Kalsner L, Basinger A, Slavotinek AM, Perry H, Saenz M, Szybowska M, Wilson LC, Kumar A, Brain C, Balasubramanian M, Dubbs H, Ortiz-Gonzalez XR, Zackai E, Stein Q, Powell CM, Schrier Vergano S, Britt A, Sun A, Smith W, Bebin EM, Picker J, Kirby A, Pinz H, Bombei H, Mahida S, Cohen JS, Fatemi A, Vernon HJ, McClellan R, Fleming LR, Knyszek B, Steinraths M, Velasco Gonzalez C, Beck AE, Golden-Grant KL, Egense A, Parikh A, Raimondi C, Angle B, Allen W, Schott S, Algrabli A, Robin NH, Ray JW, Everman DB, Gambello MJ, Chung WK. Natural history and genotype-phenotype correlations in 72 individuals with SATB2-associated syndrome. Am J Med Genet A 2018; 176:925-935. [PMID: 29436146 DOI: 10.1002/ajmg.a.38630] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/16/2018] [Indexed: 11/07/2022]
Abstract
SATB2-associated syndrome (SAS) is an autosomal dominant disorder characterized by significant neurodevelopmental disabilities with limited to absent speech, behavioral issues, and craniofacial anomalies. Previous studies have largely been restricted to case reports and small series without in-depth phenotypic characterization or genotype-phenotype correlations. Seventy two study participants were identified as part of the SAS clinical registry. Individuals with a molecularly confirmed diagnosis of SAS were referred after clinical diagnostic testing. In this series we present the most comprehensive phenotypic and genotypic characterization of SAS to date, including prevalence of each clinical feature, neurodevelopmental milestones, and when available, patient management. We confirm that the most distinctive features are neurodevelopmental delay with invariably severely limited speech, abnormalities of the palate (cleft or high-arched), dental anomalies (crowding, macrodontia, abnormal shape), and behavioral issues with or without bone or brain anomalies. This comprehensive clinical characterization will help clinicians with the diagnosis, counseling and management of SAS and help provide families with anticipatory guidance.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Constance L Smith-Hicks
- Division of Neurogenetics, Department of Neurology, Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Carol Greene
- Department of Pediatrics, University of Maryland Baltimore, Baltimore, Maryland
| | - Mary-Alice Abbott
- Department of Pediatrics, Baystate Medical Center, Springfield, Massachusetts
| | - Victoria M Siu
- Division of Medical Genetics, Department of Pediatrics, University of Western Ontario, London, Ontario, Canada
| | - Amy R U L Calhoun
- Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City, Iowa
| | - Arti Pandya
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Chumei Li
- Clinical Genetics Program, McMaster University Medical Center, Hamilton, Ontario, Canada
| | - Elizabeth A Sellars
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Katherine Bosanko
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Louisa Kalsner
- Departments of Neurology and Pediatrics, Connecticut Children's Medical Center and University of Connecticut Health Center, Farmington, Connecticut
| | | | - Anne M Slavotinek
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California
| | - Hazel Perry
- Division of Genetics, Department of Pediatrics, University of California San Francisco, San Francisco, California
| | | | - Marta Szybowska
- Clinical Genetics Program, McMaster University Medical Center, Hamilton, Ontario, Canada
| | - Louise C Wilson
- Department of Genetics, Great Ormond Street for Children NHS Foundation Trust, London, UK
| | - Ajith Kumar
- Department of Genetics, Great Ormond Street for Children NHS Foundation Trust, London, UK
| | - Caroline Brain
- Department of Endocrinology, Great Ormond Street for Children NHS Foundation Trust, London, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Holly Dubbs
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Elaine Zackai
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Quinn Stein
- Divisions of Pediatric Neurology and Genetics, Sanford Children's Specialty Clinic, Sanford Children's Hospital, Sioux Falls, South Dakota
| | - Cynthia M Powell
- Department of Pediatrics, Division of Genetics and Metabolism, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Samantha Schrier Vergano
- Division of Medical Genetics and Metabolism, Children's Hospital of The King's Daughters, Norfolk, Virginia
| | - Allison Britt
- Division of Medical Genetics, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | - Angela Sun
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington.,Seattle Children's Hospital, Seattle, Washington
| | - Wendy Smith
- Department of Pediatrics, The Barbara Bush Children's Hospital, Maine Medical Center, Portland, Maine
| | - E Martina Bebin
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Amelia Kirby
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Hospital, Saint Louis, Missouri
| | - Hailey Pinz
- Division of Medical Genetics, SSM Health Cardinal Glennon Children's Hospital, Saint Louis, Missouri
| | - Hannah Bombei
- Division of Medical Genetics, Department of Pediatrics, University of Iowa, Iowa City, Iowa
| | - Sonal Mahida
- Division of Neurogenetics, Department of Neurology, Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julie S Cohen
- Division of Neurogenetics, Department of Neurology, Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ali Fatemi
- Division of Neurogenetics, Department of Neurology, Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hilary J Vernon
- Division of Neurogenetics, Department of Neurology, Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rebecca McClellan
- Division of Neurogenetics, Department of Neurology, Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Leah R Fleming
- Clinical Genetics and Genomics, St. Luke's Children's Hospital, Boise, Idaho
| | - Brittney Knyszek
- Clinical Genetics and Genomics, St. Luke's Children's Hospital, Boise, Idaho
| | - Michelle Steinraths
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cruz Velasco Gonzalez
- Biostatistics Program, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Anita E Beck
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington.,Seattle Children's Hospital, Seattle, Washington
| | | | - Alena Egense
- Department of Pediatrics, University of Maryland Baltimore, Baltimore, Maryland
| | - Aditi Parikh
- University of Toledo Department of Pediatrics, Toledo, Ohio.,University Hospitals Cleveland Medical Center, Cleveland, Ohio.,Department of Genetics and Genome Sciences Case Western Reserve University School of Medicine, Cleveland, Ohio
| | | | - Brad Angle
- Advocate Children's Hospital, Park Ridge, Illinois
| | - William Allen
- Fullerton Genetics Center, Asheville, North Carolina
| | | | | | | | - Joseph W Ray
- Division of Medical Genetics, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas
| | | | | | - Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, New York
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16
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Zarate YA, Steinraths M, Matthews A, Smith WE, Sun A, Wilson LC, Brain C, Allgove J, Jacobs B, Fish JL, Powell CM, Wasserman WW, van Karnebeek CD, Wakeling EL, Ma NS. Bone health and SATB2-associated syndrome. Clin Genet 2017; 93:588-594. [PMID: 28787087 DOI: 10.1111/cge.13121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/27/2017] [Accepted: 08/02/2017] [Indexed: 12/20/2022]
Abstract
SATB2-associated syndrome (SAS) is a rare disorder caused by alterations in the special AT-rich sequence-binding protein 2 (SATB2). Skeletal abnormalities such as tibial bowing, osteomalacia, osteopenia or osteoporosis have been reported suggesting a higher frequency of skeletal complications in SAS. The optimal timing, necessity, and methodology for routine assessment of bone health in individuals with SAS, however, remain unclear. We report molecular and phenotypic features of 7 individuals with SAS documented to have low bone mineral density (BMD) ascertained by dual-energy X-ray absorptiometry (DXA), often preceded by tibial bowing. The lowest BMD Z-scores ranged -2.3 to -5.6. In 4 individuals, total alkaline phosphatase levels were elevated (2 with elevated bone fraction) around the time of low BMD documentation. A clinically significant fracture history and a diagnosis of pediatric osteoporosis were present in 4 individuals. Pamidronate treatment in 2 children improved BMD. In conclusion, low BMD, fractures, and tibial bowing are relatively common skeletal complications in individuals with SAS. DXA is a useful tool when evaluating a child with SAS suspected to have low BMD and the results might alter clinical management.
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Affiliation(s)
- Y A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - M Steinraths
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - A Matthews
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - W E Smith
- Department of Pediatrics, The Barbara Bush Children's Hospital, Maine Medical Center, Portland, Maine
| | - A Sun
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington
| | - L C Wilson
- Department of Genetics, Great Ormond Street for Children NHS Foundation Trust, London, UK
| | - C Brain
- Department of Endocrinology, Great Ormond Street for Children NHS Foundation Trust, London, UK
| | - J Allgove
- Department of Endocrinology, Great Ormond Street for Children NHS Foundation Trust, London, UK
| | - B Jacobs
- Department of Pediatrics, Royal National Orthopaedic Hospital NHS Trust, London, UK
| | - J L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
| | - C M Powell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - W W Wasserman
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada.,Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, Vancouver, Canada
| | - C D van Karnebeek
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, Vancouver, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, Canada.,Department of Pediatrics and Clinical Genetics, Emma Children's Hospital, Academic Medical Centre, Amsterdam, The Netherlands
| | - E L Wakeling
- North West Thames Regional Genetics Service, London North West Healthcare NHS Trust, Harrow, UK
| | - N S Ma
- Division of Endocrinology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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17
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Resnick CM, Estroff JA, Kooiman TD, Calabrese CE, Koudstaal MJ, Padwa BL. Pathogenesis of Cleft Palate in Robin Sequence: Observations From Prenatal Magnetic Resonance Imaging. J Oral Maxillofac Surg 2017; 76:1058-1064. [PMID: 29125932 DOI: 10.1016/j.joms.2017.10.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/19/2017] [Accepted: 10/05/2017] [Indexed: 11/20/2022]
Abstract
PURPOSE The etiology of the palatal cleft in Robin sequence (RS) is unknown. The purpose of this study was to assess the position of the fetal tongue at prenatal magnetic resonance imaging (MRI) and to suggest a potential relation between tongue position and development of the cleft palate seen in most patients with RS. MATERIALS AND METHODS This is a retrospective case-and-control study including fetuses with prenatal MRIs performed in the authors' center from 2002 to 2017. Inclusion criteria were 1) prenatal MRI of adequate quality, 2) liveborn infant, and 3) postnatal diagnosis of RS (Robin group) or cleft lip and palate (CLP group). Patients with postnatal RS without a palatal cleft were excluded. A control group with normal facial morphology was matched by gestational age. The outcome variable was tongue position at fetal MRI, described as within the cleft, along the floor of the mouth (normal), other, or indeterminate. RESULTS One hundred twenty-two patients with mean gestational age at MRI of 25.8 ± 4.9 weeks were included (Robin, n = 21 [17%]; CLP, n = 47 [39%]; control, n = 54 [44%]). The tongue was visualized within the palatal cleft in 76.2% of the Robin group and 4.3% of the CLP group. The tongue was found along the floor of the mouth (normal) in the remainder of the Robin and CLP groups and in 100% of the control group. CONCLUSION These findings suggest a relation between in utero tongue position and the development of cleft palate in RS.
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Affiliation(s)
- Cory M Resnick
- Assistant Professor of Oral and Maxillofacial Surgery, Harvard School of Dental Medicine and Harvard Medical School, Boston; Oral and Maxillofacial Surgeon, Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA.
| | - Judy A Estroff
- Associate Professor of Radiology, Harvard Medical School, Boston; Radiologist, Division Chief, Fetal-Neonatal Imaging, Department of Radiology, Advanced Fetal Care Center, Boston Children's Hospital, Boston, MA
| | - Tessa D Kooiman
- Medical Student, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Carly E Calabrese
- Clinical Research Specialist, Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA
| | - Maarten J Koudstaal
- Department of Oral and Maxillofacial Surgery, Erasmus Medical Center, Rotterdam, The Netherlands; Research Associate, Harvard School of Dental Medicine and Harvard Medical School, Boston, MA; Oral and Maxillofacial Surgeon, Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA
| | - Bonnie L Padwa
- Associate Professor, Harvard School of Dental Medicine and Harvard Medical School, Boston; Oral Surgeon-in-Chief, Department of Plastic and Oral Surgery, Boston Children's Hospital, Boston, MA
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18
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Duncan KM, Mukherjee K, Cornell RA, Liao EC. Zebrafish models of orofacial clefts. Dev Dyn 2017; 246:897-914. [PMID: 28795449 DOI: 10.1002/dvdy.24566] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 07/06/2017] [Accepted: 07/31/2017] [Indexed: 12/12/2022] Open
Abstract
Zebrafish is a model organism that affords experimental advantages toward investigating the normal function of genes associated with congenital birth defects. Here we summarize zebrafish studies of genes implicated in orofacial cleft (OFC). The most common use of zebrafish in this context has been to explore the normal function an OFC-associated gene product in craniofacial morphogenesis by inhibiting expression of its zebrafish ortholog. The most frequently deployed method has been to inject embryos with antisense morpholino oligonucleotides targeting the desired transcript. However, improvements in targeted mutagenesis strategies have led to widespread adoption of CRISPR/Cas9 technology. A second application of zebrafish has been for functional assays of gene variants found in OFC patients; such in vivo assays are valuable because the success of in silico methods for testing allele severity has been mixed. Finally, zebrafish have been used to test the tissue specificity of enhancers that harbor single nucleotide polymorphisms associated with risk for OFC. We review examples of each of these approaches in the context of genes that are implicated in syndromic and non-syndromic OFC. Developmental Dynamics 246:897-914, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Kaylia M Duncan
- Department of Anatomy and Cell Biology, Molecular and Cell Biology Graduate Program, University of Iowa, Iowa City, Iowa
| | - Kusumika Mukherjee
- Center for Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, Molecular and Cell Biology Graduate Program, University of Iowa, Iowa City, Iowa
| | - Eric C Liao
- Center for Regenerative Medicine, Division of Plastic and Reconstructive Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
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19
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Sansović I, Ivankov AM, Bobinec A, Kero M, Barišić I. Chromosomal microarray in clinical diagnosis: a study of 337 patients with congenital anomalies and developmental delays or intellectual disability. Croat Med J 2017; 58:231-238. [PMID: 28613040 PMCID: PMC5470123 DOI: 10.3325/cmj.2017.58.231] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Aim To determine the diagnostic yield and criteria that could help to classify and interpret the copy number variations (CNVs) detected by chromosomal microarray (CMA) technique in patients with congenital and developmental abnormalities including dysmorphia, developmental delay (DD) or intellectual disability (ID), autism spectrum disorders (ASD) and congenital anomalies (CA). Method CMA analysis was performed in 337 patients with DD/ID with or without dysmorphism, ASD, and/or CA. In 30 of 337 patients, chromosomal imbalances had previously been detected by classical cytogenetic and molecular cytogenetic methods. Results In 73 of 337 patients, clinically relevant variants were detected and better characterized. Most of them were >1 Mb. Variants of unknown clinical significance (VOUS) were discovered in 35 patients. The most common VOUS size category was <300 kb (40.5%). Deletions and de novo imbalances were more frequent in pathogenic CNV than in VOUS category. CMA had a high diagnostic yield of 43/307, excluding patients previously detected by other methods. Conclusion CMA was valuable in establishing the diagnosis in a high proportion of patients. Criteria for classification and interpretation of CNVs include CNV size and type, mode of inheritance, and genotype-phenotype correlation. Agilent ISCA v2 Human Genome 8x60 K oligonucleotide microarray format proved to be reasonable resolution for clinical use, particularly in the regions that are recommended by the International Standard Cytogenomic Array (ISCA) Consortium and associated with well-established syndromes.
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Affiliation(s)
- Ivona Sansović
- Ivona Sansović, Department of Medical Genetics and Reproductive Health, Children's Hospital Zagreb, Klaićeva 16, 10000 Zagreb, Croatia,
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20
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Thieme F, Ludwig K. The Role of Noncoding Genetic Variation in Isolated Orofacial Clefts. J Dent Res 2017; 96:1238-1247. [DOI: 10.1177/0022034517720403] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past decade, medical genetic research has generated multiple discoveries, many of which were obtained via genome-wide association studies (GWASs). A major GWAS finding is that the majority of risk variants for complex traits map to noncoding regions. This has resulted in a paradigm shift in terms of the interpretation of human genomic sequence variation, with more attention now being paid to what was previously termed “junk DNA.” Translation of genetic findings into biologically meaningful results requires 1) large-scale and cell-specific efforts to annotate non-protein–coding regions and 2) the integration of comprehensive genomic data sets. However, this represents an enormous challenge, particularly in the case of human traits that arise during embryonic development, such as orofacial clefts (OFCs). OFC is a multifactorial trait and ranks among the most common of all human congenital malformations. These 2 attributes apply in particular to its isolated forms (nonsyndromic OFC [nsOFC]). Although genetic studies (including GWASs) have yielded novel insights into the genetic architecture of nsOFC, few data are available concerning causality and affected biological pathways. Reasons for this deficiency include the complex genetic architecture at risk loci and the limited availability of functional data sets from human tissues that represent relevant embryonic sites and time points. The present review summarizes current knowledge of the role of noncoding regions in nsOFC etiology. We describe the identification of genetic risk factors for nsOFC and several of the approaches used to identify causal variants at these loci. These strategies include the use of biological and genetic information from public databases, the assessment of the full spectrum of genetic variability within 1 locus, and comprehensive in vitro and in vivo experiments. This review also highlights the role of the emerging research field “functional genomics” and its increasing contribution to our biological understanding of nsOFC.
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Affiliation(s)
- F. Thieme
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - K.U. Ludwig
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
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21
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Bengani H, Handley M, Alvi M, Ibitoye R, Lees M, Lynch SA, Lam W, Fannemel M, Nordgren A, Malmgren H, Kvarnung M, Mehta S, McKee S, Whiteford M, Stewart F, Connell F, Clayton-Smith J, Mansour S, Mohammed S, Fryer A, Morton J, Grozeva D, Asam T, Moore D, Sifrim A, McRae J, Hurles ME, Firth HV, Raymond FL, Kini U, Nellåker C, Ddd Study, FitzPatrick DR. Clinical and molecular consequences of disease-associated de novo mutations in SATB2. Genet Med 2017; 19:900-908. [PMID: 28151491 PMCID: PMC5548934 DOI: 10.1038/gim.2016.211] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/01/2016] [Indexed: 02/03/2023] Open
Abstract
PURPOSE To characterize features associated with de novo mutations affecting SATB2 function in individuals ascertained on the basis of intellectual disability. METHODS Twenty previously unreported individuals with 19 different SATB2 mutations (11 loss-of-function and 8 missense variants) were studied. Fibroblasts were used to measure mutant protein production. Subcellular localization and mobility of wild-type and mutant SATB2 were assessed using fluorescently tagged protein. RESULTS Recurrent clinical features included neurodevelopmental impairment (19/19), absent/near absent speech (16/19), normal somatic growth (17/19), cleft palate (9/19), drooling (12/19), and dental anomalies (8/19). Six of eight missense variants clustered in the first CUT domain. Sibling recurrence due to gonadal mosaicism was seen in one family. A nonsense mutation in the last exon resulted in production of a truncated protein retaining all three DNA-binding domains. SATB2 nuclear mobility was mutation-dependent; p.Arg389Cys in CUT1 increased mobility and both p.Gly515Ser in CUT2 and p.Gln566Lys between CUT2 and HOX reduced mobility. The clinical features in individuals with missense variants were indistinguishable from those with loss of function. CONCLUSION SATB2 haploinsufficiency is a common cause of syndromic intellectual disability. When mutant SATB2 protein is produced, the protein appears functionally inactive with a disrupted pattern of chromatin or matrix association.Genet Med advance online publication 02 February 2017.
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Affiliation(s)
- Hemant Bengani
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Mark Handley
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Mohsan Alvi
- Avdeling for Medisinsk Genetikk, Oslo Universitetssykehus, Oslo, Norway
| | - Rita Ibitoye
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Melissa Lees
- North East Regional Genetics Service, Great Ormond Street Hospital, London, UK
| | - Sally Ann Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin, Ireland
| | - Wayne Lam
- South East Scotland Genetic Service, Western General Hospital, Edinburgh, UK
| | | | - Ann Nordgren
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - H Malmgren
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - M Kvarnung
- Clinical Genetics Unit, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Sarju Mehta
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation, Cambridge, UK
| | - Shane McKee
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, UK
| | - Margo Whiteford
- West of Scotland Genetic Services, Queen Elizabeth University Hospital, Glasgow, UK
| | - Fiona Stewart
- Northern Ireland Regional Genetics Centre, Belfast City Hospital, Belfast, UK
| | - Fiona Connell
- South East Thames Regional Genetics Service, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Sahar Mansour
- Department of Clinical Genetics, St Georges Hospital, Tooting, UK
| | - Shehla Mohammed
- South East Thames Regional Genetics Service, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Alan Fryer
- Cheshire &Merseyside Regional Genetics Service, Liverpool Women's NHS foundation Trust, Liverpool, UK
| | - Jenny Morton
- West Midlands Regional Genetics Service, Birmingham Women's NHS Foundation Trust, Birmingham, UK
| | | | - Detelina Grozeva
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Tara Asam
- South-East Scotland Regional Genetics Laboratories, Western General Hospital, Edinburgh, UK
| | - David Moore
- South-East Scotland Regional Genetics Laboratories, Western General Hospital, Edinburgh, UK
| | - Alejandro Sifrim
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jeremy McRae
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Matthew E Hurles
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Helen V Firth
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation, Cambridge, UK
| | - F Lucy Raymond
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Usha Kini
- Department of Clinical Genetics, Oxford University Hospitals NHS Trust, Oxford, UK.,Spires Cleft Centre, John Radcliffe Hospital, Oxford, UK
| | - Christoffer Nellåker
- Nuffield Department of Obstetrics &Gynaecology, University of Oxford, Women's Centre, John Radcliffe Hospital, Oxford, UK.,Department of Engineering Science, University of Oxford, Institute of Biomedical Engineering, Oxford, UK.,Big Data Institute, University of Oxford, Oxford, UK
| | - Ddd Study
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, IGMM, University of Edinburgh, Western General Hospital, Edinburgh, UK
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22
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Muggenthaler MMA, Chowdhury B, Hasan SN, Cross HE, Mark B, Harlalka GV, Patton MA, Ishida M, Behr ER, Sharma S, Zahka K, Faqeih E, Blakley B, Jackson M, Lees M, Dolinsky V, Cross L, Stanier P, Salter C, Baple EL, Alkuraya FS, Crosby AH, Triggs-Raine B, Chioza BA. Mutations in HYAL2, Encoding Hyaluronidase 2, Cause a Syndrome of Orofacial Clefting and Cor Triatriatum Sinister in Humans and Mice. PLoS Genet 2017; 13:e1006470. [PMID: 28081210 PMCID: PMC5230738 DOI: 10.1371/journal.pgen.1006470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/08/2016] [Indexed: 01/25/2023] Open
Abstract
Orofacial clefting is amongst the most common of birth defects, with both genetic and environmental components. Although numerous studies have been undertaken to investigate the complexities of the genetic etiology of this heterogeneous condition, this factor remains incompletely understood. Here, we describe mutations in the HYAL2 gene as a cause of syndromic orofacial clefting. HYAL2, encoding hyaluronidase 2, degrades extracellular hyaluronan, a critical component of the developing heart and palatal shelf matrix. Transfection assays demonstrated that the gene mutations destabilize the molecule, dramatically reducing HYAL2 protein levels. Consistent with the clinical presentation in affected individuals, investigations of Hyal2-/- mice revealed craniofacial abnormalities, including submucosal cleft palate. In addition, cor triatriatum sinister and hearing loss, identified in a proportion of Hyal2-/- mice, were also found as incompletely penetrant features in affected humans. Taken together our findings identify a new genetic cause of orofacial clefting in humans and mice, and define the first molecular cause of human cor triatriatum sinister, illustrating the fundamental importance of HYAL2 and hyaluronan turnover for normal human and mouse development.
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Affiliation(s)
| | - Biswajit Chowdhury
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - S. Naimul Hasan
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Harold E. Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
| | - Brian Mark
- Department of Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Gaurav V. Harlalka
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, United Kingdom
| | - Michael A. Patton
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, United Kingdom
- Genetics Research Centre, St George’s University London, London, United Kingdom
| | - Miho Ishida
- Genetics and Genomic Medicine, UCL Institute of Child Health, London, United Kingdom
| | - Elijah R. Behr
- Cardiovascular Sciences Research Centre, St George's University of London, London, United Kingdom
| | - Sanjay Sharma
- Cardiovascular Sciences Research Centre, St George's University of London, London, United Kingdom
| | - Kenneth Zahka
- Pediatric Cardiology, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Eissa Faqeih
- Department of Pediatric Subspecialties, Children’s Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Brian Blakley
- Department of Otolaryngology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mike Jackson
- Department of Small Animal and Materials Imaging Facility, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Melissa Lees
- Department of Clinical Genetics, Great Ormond Street Hospital, London, United Kingdom
| | - Vernon Dolinsky
- Pharmacology & Therapeutics, University of Manitoba, Winnipeg, Manitoba, Canada
- Pediatrics & Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Leroy Cross
- Windows of Hope Genetic Information Centre, Holmes County, Ohio, United States of America
| | - Philip Stanier
- Genetics and Genomic Medicine, UCL Institute of Child Health, London, United Kingdom
| | - Claire Salter
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Emma L. Baple
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, United Kingdom
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Andrew H. Crosby
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, United Kingdom
- * E-mail: (AHC); (BTR)
| | - Barbara Triggs-Raine
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Pediatrics & Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
- Manitoba Institute of Child Health, Winnipeg, Manitoba, Canada
- * E-mail: (AHC); (BTR)
| | - Barry A. Chioza
- RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, United Kingdom
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23
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Intellectual Disability & Rare Disorders: A Diagnostic Challenge. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1031:39-54. [PMID: 29214565 DOI: 10.1007/978-3-319-67144-4_3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rare disorders constitute a large and heterogeneous group of diagnoses of which many cause chronic disabilities with significant impact on the lives of affected individuals and their families as well as on the health-care system. Each individual disorder is rare, but when considered as a group, rare disorders are common with a total prevalence of approximately 6-8%. The clinical presentation of these disorders includes a broad diversity of symptoms and signs, often involving the nervous system and resulting in symptoms such as intellectual disability, neuropsychiatric disorders, epilepsy and motor dysfunction. The methods for establishing an etiological diagnosis in patients with rare disorders have improved dramatically during recent years. With the introduction of genomic screening methods, it has been shown that the cause is genetic in the majority of the patients and many will receive an etiological diagnosis in a clinical setting. However, there are a lot of challenges in diagnosing these disorders and despite recent years' advances, a large number of patients with rare disorders still go without an etiological diagnosis. In this chapter we will review the etiology of rare disorders with focus on intellectual disability and what has been learned from massive parallel sequencing studies in deciphering the genetic basis. Furthermore, we will discuss challenges in the etiological diagnostics of these disorders including issues that regard interpretation of the numerous genetic variants detected by genomic screening methods and challenges in the translation of massive parallel sequencing technologies into clinical practice.
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24
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Jia ZL, He S, Jiang SY, Zhang BH, Duan SJ, Shi JY, Huang N, Zhu WC, Shi B. Rs12941170 at SOX9 gene associated with orofacial clefts in Chinese. Arch Oral Biol 2016; 76:14-19. [PMID: 28068523 DOI: 10.1016/j.archoralbio.2016.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 10/20/2016] [Accepted: 12/27/2016] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Non-syndromic orofacial cleftings (NSOCs) are considered as complex trait, which results from genetic and/or environmental modifiers. Current findings could only explain small portion of the NSOCs. SOX9 gene plays an important role during craniofacial development in animal models and the Pierre Robin sequence (PRS). However, its role in non-syndromic clefts remains unknown. DESIGN In this study, we selected eight SNPs in and around SOX9 gene to make maximum coverage, and genotyped them by using RFLP-PCR and ligase detection reaction (LDR) methods to test its associations among 151 NSOCs (53 NSCLP, 52 NSCLO and 46 NSCPO) from Western Han Chinese population. RESULTS Allelic TDT results showed that G allele at rs12941170 of SOX9 was under-transmitted among NSOCs (p=0.00014, OR=0.55 and 95%CI: 0.40-0.75), which could indicate that the G allele is protective against NSOCs; parent-of-origin effect analysis showed that G allele at rs12941170 was maternally under-transmitted (p=0.002), while there was no statistically difference between the maternal and paternal transmission of it. To test if the adjacent SNPs travel together from parents to the affected individual, we carried out the sliding window haplotype analysis, it is interesting to find that the haplotypes carrying the G allele at rs12941170 also was under-transmitted for NSOCs, NSCL/P, NSCLP and NSCPO (lowest p=0.00033). CONCLUSIONS This study suggested that G allele at rs12941170 was protective, which could decrease the risk for NSOCs from Western Han Chinese population, and it will provide new reference for future research and genetic counseling in NSOCs.
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Affiliation(s)
- Zhong-Lin Jia
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China
| | - Sha He
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China; Department of Stomatology, The third People's hospital of Chengdu, Chengdu, PR China
| | - Shu-Yuan Jiang
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Bi-He Zhang
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Shi-Jun Duan
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Jia-Yu Shi
- Division of Growth and Development and Section of Orthodontics, School of Dentistry, University of California, Los Angeles, CA 90095, United States
| | - Ning Huang
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Wen-Chao Zhu
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China
| | - Bing Shi
- State Key Laboratory of Oral Disease, West China hospital of Stomatology, Sichuan University, Chengdu, PR China; Department of Cleft Lip and Palate Surgery, West China College of Stomatology, Sichuan University, Chengdu, PR China.
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25
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Zarate YA, Fish JL. SATB2-associated syndrome: Mechanisms, phenotype, and practical recommendations. Am J Med Genet A 2016; 173:327-337. [PMID: 27774744 PMCID: PMC5297989 DOI: 10.1002/ajmg.a.38022] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/29/2016] [Indexed: 12/11/2022]
Abstract
The SATB2‐associated syndrome is a recently described syndrome characterized by developmental delay/intellectual disability with absent or limited speech development, craniofacial abnormalities, behavioral problems, dysmorphic features, and palatal and dental abnormalities. Alterations of the SATB2 gene can result from a variety of different mechanisms that include contiguous deletions, intragenic deletions and duplications, translocations with secondary gene disruption, and point mutations. The multisystemic nature of this syndrome demands a multisystemic approach and we propose evaluation and management guidelines. The SATB2‐associated syndrome registry has now been started and that will allow gathering further clinical information and refining the provided surveillance recommendations. © 2016 The Authors. American Journal of Medical Genetics Part A Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Jennifer L Fish
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts
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Tooth agenesis and orofacial clefting: genetic brothers in arms? Hum Genet 2016; 135:1299-1327. [PMID: 27699475 PMCID: PMC5065589 DOI: 10.1007/s00439-016-1733-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/21/2016] [Indexed: 12/16/2022]
Abstract
Tooth agenesis and orofacial clefts represent the most common developmental anomalies and their co-occurrence is often reported in patients as well in animal models. The aim of the present systematic review is to thoroughly investigate the current literature (PubMed, EMBASE) to identify the genes and genomic loci contributing to syndromic or non-syndromic co-occurrence of tooth agenesis and orofacial clefts, to gain insight into the molecular mechanisms underlying their dual involvement in the development of teeth and facial primordia. Altogether, 84 articles including phenotype and genotype description provided 9 genomic loci and 26 gene candidates underlying the co-occurrence of the two congenital defects: MSX1, PAX9, IRF6, TP63, KMT2D, KDM6A, SATB2, TBX22, TGFα, TGFβ3, TGFβR1, TGFβR2, FGF8, FGFR1, KISS1R, WNT3, WNT5A, CDH1, CHD7, AXIN2, TWIST1, BCOR, OFD1, PTCH1, PITX2, and PVRL1. The molecular pathways, cellular functions, tissue-specific expression and disease association were investigated using publicly accessible databases (EntrezGene, UniProt, OMIM). The Gene Ontology terms of the biological processes mediated by the candidate genes were used to cluster them using the GOTermMapper (Lewis-Sigler Institute, Princeton University), speculating on six super-clusters: (a) anatomical development, (b) cell division, growth and motility, (c) cell metabolism and catabolism, (d) cell transport, (e) cell structure organization and (f) organ/system-specific processes. This review aims to increase the knowledge on the mechanisms underlying the co-occurrence of tooth agenesis and orofacial clefts, to pave the way for improving targeted (prenatal) molecular diagnosis and finally to reflect on therapeutic or ultimately preventive strategies for these disabling conditions in the future.
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27
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Basart H, van Oers HA, Paes EC, Breugem CC, Don Griot JPW, van der Horst CMAM, Haverman L, Hennekam RC. Health-related quality of life in children with Robin sequence. Am J Med Genet A 2016; 173:54-61. [DOI: 10.1002/ajmg.a.37968] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 08/12/2016] [Indexed: 02/01/2023]
Affiliation(s)
- Hanneke Basart
- Department of Pediatrics, Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
- Department of Plastic and Reconstructive Surgery, Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Hedy A. van Oers
- Psychosocial Department, Emma Children's Hospital, Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Emma C. Paes
- Department of Plastic and Reconstructive Surgery; Wilhelmina Pediatric Hospital; Utrecht The Netherlands
| | - Corstiaan C. Breugem
- Department of Plastic and Reconstructive Surgery; Wilhelmina Pediatric Hospital; Utrecht The Netherlands
| | - J. Peter W. Don Griot
- Department of Plastic and Reconstructive Surgery, VU Medical Center; Free University; Amsterdam The Netherlands
| | - Chantal M. A. M. van der Horst
- Department of Plastic and Reconstructive Surgery, Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Lotte Haverman
- Psychosocial Department, Emma Children's Hospital, Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
| | - Raoul C. Hennekam
- Department of Pediatrics, Academic Medical Center; University of Amsterdam; Amsterdam The Netherlands
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28
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Gomez-Ospina N, Bernstein JA. Clinical, cytogenetic, and molecular outcomes in a series of 66 patients with Pierre Robin sequence and literature review: 22q11.2 deletion is less common than other chromosomal anomalies. Am J Med Genet A 2016; 170A:870-80. [PMID: 26756138 DOI: 10.1002/ajmg.a.37538] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 12/17/2015] [Indexed: 01/01/2023]
Abstract
Pierre Robin sequence (PRS) is an important craniofacial anomaly that can be seen as an isolated finding or manifestation of multiple syndromes. 22q11.2 deletion and Stickler syndrome are cited as the two most common conditions associated with PRS, but their frequencies are debated. We performed a retrospective study of 66 patients with PRS and reviewed their genetic testing, diagnoses, and clinical findings. The case series is complemented by a comprehensive literature review of the nature and frequency of genetic diagnosis in PRS. In our cohort 65% of patients had associated anomalies; of these, a genetic diagnosis was established in 56%. Stickler syndrome was the most common diagnosis, comprising approximately 11% of all cases, followed by Treacher Collins syndrome (9%). The frequency of 22q11.2 deletion was 1.5%. Chromosome arrays, performed for 72% of idiopathic PRS with associated anomalies, revealed two cases of 18q22→qter deletion, a region not previously reported in association with PRS. A review of the cytogenetic anomalies identified in this population supports an association between the 4q33-qter, 17q24.3, 2q33.1, and 11q23 chromosomal loci and PRS. We found a low frequency of 22q11.2 deletion in PRS, suggesting it is less commonly implicated in this malformation. Our data also indicate a higher frequency of cytogenetic anomalies in PRS patients with associated anomalies, and a potential new link with the 18q22→qter locus. The present findings underscore the utility of chromosomal microarrays in cases of PRS with associated anomalies and suggest that delaying testing for apparently isolated cases should be considered.
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Zarate YA, Perry H, Ben-Omran T, Sellars EA, Stein Q, Almureikhi M, Simmons K, Klein O, Fish J, Feingold M, Douglas J, Kruer MC, Si Y, Mao R, McKnight D, Gibellini F, Retterer K, Slavotinek A. Further supporting evidence for the SATB2-associated syndrome found through whole exome sequencing. Am J Med Genet A 2016; 167A:1026-32. [PMID: 25885067 DOI: 10.1002/ajmg.a.36849] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 09/27/2014] [Indexed: 12/16/2022]
Abstract
The SATB2-associated syndrome (SAS) was recently proposed as a clinically recognizable syndrome that results from deleterious alterations of the SATB2 gene in humans. Although interstitial deletions at 2q33 encompassing SATB2, either alone or contiguously with other genes, have been reported before, there is limited literature regarding intragenic mutations of this gene and the resulting phenotype. We describe five patients in whom whole exome sequencing identified five unique de novo mutations in the SATB2 gene (one splice site, one frameshift, and three nonsense mutations). The five patients had overlapping features that support the characteristic features of the SAS: intellectual disability with limited speech development and craniofacial abnormalities including cleft palate, dysmorphic features, and dental abnormalities. Furthermore, Patient 1 also had features not previously described that represent an expansion of the phenotype. Osteopenia was seen in two of the patients, suggesting that this finding could be added to the list of distinctive findings. We provide supporting evidence that analysis for deletions or point mutations in SATB2 should be considered in children with intellectual disability and severely impaired speech, cleft or high palate, teeth abnormalities, and osteopenia.
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Affiliation(s)
- Yuri A Zarate
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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Fish JL. Developmental mechanisms underlying variation in craniofacial disease and evolution. Dev Biol 2015; 415:188-197. [PMID: 26724698 DOI: 10.1016/j.ydbio.2015.12.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/17/2015] [Accepted: 12/21/2015] [Indexed: 01/14/2023]
Abstract
Craniofacial disease phenotypes exhibit significant variation in penetrance and severity. Although many genetic contributions to phenotypic variation have been identified, genotype-phenotype correlations remain imprecise. Recent work in evolutionary developmental biology has exposed intriguing developmental mechanisms that potentially explain incongruities in genotype-phenotype relationships. This review focuses on two observations from work in comparative and experimental animal model systems that highlight how development structures variation. First, multiple genetic inputs converge on relatively few developmental processes. Investigation of when and how variation in developmental processes occurs may therefore help predict potential genetic interactions and phenotypic outcomes. Second, genetic mutation is typically associated with an increase in phenotypic variance. Several models outlining developmental mechanisms underlying mutational increases in phenotypic variance are discussed using Satb2-mediated variation in jaw size as an example. These data highlight development as a critical mediator of genotype-phenotype correlations. Future research in evolutionary developmental biology focusing on tissue-level processes may help elucidate the "black box" between genotype and phenotype, potentially leading to novel treatment, earlier diagnoses, and better clinical consultations for individuals affected by craniofacial anomalies.
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Affiliation(s)
- Jennifer L Fish
- University of Massachusetts Lowell, Department of Biological Sciences, 198 Riverside Street, Olsen Hall, Room 619, Lowell, MA 01854, United States.
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31
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Benabdallah NS, Bickmore WA. Regulatory Domains and Their Mechanisms. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:45-51. [PMID: 26590168 DOI: 10.1101/sqb.2015.80.027268] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The concept of gene regulation is being refined as our understanding of the role of enhancer elements grows. Although described more than 30 years ago, the mechanisms through which these cis-regulating elements operate remain under debate. With the recognition that most of the human genetic variation contributing to common disease risk lies outside of genes and probably in enhancers, unraveling these mechanisms becomes ever more important. Originally, a popular view was to consider regulatory elements as an entry site for the transcription machinery that could scan the intervening chromatin until the cognate core promoter was located. Now, the most prominent model for distal enhancer-promoter interaction involves direct enhancer/promoter contacts with a looping out of intervening chromatin. However, a rising awareness of the importance of chromatin architecture and organization forces us to consider enhancer-promoter communication in light of the polymer folding properties of chromatin. Here, we discuss how three-dimensional chromatin folding, topological domains, and the constrained motion, plasticity, and accessibility of chromatin could offer a structural basis for regulatory domains that greatly enhances the probability of enhancer-promoter and transcription factor-promoter interactions and gene activation.
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Affiliation(s)
- Nezha S Benabdallah
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH42XU, United Kingdom Edinburgh Super Resolution Imaging Consortium, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH42XU, United Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH42XU, United Kingdom
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Conte F, Oti M, Dixon J, Carels CEL, Rubini M, Zhou H. Systematic analysis of copy number variants of a large cohort of orofacial cleft patients identifies candidate genes for orofacial clefts. Hum Genet 2015; 135:41-59. [PMID: 26561393 PMCID: PMC4698300 DOI: 10.1007/s00439-015-1606-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/15/2015] [Indexed: 12/16/2022]
Abstract
Orofacial clefts (OFCs) represent a large fraction of human birth defects and are one of the most common phenotypes affected by large copy number variants (CNVs). Due to the limited number of CNV patients in individual centers, CNV analyses of a large number of OFC patients are challenging. The present study analyzed 249 genomic deletions and 226 duplications from a cohort of 312 OFC patients reported in two publicly accessible databases of chromosome imbalance and phenotype in humans, DECIPHER and ECARUCA. Genomic regions deleted or duplicated in multiple patients were identified, and genes in these overlapping CNVs were prioritized based on the number of genes encompassed by the region and gene expression in embryonic mouse palate. Our analyses of these overlapping CNVs identified two genes known to be causative for human OFCs, SATB2 and MEIS2, and 12 genes (DGCR6, FGF2, FRZB, LETM1, MAPK3, SPRY1, THBS1, TSHZ1, TTC28, TULP4, WHSC1, WHSC2) that are associated with OFC or orofacial development. Additionally, we report 34 deleted and 24 duplicated genes that have not previously been associated with OFCs but are associated with the BMP, MAPK and RAC1 pathways. Statistical analyses show that the high number of overlapping CNVs is not due to random occurrence. The identified genes are not located in highly variable genomic regions in healthy populations and are significantly enriched for genes that are involved in orofacial development. In summary, we report a CNV analysis pipeline of a large cohort of OFC patients and identify novel candidate OFC genes.
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Affiliation(s)
- Federica Conte
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands.,Medical Genetic Unit, Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Martin Oti
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands
| | - Jill Dixon
- Faculty of Medical and Human Sciences, University of Manchester, Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Carine E L Carels
- Department of Orthodontics and Craniofacial Biology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michele Rubini
- Medical Genetic Unit, Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy.
| | - Huiqing Zhou
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, The Netherlands. .,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Welsh IC, Kwak H, Chen FL, Werner M, Shopland LS, Danko CG, Lis JT, Zhang M, Martin JF, Kurpios NA. Chromatin Architecture of the Pitx2 Locus Requires CTCF- and Pitx2-Dependent Asymmetry that Mirrors Embryonic Gut Laterality. Cell Rep 2015; 13:337-49. [PMID: 26411685 PMCID: PMC4617833 DOI: 10.1016/j.celrep.2015.08.075] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/20/2015] [Accepted: 08/24/2015] [Indexed: 11/24/2022] Open
Abstract
Expression of Pitx2 on the left side of the embryo patterns left-right (LR) organs including the dorsal mesentery (DM), whose asymmetric cell behavior directs gut looping. Despite the importance of organ laterality, chromatin-level regulation of Pitx2 remains undefined. Here, we show that genes immediately neighboring Pitx2 in chicken and mouse, including a long noncoding RNA (Pitx2 locus-asymmetric regulated RNA or Playrr), are expressed on the right side and repressed by Pitx2. CRISPR/Cas9 genome editing of Playrr, 3D fluorescent in situ hybridization (FISH), and variations of chromatin conformation capture (3C) demonstrate that mutual antagonism between Pitx2 and Playrr is coordinated by asymmetric chromatin interactions dependent on Pitx2 and CTCF. We demonstrate that transcriptional and morphological asymmetries driving gut looping are mirrored by chromatin architectural asymmetries at the Pitx2 locus. We propose a model whereby Pitx2 auto-regulation directs chromatin topology to coordinate LR transcription of this locus essential for LR organogenesis.
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Affiliation(s)
- Ian C Welsh
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Frances L Chen
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Melissa Werner
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Lindsay S Shopland
- The Jackson Laboratory, Bar Harbor, ME, 04609, USA; Eastern Maine Medical Center Cancer Care, 33 Whiting Hill Road, Brewer, ME 04412, USA
| | - Charles G Danko
- Department of Biomedical Sciences, The Baker Institute for Animal Health, Cornell University, Ithaca, NY 14853, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Min Zhang
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA; Texas Heart Institute, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Natasza A Kurpios
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA.
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Abstract
The formation of the face and skull involves a complex series of developmental events mediated by cells derived from the neural crest, endoderm, mesoderm, and ectoderm. Although vertebrates boast an enormous diversity of adult facial morphologies, the fundamental signaling pathways and cellular events that sculpt the nascent craniofacial skeleton in the embryo have proven to be highly conserved from fish to man. The zebrafish Danio rerio, a small freshwater cyprinid fish from eastern India, has served as a popular model of craniofacial development since the 1990s. Unique strengths of the zebrafish model include a simplified skeleton during larval stages, access to rapidly developing embryos for live imaging, and amenability to transgenesis and complex genetics. In this chapter, we describe the anatomy of the zebrafish craniofacial skeleton; its applications as models for the mammalian jaw, middle ear, palate, and cranial sutures; the superior imaging technology available in fish that has provided unprecedented insights into the dynamics of facial morphogenesis; the use of the zebrafish to decipher the genetic underpinnings of craniofacial biology; and finally a glimpse into the most promising future applications of zebrafish craniofacial research.
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Basart H, Paes EC, Maas SM, van den Boogaard MJH, van Hagen JM, Breugem CC, Cobben JM, Don Griot JPW, Lachmeijer AMA, Lichtenbelt KD, van Nunen DPF, van der Horst CM, Hennekam RC. Etiology and pathogenesis of robin sequence in a large Dutch cohort. Am J Med Genet A 2015; 167A:1983-92. [DOI: 10.1002/ajmg.a.37154] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/05/2015] [Indexed: 11/05/2022]
Affiliation(s)
- Hanneke Basart
- Department of Pediatrics; Academic Medical Center; University of Amsterdam; Amsterdam Netherlands
- Department of Plastic and Reconstructive Surgery; Academic Medical Center; University of Amsterdam; Amsterdam Netherlands
| | - Emma C. Paes
- Department of Plastic; Reconstructive and Hand Surgery; University Medical Center Utrecht/ Wilhelmina Children's Hospital; Utrecht Netherlands
| | - Saskia M. Maas
- Department of Pediatrics; Academic Medical Center; University of Amsterdam; Amsterdam Netherlands
| | | | | | - Corstiaan C. Breugem
- Department of Plastic; Reconstructive and Hand Surgery; University Medical Center Utrecht/ Wilhelmina Children's Hospital; Utrecht Netherlands
| | - Jan Maarten Cobben
- Department of Pediatrics; Academic Medical Center; University of Amsterdam; Amsterdam Netherlands
| | - J. Peter W. Don Griot
- Department of Plastic; Reconstructive and Hand Surgery; VU Medical Center; Amsterdam Netherlands
| | | | - Klaske D. Lichtenbelt
- Department of Clinical Genetics; Utrecht Medical Center/Wilhelmina Children's Hospital; Utrecht Netherlands
| | - Daan P. F. van Nunen
- Department of Plastic; Reconstructive and Hand Surgery; University Medical Center Utrecht/ Wilhelmina Children's Hospital; Utrecht Netherlands
| | - Chantal M. van der Horst
- Department of Plastic and Reconstructive Surgery; Academic Medical Center; University of Amsterdam; Amsterdam Netherlands
| | - Raoul C. Hennekam
- Department of Pediatrics; Academic Medical Center; University of Amsterdam; Amsterdam Netherlands
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Papoulidis I, Paspaliaris V, Papageorgiou E, Siomou E, Dagklis T, Sotiriou S, Thomaidis L, Manolakos E. Deletion of 4.4 Mb at 2q33.2q33.3 May Cause Growth Deficiency in a Patient with Mental Retardation, Facial Dysmorphic Features and Speech Delay. Cytogenet Genome Res 2015; 145:19-24. [PMID: 25925190 DOI: 10.1159/000381568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2015] [Indexed: 11/19/2022] Open
Abstract
A patient with a rare interstitial deletion of chromosomal band 2q33.2q33.3 is described. The clinical features resembled the 2q33.1 microdeletion syndrome (Glass syndrome), including mental retardation, facial dysmorphism, high-arched narrow palate, growth deficiency, and speech delay. The chromosomal aberration was characterized by whole genome BAC aCGH. A comparison of the current patient and Glass syndrome features revealed that this case displayed a relatively mild phenotype. Overall, it is suggested that the deleted region of 2q33 causative for Glass syndrome may be larger than initially suggested.
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Affiliation(s)
- Ioannis Papoulidis
- Access To Genome - ATG P.C., Clinical Laboratory Genetics, Thessaloniki, Greece
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37
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A prenatally ascertained de novo terminal deletion of chromosomal bands 1q43q44 associated with multiple congenital abnormalities in a female fetus. Case Rep Genet 2015; 2015:517678. [PMID: 25722899 PMCID: PMC4334433 DOI: 10.1155/2015/517678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/22/2014] [Accepted: 01/13/2015] [Indexed: 11/17/2022] Open
Abstract
Terminal deletions in the long arm of chromosome 1 result in a postnatally recognizable disorder described as 1q43q44 deletion syndrome. The size of the deletions and the resulting phenotype varies among patients. However, some features are common among patients as the chromosomal regions included in the deletions. In the present case, ultrasonography at 22 weeks of gestation revealed choroid plexus cysts (CPCs) and a single umbilical artery (SUA) and therefore amniocentesis was performed. Chromosomal analysis revealed a possible terminal deletion in 1q and high resolution array CGH confirmed the terminal 1q43q44 deletion and estimated the size to be approximately 8 Mb. Following termination of pregnancy, performance of fetopsy allowed further clinical characterization. We report here a prenatal case with the smallest pure terminal 1q43q44 deletion, that has been molecularly and phenotypically characterized. In addition, to our knowledge this is the first prenatal case reported with 1q13q44 terminal deletion and Pierre-Robin sequence (PRS). Our findings combined with review data from the literature show the complexity of the genetic basis of the associated syndrome.
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38
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Price KE, Haddad Y, Fakhouri WD. Analysis of the Relationship Between Micrognathia and Cleft Palate: A Systematic Review. Cleft Palate Craniofac J 2015; 53:e34-44. [PMID: 25658963 DOI: 10.1597/14-238] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Objective To gather data from relevant experimental and observational studies to determine the relationship between micrognathia and cleft palate. The goal is to raise awareness and motivate clinicians to consider the cause and effect relationship when confronted with patients with cleft palate, even if there is no clearly noticeable mandibular abnormality. Design Several electronic databases were systematically examined to find articles for this review, using search terms including "cleft palate," "micrognathia," "tongue," and "airway obstruction." PubMed was the source of all the articles chosen to be included. Exclusion criteria included case reports, articles focused on treatment options, and articles only tangentially related to cleft palate and/or micrognathia. Results A total of 930 articles were screened for relevance, and 82 articles were chosen for further analysis. Evidence gathered in this review includes a variety of etiological factors that are causative or associated with both micrognathia and cleft palate. Observational studies relating the two abnormalities are also included. Much of the included literature recognizes a cause-and-effect relationship between micrognathia and cleft palate. Conclusion On the basis of the published data, we suggest that micrognathia does induce cleft palate in humans and animals. With knowledge of this causative relationship, clinicians should consider the importance of gathering cephalometric data on the mandibles and tongues of patients presenting with isolated cleft palate to determine whether they have micrognathia as well. With more data, patterns may emerge that could give insight into the complex etiology of nonsyndromic cleft palate.
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Schilders K, Ochieng JK, van de Ven CP, Gontan C, Tibboel D, Rottier RJ. Role of SOX2 in foregut development in relation to congenital abnormalities. World J Med Genet 2014; 4:94-104. [DOI: 10.5496/wjmg.v4.i4.94] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/14/2014] [Accepted: 09/10/2014] [Indexed: 02/06/2023] Open
Abstract
The uptake of the two essential ingredients for life, oxygen and nutrients, occurs primarily through the oral cavity, but these two lifelines need to be separated with high accuracy once inside the body. The two systems, the gas exchange pulmonary system and the gastro-intestinal feeding system, are derived from the same primitive embryonic structure during development, the foregut, which need to be separated before birth. In certain newborns, this separation occurs not or insufficiently, leading to life threatening conditions, sometimes incompatible with life. The development of the foregut, trachea and lungs is influenced and coordinated by a multitude of signaling cascades and transcription factors. In this review, we will highlight the development of the foregut and pulmonary system and focus on associated congenital abnormalities in light of known genetic alterations with specific attention to the transcription factor SOX2.
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Liedén A, Kvarnung M, Nilssson D, Sahlin E, Lundberg ES. Intragenic duplication--a novel causative mechanism for SATB2-associated syndrome. Am J Med Genet A 2014; 164A:3083-7. [PMID: 25251319 DOI: 10.1002/ajmg.a.36769] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 08/01/2014] [Indexed: 12/15/2022]
Abstract
Previous studies have shown that genetic aberrations involving the special AT-rich sequence-binding protein 2 (SATB2) gene result in a variable phenotype of syndromic intellectual disability. Although only a small number of patients have been described, there is already considerable variation in regard to the underlying molecular mechanism spanning from structural variation to point mutations. We here describe a male patient with intellectual disability, speech and language impairment, cleft palate, malformed teeth, and oligodontia. Array CGH analysis identified a small intragenic duplication in the SATB2 gene that included three coding exons. The result was confirmed by multiplex ligation-dependent probe amplification and low coverage whole genome mate pair sequencing. WGS breakpoint analysis directly confirmed the duplication as intragenic. This is the first reported patient with an intragenic duplication in SATB2 in combination with a phenotype that is highly similar to previously described patients with small deletions or point mutations of the same gene. Our findings expand the spectra of SATB2 mutations and confirm the presence of a distinct SATB2-phenotype with severe ID and speech impairment, cleft palate and/or high arched palate, and abnormalities of the teeth. For patients that present with this clinical picture, a high-resolution exon targeted array CGH and/or WGS, in addition to sequencing of SATB2, should be considered.
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Affiliation(s)
- Agne Liedén
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Martinez N, Vallerskog T, West K, Nunes-Alves C, Lee J, Martens GW, Behar SM, Kornfeld H. Chromatin decondensation and T cell hyperresponsiveness in diabetes-associated hyperglycemia. THE JOURNAL OF IMMUNOLOGY 2014; 193:4457-68. [PMID: 25246495 DOI: 10.4049/jimmunol.1401125] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Diabetes is linked to increased inflammation and susceptibility to certain infectious diseases including tuberculosis (TB). We previously reported that aerosol TB in mice with chronic (≥ 12 wk) hyperglycemia features increased bacterial load, overproduction of several cytokines, and increased immune pathology compared with normoglycemic controls. A similar phenotype exists in human patients with diabetes with TB. The mechanisms of increased T cell activation in diabetes are unknown. In the current study, we tested the hypothesis that hyperglycemia modifies the intrinsic responsiveness of naive T cells to TCR stimulation. Purified T cells from chronically hyperglycemic (HG) mice produced higher levels of Th1, Th2, and Th17 cytokines and proliferated more than T cells from normoglycemic controls after anti-CD3e or Ag stimulation. In this way, naive T cells from HG mice resembled Ag-experienced cells, although CD44 expression was not increased. Chromatin decondensation, another characteristic of Ag-experienced T cells, was increased in naive T cells from HG mice. That phenotype depended on expression of the receptor for advanced glycation end products and could be reversed by inhibiting p38 MAPK. Chromatin decondensation and hyperresponsiveness to TCR stimulation persisted following transfer of T cells from HG mice into normoglycemic mice. We propose that chronic hyperglycemia causes receptor for advanced glycation end products-mediated epigenetic modification of naive T cells leading to p38 MAPK-dependent chromatin decondensation. This preactivation state facilitates transcription factor access to DNA, increasing cytokine production and proliferation following TCR stimulation. This mechanism may contribute to pathological inflammation associated with diabetes and might offer a novel therapeutic target.
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Affiliation(s)
- Nuria Martinez
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Therese Vallerskog
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Kim West
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Claudio Nunes-Alves
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655
| | - Jinhee Lee
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Gregory W Martens
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655; and
| | - Samuel M Behar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655
| | - Hardy Kornfeld
- Department of Medicine, University of Massachusetts Medical School, Worcester, MA 01655; and
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Ansari M, Rainger JK, Murray JE, Hanson I, Firth HV, Mehendale F, Amiel J, Gordon CT, Percesepe A, Mazzanti L, Fryer A, Ferrari P, Devriendt K, Temple IK, FitzPatrick DR. A syndromic form of Pierre Robin sequence is caused by 5q23 deletions encompassing FBN2 and PHAX. Eur J Med Genet 2014; 57:587-95. [PMID: 25195018 DOI: 10.1016/j.ejmg.2014.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/22/2014] [Indexed: 12/19/2022]
Abstract
Pierre Robin sequence (PRS) is an aetiologically distinct subgroup of cleft palate. We aimed to define the critical genomic interval from five different 5q22-5q31 deletions associated with PRS or PRS-associated features and assess each gene within the region as a candidate for the PRS component of the phenotype. Clinical array-based comparative genome hybridisation (aCGH) data were used to define a 2.08 Mb minimum region of overlap among four de novo deletions and one mother-son inherited deletion associated with at least one component of PRS. Commonly associated anomalies were talipes equinovarus (TEV), finger contractures and crumpled ear helices. Expression analysis of the orthologous genes within the PRS critical region in embryonic mice showed that the strongest candidate genes were FBN2 and PHAX. Targeted aCGH of the critical region and sequencing of these genes in a cohort of 25 PRS patients revealed no plausible disease-causing mutations. In conclusion, deletion of ∼2 Mb on 5q23 region causes a clinically recognisable subtype of PRS. Haploinsufficiency for FBN2 accounts for the digital and auricular features. A possible critical region for TEV is distinct and telomeric to the PRS region. The molecular basis of PRS in these cases remains undetermined but haploinsufficiency for PHAX is a plausible mechanism.
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Affiliation(s)
- Morad Ansari
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jacqueline K Rainger
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jennie E Murray
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; Southeast Scotland Clinical Genetics Services, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Isabel Hanson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Helen V Firth
- DECIPHER, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Felicity Mehendale
- Cleft Lip and Palate Service, Royal Hospital for Sick Children, Edinburgh EH9 1LF, UK
| | - Jeanne Amiel
- INSERM U-1163 Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Christopher T Gordon
- INSERM U-1163 Institut Imagine, Université Paris Descartes-Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, APHP, Paris, France
| | - Antonio Percesepe
- Departments of Medical Genetics and Pediatrics, University Hospital of Modena, Italy
| | | | - Alan Fryer
- Department of Clinical Genetics, Alder Hey Children's Hospital, Liverpool L12 2AP, UK
| | - Paola Ferrari
- Departments of Medical Genetics and Pediatrics, University Hospital of Modena, Italy
| | | | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton and Wessex Clinical Genetics Service, University Hospital NHS Trust, Princess Anne Hospital, Coxford Road, Southampton SO16 5YA, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK; Southeast Scotland Clinical Genetics Services, Western General Hospital, Edinburgh EH4 2XU, UK.
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Kaiser AS, Maas B, Wolff A, Sutter C, Janssen JWG, Hinderhofer K, Moog U. Characterization of the first intragenic SATB2 duplication in a girl with intellectual disability, nearly absent speech and suspected hypodontia. Eur J Hum Genet 2014; 23:704-7. [PMID: 25118029 DOI: 10.1038/ejhg.2014.163] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 12/25/2022] Open
Abstract
SATB2, a gene encoding a highly conserved DNA-binding protein, is known to have an important role in craniofacial and neuronal development. Only a few patients with SATB2 variants have been described so far. Recently, Döcker et al provided a summary of these patients and delineated the SAS (SATB2-associated syndrome). We here report on a girl with intellectual disability, nearly absent speech and suspected hypodontia who was shown to carry an intragenic SATB2 tandem duplication hypothesized to lead to haploinsufficiency of SATB2. Preliminary information on this patient had already been included in the article by Döcker et al. We want to give a detailed description of the patient's phenotype and genotype, providing further insight into the spectrum of the molecular mechanisms leading to SAS.
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Affiliation(s)
- Ann-Sophie Kaiser
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Bianca Maas
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Anna Wolff
- Department of Conservative Dentistry, Heidelberg University, Heidelberg, Germany
| | - Christian Sutter
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | | | | | - Ute Moog
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
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Genetics of cleft lip and/or cleft palate: Association with other common anomalies. Eur J Med Genet 2014; 57:381-93. [DOI: 10.1016/j.ejmg.2014.04.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/03/2014] [Indexed: 12/16/2022]
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Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
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