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Li RM, Lu YC, Li Z, Wang JY, Chang J, Lei SQ, Zeng Q, Sang YM. [Floating-Harbor syndrome: a case report and literature review]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2019; 21:1208-1211. [PMID: 31874661 PMCID: PMC7389003 DOI: 10.7499/j.issn.1008-8830.2019.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/06/2019] [Indexed: 06/10/2023]
Abstract
Floating-Harbor syndrome (FHS) is an autosomal dominant genetic disease caused by SRCAP mutation. This article reports the clinical features of a boy with FHS. The boy, aged 11 years and 7 months, attended the hospital due to short stature for more than 8 years and had the clinical manifestations of unusual facial features (triangularly shaped face, thin lips and long eyelashes), skeletal dysplasia (curvature finger), expressive language disorder, and retardation of bone age. Genetic detection revealed a novel heterozygous mutation, c.7330 C>T(p.R2444X), in the SRCAP gene. The boy was diagnosed with FHS based on these clinical manifestations and gene detection results. FHS is rare in clinical practice, which may lead to missed diagnosis and misdiagnosis, and gene detection may help with the clinical diagnosis of FHS in children.
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Affiliation(s)
- Rong-Min Li
- Baoding Key Laboratory of Clinical Research on Children's Respiratory and Digestive Diseases/Baoding Children's Hospital, Baoding, Hebei 071000.
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52
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Schmidt J, Wollnik B. Hallermann-Streiff syndrome: A missing molecular link for a highly recognizable syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 178:398-406. [PMID: 30580479 DOI: 10.1002/ajmg.c.31668] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/23/2018] [Accepted: 10/29/2018] [Indexed: 12/31/2022]
Abstract
The use of modern next-generation sequencing-based approaches for gene identification has tremendously improved our understanding of the molecular pathogenesis of the great majority of well-known syndromes, whereas only a few remain to be elucidated. Hallermann-Streiff syndrome is such a disorder for which the molecular basis is still unknown although it represents a highly recognizable phenotype. Clinically, patients with Hallermann-Streiff syndrome show typical craniofacial dysmorphism, eye malformations, a distinctive facial appearance, abnormalities of hair and skin, short stature, and, interestingly, they might also present with aspects of premature aging. The clinical diagnosis is mainly given by the very typical facial gestalt of patients. In this review, we (a) summarize the current knowledge on the phenotypic traits, focusing on described classic cases, (b) discuss the missing molecular link, and (c) present innovative future strategies for gene identification.
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Affiliation(s)
- Julia Schmidt
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
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53
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Intracranial vascular pathology in two further patients with Floating-Harbor syndrome: Proposals for cerebrovascular disease risk management. Eur J Med Genet 2019; 63:103785. [PMID: 31605816 DOI: 10.1016/j.ejmg.2019.103785] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/15/2019] [Accepted: 10/06/2019] [Indexed: 01/22/2023]
Abstract
Floating-Harbor syndrome (FHS) is a rare, heritable disorder caused by variants in the SRCAP gene. Most individuals with FHS have characteristic facial features, short stature, and speech and language impairment. Although FHS has been likely under-diagnosed due to a combination of lack of recognition of the clinical phenotype and limited access to genomic testing, it is a rare condition with around 100 individuals reported in the medical literature. Case series have been biased towards younger individuals (vast majority <20 years of age) meaning that it has been challenging to provide accurate medical advice for affected individuals in adulthood. We report two young adults with FHS who presented with intracranial haemorrhage likely secondary to cerebrovascular aneurysms, with devastating consequences, making a total of four FHS patients reported with significant cerebrovascular abnormalities. Three of four patients had hypertension, at least one in conjunction with normal renal structure. We consider possible relationships between hypertension, renal pathology and aneurysms in the context of FHS, and consider mechanisms through which disruption of the SRCAP protein may lead to vascular pathology. We recommend that clinicians should have a low threshold to investigate symptoms suggestive of cerebrovascular disease in FHS. We advise that patients with FHS should have annual blood pressure monitoring from adolescence, renal ultrasound at diagnosis repeated in adulthood, and timely investigation of any neurological symptoms. For patients with FHS, particularly with hypertension, we advise that clinicians should consider at least one MRA (Magnetic Resonance Imaging with Angiography) to check for cerebral aneurysms.
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54
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Flaus A, Owen-Hughes T. The Face of Chromatin Variants. Cell 2019; 178:1284-1286. [PMID: 31491382 DOI: 10.1016/j.cell.2019.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A developmental program affecting human face shape is shown by Greenberg et al. (2019) to hinge on the ability to distinguish a single methyl group between two histone variant isoforms and the action of the chromatin-remodeling enzyme SRCAP. This challenges researchers to link atomic structure to a morphological defect.
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Affiliation(s)
- Andrew Flaus
- Centre for Chromosome Biology, Biochemistry, School of Natural Sciences, National University of Ireland Galway, Ireland
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.
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55
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Ko J, Pomerantz JH, Perry H, Shieh JT, Slavotinek AM, Oberoi S, Klein OD. Case Report of Floating-Harbor Syndrome With Bilateral Cleft Lip. Cleft Palate Craniofac J 2019; 57:132-136. [PMID: 31248274 DOI: 10.1177/1055665619858257] [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] [Indexed: 11/17/2022] Open
Abstract
Floating-Harbor syndrome (FHS) is a rare genetic disorder caused by heterozygous mutations in the Snf2-related CREBBP activator protein (SRCAP) gene. The syndrome is characterized by proportional short stature, delayed bone maturation, delayed speech development, and facial dysmorphism. Submucous cleft palate and cleft lip have been reported in FHS, but to our knowledge orofacial clefting in this condition has not been assessed in detail. Here, we report on a case of bilateral cleft lip in a patient with FHS confirmed by exome sequencing.
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Affiliation(s)
- Jaemin Ko
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Jason H Pomerantz
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA.,Division of Plastic and Reconstructive Surgery, Department of Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Hazel Perry
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Joseph T Shieh
- Division of Medical Genetics, Department of Pediatrics, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Anne M Slavotinek
- Division of Medical Genetics, Department of Pediatrics, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Snehlata Oberoi
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA
| | - Ophir D Klein
- Program in Craniofacial Biology and Division of Craniofacial Anomalies, Department of Orofacial Sciences, University of California, San Francisco, CA, USA.,Division of Medical Genetics, Department of Pediatrics, and Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
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56
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Zhang S, Chen S, Qin H, Yuan H, Pi Y, Yang Y, Huang H, Li G, Sun Y, Wang Z, Ma H, Fu X, Zhou T, Wang J, Zhang H, Shen Y. Novel genotypes and phenotypes among Chinese patients with Floating-Harbor syndrome. Orphanet J Rare Dis 2019; 14:144. [PMID: 31200758 PMCID: PMC6570847 DOI: 10.1186/s13023-019-1111-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022] Open
Abstract
Background Floating-Harbor syndrome (FHS) is a rare syndromic short stature disorder caused by truncating variants in SRCAP. Few Chinese FHS patients had been reported so far and limited knowledge regarding the benefit of growth hormone treatment existed. Methods We ascertained 12 short stature patients with molecularly confirmed diagnosis of FHS by whole exome sequencing. We performed a comprehensive clinical evaluation for all patients and assessed the responsiveness of growth hormone treatment in a subset of the patients. Results Five distinct pathogenic/likely pathogenic variants were identified in 12 independent FHS patients including two previously reported variants (c.7303C > T/p.Arg2435Ter and c.7330C > T/p.Arg2444Ter) and three novel variants (c.7189G > T/p.Glu2397Ter, c.7245_7246delAT/p.Ser2416ArgfsTer26 and c.7466C > G/p.Ser2489Ter). The c.7303C > T/p.Arg2435Ter mutation appears more common in Chinese FHS patients. The clinical presentations of Chinese FHS patients are very similar to those of previously reported patients of different ethnicities. Yet we noticed micropenis and ear abnormalities in multiple patients, suggesting that these may be novel phenotypes of Floating-Harbor syndrome. Eight patients (one with GH deficiency, one with undetermined GH level, six without GH deficiency) underwent growth hormone treatment, 3 patients had good responses, one with modest and two with poor responses. Conclusion We described novel genotypes and phenotypes in a Chinese FHS patient cohort. We showed that about half of FHS patients exhibited modest to good response to GH treatment regardless of their respective GH deficiency status. We didn’t find any correlation between different mutations and response to GH treatment. Electronic supplementary material The online version of this article (10.1186/s13023-019-1111-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shujie Zhang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, People's Republic of China.,Department of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530003, People's Republic of China
| | - Shaoke Chen
- Department of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530003, People's Republic of China
| | - Haisong Qin
- Department of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530003, People's Republic of China
| | - Haiming Yuan
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, People's Republic of China
| | - Yalei Pi
- Department of pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People's Republic of China
| | - Yu Yang
- Department of Endocrinology, Metabolism, and Genetics, Jiangxi Provincial Children's Hospital, Nanchang, 330006, People's Republic of China
| | - Hui Huang
- Department of Endocrinology, Metabolism, and Genetics, Jiangxi Provincial Children's Hospital, Nanchang, 330006, People's Republic of China
| | - Guimei Li
- Department of Pediatrics Endocrinology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250021, People's Republic of China
| | - Yan Sun
- Department of Pediatrics Endocrinology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250021, People's Republic of China
| | - Zhihua Wang
- Department of Endocrinology, Genetics and Metabolism, Xi'an Children's Hospital Affiliated with the School of Medicine, Xi'an Jiaotong University, Xi'an, 710000, People's Republic of China
| | - Huamei Ma
- Department of Pediatrics, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China
| | - Xiaoling Fu
- Department of Pediatrics, The Peoples Hospital of The Guizhou Province, Guiyang, 550002, People's Republic of China
| | - Ting Zhou
- Department of Endocrinology, Children's Hospital of Chongqing Medical University, Chongqing, 400014, People's Republic of China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, People's Republic of China
| | - Huifeng Zhang
- Department of pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, People's Republic of China.
| | - Yiping Shen
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200000, People's Republic of China. .,Department of Genetics and Metabolism, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530003, People's Republic of China. .,Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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57
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Uehara T, Takenouchi T, Yamaguchi Y, Daimon Y, Suzuki H, Sakaguchi Y, Kosaki K. CNOT2
as the critical gene for phenotypes of 12q15 microdeletion syndrome. Am J Med Genet A 2019; 179:659-662. [DOI: 10.1002/ajmg.a.61068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/06/2019] [Accepted: 01/23/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Tomoko Uehara
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
| | - Toshiki Takenouchi
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
- Department of Pediatrics; Keio University School of Medicine; Tokyo Japan
| | - Yu Yamaguchi
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
- Department of Clinial Genetics; Gunma Children's Medical Center; Gunma Japan
| | - Yumi Daimon
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
- Department of Pediatrics; Hino Municipal Hospital; Tokyo Japan
| | - Hisato Suzuki
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
| | - Yuri Sakaguchi
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics; Keio University School of Medicine; Tokyo Japan
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58
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Al-Qattan MM, Jarman A, Rafique A, Al-Hassnan ZN, Al-Qattan HM. Rubinstein-Taybi syndrome in a Saudi boy with distinct features and variants in both the CREBBP and EP300 genes: a case report. BMC MEDICAL GENETICS 2019; 20:12. [PMID: 30635043 PMCID: PMC6330443 DOI: 10.1186/s12881-019-0747-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/04/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND Rubinstein-Taybi syndrome (RSTS) Type 1 (OMIM 180849) is characterized by three main features: intellectual disability; broad and frequently angulated thumbs and halluces; and characteristic facial dysmorphism. CASE PRESENTATION We report on a Saudi boy with RSTS Type 1 and the following distinct features: a midline notch of the upper lip, a bifid tip of the tongue, a midline groove of the lower lip, plump fingers with broad / flat fingertips, and brachydactyly. The child was found to be heterozygous in the CREBBP gene for a sequence variant designated c.4963del, which is predicted to result in premature protein termination p.Leu1655Cysfs*89. The child and his father were also found to be heterozygous in the EP300 gene for a sequence variant designated c.586A > G, which is predicted to result in the amino-acid substitution p.Ile196Val. CONCLUSION Our report expands the clinical spectrum of RSTS to include several distinct facial and limb features. The variant of the CREBBP gene is known to be causative of RSTS Type 1. The variant in the EP300 gene is benign since the father carried the same variant and exhibited no abnormalities. However, functional studies are required to investigate if this benign EP300 variant influences the phenotype in the presence of disease-causing CREBBP gene mutations.
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Affiliation(s)
- Mohammad M Al-Qattan
- Division of Plastic Surgery, King Saud University, PO Box 18097, Riyadh, 11415, Saudi Arabia. .,Division of Plastic Surgery, King Faisal Specialist Hospital and Research Center, PO Box 18097, Riyadh, 11415, Saudi Arabia. .,Division of Plastic Surgery, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, PO Box 18097, Riyadh, 11415, Saudi Arabia.
| | - Abdulaziz Jarman
- Division of Plastic Surgery, King Faisal Specialist Hospital and Research Center, PO Box 18097, Riyadh, 11415, Saudi Arabia
| | - Atif Rafique
- Division of Plastic Surgery, King Faisal Specialist Hospital and Research Center, PO Box 18097, Riyadh, 11415, Saudi Arabia
| | - Zuhair N Al-Hassnan
- Department of Medical Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Heba M Al-Qattan
- Division of Plastic Surgery, King Saud University, PO Box 18097, Riyadh, 11415, Saudi Arabia
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59
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Shields LBE, Peppas DS, Rosenberg E. Renal Calculus in Floating-Harbor Syndrome: A Case Report. J Pediatr Health Care 2019; 33:97-101. [PMID: 30205917 DOI: 10.1016/j.pedhc.2018.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/12/2018] [Accepted: 07/18/2018] [Indexed: 11/24/2022]
Abstract
Floating-Harbor syndrome is a rare condition marked by short stature and delayed bone age, characteristic facial features, and speech impairment. Floating-Harbor syndrome commonly results from a sporadic genetic mutation. Renal abnormalities have rarely been encountered. We report the first patient with Floating-Harbor syndrome who spontaneously passed a renal calculus consisting of calcium oxalate monohydrate and calcium oxalate dihydrate. A renal ultrasound showed echotexture within the renal pyramids, hydronephrosis, and a cyst. Pediatric nurse practitioners should be alert to the unique features associated with Floating-Harbor syndrome and be prepared to monitor and treat the renal abnormalities that may accompany this uncommon condition.
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60
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Zech M, Lam DD, Weber S, Berutti R, Poláková K, Havránková P, Fečíková A, Strom TM, Růžička E, Jech R, Winkelmann J. A unique de novo gain-of-function variant in CAMK4 associated with intellectual disability and hyperkinetic movement disorder. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003293. [PMID: 30262571 PMCID: PMC6318768 DOI: 10.1101/mcs.a003293] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/04/2018] [Indexed: 01/12/2023] Open
Abstract
Calcium/calmodulin-dependent protein kinases (CaMKs) are key mediators of calcium signaling and underpin neuronal health. Although widely studied, the contribution of CaMKs to Mendelian disease is rather enigmatic. Here, we describe an unusual neurodevelopmental phenotype, characterized by milestone delay, intellectual disability, autism, ataxia, and mixed hyperkinetic movement disorder including severe generalized dystonia, in a proband who remained etiologically undiagnosed despite exhaustive testing. We performed trio whole-exome sequencing to identify a de novo essential splice-site variant (c.981+1G>A) in CAMK4, encoding CaMKIV. Through in silico evaluation and cDNA analyses, we demonstrated that c.981+1G>A alters CAMK4 pre-mRNA processing and results in a stable mRNA transcript containing a 77-nt out-of-frame deletion and a premature termination codon within the last exon. The expected protein, p.Lys303Serfs*28, exhibits selective loss of the carboxy-terminal regulatory domain of CaMKIV and bears striking structural resemblance to previously reported synthetic mutants that confer constitutive CaMKIV activity. Biochemical studies in proband-derived cells confirmed an activating effect of c.981+1G>A and indicated that variant-induced excessive CaMKIV signaling is sensitive to pharmacological manipulation. Additionally, we found that variants predicted to cause selective depletion of CaMKIV's regulatory domain are unobserved in diverse catalogs of human variation, thus revealing that c.981+1G>A is a unique molecular event. We propose that our proband's phenotype is explainable by a dominant CAMK4 splice-disrupting mutation that acts through a gain-of-function mechanism. Our findings highlight the importance of CAMK4 in human neurodevelopment, provide a foundation for future clinical research of CAMK4, and suggest the CaMKIV signaling pathway as a potential drug target in neurological disease.
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Affiliation(s)
- Michael Zech
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, 85764, Germany.,Klinik und Poliklinik für Neurologie, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Daniel D Lam
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, 85764, Germany
| | - Sandrina Weber
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, 85764, Germany
| | - Riccardo Berutti
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, 85764, Germany
| | - Kamila Poláková
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Petra Havránková
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Anna Fečíková
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Tim M Strom
- Institut für Humangenetik, Helmholtz Zentrum München, Munich, 85764, Germany.,Institut für Humangenetik, Technische Universität München, Munich, 81675, Germany
| | - Evžen Růžička
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Robert Jech
- Department of Neurology and Center of Clinical Neuroscience, First Faculty of Medicine, Charles University and General Faculty Hospital, Prague, 120 00, Czech Republic
| | - Juliane Winkelmann
- Institut für Neurogenomik, Helmholtz Zentrum München, Munich, 85764, Germany.,Institut für Humangenetik, Technische Universität München, Munich, 81675, Germany.,Lehrstuhl für Neurogenetik, Technische Universität München, Munich, 80333, Germany.,Munich Cluster for Systems Neurology, SyNergy, Munich, 81377, Germany
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61
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Floating-Harbor Syndrome: Presentation of the First Romanian Patient with a SRCAP Mutation and Review of the Literature. Balkan J Med Genet 2018; 21:83-86. [PMID: 30425916 PMCID: PMC6231312 DOI: 10.2478/bjmg-2018-0005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Floating-Harbor syndrome (FHS) is a rare autosomal dominant syndrome characterized by short stature with delayed bone age, retarded speech development, intellectual disability and dysmorphic facial features. Recently, dominant mutations almost exclusively clustered in the final exon of the Snf2-related CREBBP activator protein (SRCAP) gene were identified to cause FHS. Here, we report a boy with short stature, speech delay, mild intellectual disability, dysmorphic features, and with genetically confirmed FHS. To the best of our knowledge, this is the first molecularly confirmed case with this syndrome reported in Romania. An intensive program of cognitive and speech stimulation, as well as yearly neurological, psychological, ophthalmological, otorhinolaryngological, pediatric and endocrinological monitoring for our patient were designed. We propose a checklist of clinical features suggestive of FHS, based on the main clinical features, in order to facilitate the diagnosis and clinical management of this rare condition.
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62
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Assoum M, Lines MA, Elpeleg O, Darmency V, Whiting S, Edvardson S, Devinsky O, Heinzen E, Hernan RR, Antignac C, Deleuze JF, Des Portes V, Bertholet-Thomas A, Belot A, Geller E, Lemesle M, Duffourd Y, Thauvin-Robinet C, Thevenon J, Chung W, Lowenstein DH, Faivre L. Further delineation of the clinical spectrum of de novo TRIM8 truncating mutations. Am J Med Genet A 2018; 176:2470-2478. [PMID: 30244534 DOI: 10.1002/ajmg.a.40357] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 04/22/2018] [Accepted: 05/17/2018] [Indexed: 12/21/2022]
Abstract
De novo mutations of the TRIM8 gene, which codes for a tripartite motif protein, have been identified using whole exome sequencing (WES) in two patients with epileptic encephalopathy (EE), but these reports were not sufficient to conclude that TRIM8 was a novel gene responsible for EE. Here we report four additional patients presenting with EE and de novo truncating mutations of TRIM8 detected by WES, and give further details of the patient previously reported by the Epi4K consortium. Epilepsy of variable severity was diagnosed in children aged 2 months to 3.5 years of age. All patients had developmental delay of variable severity with no or very limited language, often associated with behavioral anomalies and unspecific facial features or MRI brain abnormalities. The phenotypic variability observed in these patients appeared related to the severity of the epilepsy. One patient presented pharmacoresistant EE with regression, recurrent infections and nephrotic syndrome, compatible with the brain and kidney expression of TRIM8. Interestingly, all mutations were located at the highly conserved C-terminus section of TRIM8. This collaborative study confirms that TRIM8 is a novel gene responsible for EE, possibly associated with nephrotic syndrome. This report brings new evidence on the pathogenicity of TRIM8 mutations and highlights the value of data-sharing to delineate the phenotypic characteristics and biological basis of extremely rare disorders.
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Affiliation(s)
- Mirna Assoum
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France
| | - Matthew A Lines
- Division of Metabolics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Véronique Darmency
- Service de Neurophysiologie Clinique Pole Neurosciences Hôpital d'Enfants, Dijon, France
| | - Sharon Whiting
- Division of Neurology, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Simon Edvardson
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Orrin Devinsky
- NYU and Saint Barnabas Epilepsy Centers NYU School of Medicine, New York, New York
| | - Erin Heinzen
- Institute for Genomic Medicine Columbia University Medical Center, New York, New York
| | - Rebecca Rose Hernan
- Department of Pediatrics and Molecular Genetics, Columbia University, New York, New York
| | - Corinne Antignac
- Laboratoire de Génétique Moléculaire, Institut de Recherche Necker Enfants Malades, CHU Paris - Hôpital Necker-Enfants Malades, Paris, France.,Equipe Néphropathies héréditaires et rein en développement, Inserm U983, Institut Imagine, Hôpital Necker-Enfants Malades, Paris, France
| | | | - Vincent Des Portes
- Centre de référence « Déficiences Intellectuelles de causes rares », HFME, HCL F-69675, Bron, France.,ISC CNRS UMR 5304, Université de Lyon, Lyon, France
| | - Aurélie Bertholet-Thomas
- Centre de référence des rhumatismes inflammatoires et des maladies auto-immunes systémiques rares de l'enfant (RAISE), HFME HCL INSERM U1111, Lyon, France.,Service de Néphrologie, Rhumatologie et Dermatologie pédiatriques, Hôpital Femme Mère Enfant Hospices Civils de Lyon GH Est, Bron, France
| | - Alexandre Belot
- Centre de référence des rhumatismes inflammatoires et des maladies auto-immunes systémiques rares de l'enfant (RAISE), HFME HCL INSERM U1111, Lyon, France.,Service de Néphrologie, Rhumatologie et Dermatologie pédiatriques, Hôpital Femme Mère Enfant Hospices Civils de Lyon GH Est, Bron, France
| | - Eric Geller
- NYU and Saint Barnabas Epilepsy Centers NYU School of Medicine, New York, New York
| | - Martine Lemesle
- Service de Neurophysiologie Clinique Pole Neurosciences Hôpital d'Enfants, Dijon, France
| | - Yannis Duffourd
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire TRANSLAD CHU Dijon et Université de Bourgogne-Franche Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est CHU, Dijon, France
| | - Christel Thauvin-Robinet
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire TRANSLAD CHU Dijon et Université de Bourgogne-Franche Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est CHU, Dijon, France.,Centre de Référence Déficience Intellectuelle de causes rares (Defi-Bourgogne), CHU, Dijon, France
| | - Julien Thevenon
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire TRANSLAD CHU Dijon et Université de Bourgogne-Franche Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est CHU, Dijon, France
| | - Wendy Chung
- Kennedy Family Professor of Pediatrics and Medicine, Columbia University, New York, New York
| | - Daniel H Lowenstein
- Department of Neurology, University of California, San Francisco, San Francisco, California
| | - Laurence Faivre
- Génétique des Anomalies du Développement, UMR1231, Université de Bourgogne, Dijon, France.,Fédération Hospitalo-Universitaire TRANSLAD CHU Dijon et Université de Bourgogne-Franche Comté, Dijon, France.,Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est CHU, Dijon, France.,Centre de Référence Déficience Intellectuelle de causes rares (Defi-Bourgogne), CHU, Dijon, France
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63
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Choi EM, Lee DH, Kang SJ, Shim YJ, Kim HS, Kim JS, Jeong JI, Ha JS, Jang JH. The first Korean case with Floating-Harbor syndrome with a novel SRCAP mutation diagnosed by targeted exome sequencing. KOREAN JOURNAL OF PEDIATRICS 2018; 61:403-406. [PMID: 30304910 PMCID: PMC6313083 DOI: 10.3345/kjp.2018.06289] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 07/31/2018] [Indexed: 12/02/2022]
Abstract
Floating-Harbor syndrome is a rare autosomal dominant genetic disorder associated with SRCAP mutation. To date, approximately 50 cases of Floating-Harbor syndrome have been reported, but none have been reported in Korea yet. Floating-Harbor syndrome is characterized by delayed bony maturation, unique facial features, and language impairment. Here, we present a 6-year-old boy with a triangular face, deep-set protruding eyes, low-set ears, wide nose with narrow nasal bridge, short philtrum, long thin lips, clinodactyly, and developmental delay that was transferred to our pediatric clinic for genetic evaluation. He showed progressive delay in the area of language and cognition-adaption as he grew. He had previously undergone chromosomal analysis at another hospital due to his language delay, but his karyotype was normal. We performed targeted exome sequencing, considering several syndromes with similar phenotypes. Library preparation was performed with the TruSight One sequencing panel, which enriches the sample for about 4,800 genes of clinical relevance. Massively parallel sequencing was conducted with NextSeq. An identified variant was confirmed by Sanger sequencing of the patient and his parents. Finally, the patient was confirmed as the first Korean case of Floating-Harbor syndrome with a novel SRCAP (Snf2 related CREBBP activator protein) mutation (c.7732dupT, p.Ser2578Phefs*6), resulting in early termination of the protein; it was not found in either of his healthy parents or a control population. To our knowledge, this is the first study to describe a boy with Floating-Harbor syndrome with a novel SRCAP mutation diagnosed by targeted exome sequencing in Korea.
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Affiliation(s)
- Eun Mi Choi
- Department of Pediatrics, Keimyung University Dongsan Medical Center, Keimyung University School of Medicine, Daegu, Korea
| | - Dong Hyun Lee
- Department of Pediatrics, Keimyung University Dongsan Medical Center, Keimyung University School of Medicine, Daegu, Korea
| | - Seok Jin Kang
- Department of Pediatrics, Keimyung University Dongsan Medical Center, Keimyung University School of Medicine, Daegu, Korea
| | - Ye Jee Shim
- Department of Pediatrics, Keimyung University Dongsan Medical Center, Keimyung University School of Medicine, Daegu, Korea
| | - Heung Sik Kim
- Department of Pediatrics, Keimyung University Dongsan Medical Center, Keimyung University School of Medicine, Daegu, Korea
| | - Jun Sik Kim
- Department of Pediatrics, Keimyung University Dongsan Medical Center, Keimyung University School of Medicine, Daegu, Korea
| | - Jong In Jeong
- Department of Otorhinolaryngology, Keimyung University Dongsan Medical Center, Keimyung University School of Medicine, Daegu, Korea
| | - Jung-Sook Ha
- Department of Laboratory Medicine, Keimyung University Dongsan Medical Center, Keimyung University School of Medicine, Daegu, Korea
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64
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Balak C, Belnap N, Ramsey K, Joss S, Devriendt K, Naymik M, Jepsen W, Siniard AL, Szelinger S, Parker ME, Richholt R, Izatt T, LaFleur M, Terraf P, Llaci L, De Both M, Piras IS, Rangasamy S, Schrauwen I, Craig DW, Huentelman M, Narayanan V. A novel
FBXO28
frameshift mutation in a child with developmental delay, dysmorphic features, and intractable epilepsy: A second gene that may contribute to the 1q41‐q42 deletion phenotype. Am J Med Genet A 2018; 176:1549-1558. [DOI: 10.1002/ajmg.a.38712] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Chris Balak
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Newell Belnap
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Keri Ramsey
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Shelagh Joss
- West of Scotland Genetics ServiceQueen Elizabeth University HospitalGlasgow United Kingdom
| | - Koen Devriendt
- Center for Human Genetics (Centrum Menselijke Erfelijkheid)University of LeuvenLeuven Belgium
| | - Marcus Naymik
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Wayne Jepsen
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Ashley L. Siniard
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Szabolcs Szelinger
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- UCLA Pathology & Laboratory MedicineUCLA Center for the Health SciencesLos Angeles California
| | - Mary E. Parker
- Department of Physical TherapyTexas State UniversitySan Marcos Texas
- U.R. Our Hope, Undiagnosed and Rare Disorder OrganizationAustin Texas
| | - Ryan Richholt
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Tyler Izatt
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Madison LaFleur
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Panieh Terraf
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Lorida Llaci
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Matt De Both
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Ignazio S. Piras
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Sampathkumar Rangasamy
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Isabelle Schrauwen
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- Department of Molecular and Human Genetics, Center for Statistical GeneticsBaylor College of MedicineHouston Texas
| | - David W. Craig
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
- Department of Translational GenomicsKeck School of Medicine of USCLos Angeles California
| | - Matt Huentelman
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
| | - Vinodh Narayanan
- Neurogenomics Division, Center for Rare Childhood Disorders (C4RCD)Translational Genomics Research InstitutePhoenix Arizona
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65
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Ito Y, Carss KJ, Duarte ST, Hartley T, Keren B, Kurian MA, Marey I, Charles P, Mendonça C, Nava C, Pfundt R, Sanchis-Juan A, van Bokhoven H, van Essen A, van Ravenswaaij-Arts C, Boycott KM, Kernohan KD, Dyack S, Raymond FL, Aitman T, Bennett D, Caulfield M, Chinnery P, Gale D, Koziell A, Kuijpers TW, Laffan MA, Maher E, Markus HS, Morrell NW, Ouwehand WH, Perry DJ, Raymond FL, Roberts I, Smith KG, Thrasher A, Watkins H, Williamson C, Woods G, Ashford S, Bradley JR, Fletcher D, Hammerton T, James R, Kingston N, Penkett CJ, Stirrups K, Veltman M, Young T, Brown M, Clements-Brod N, Davis J, Dewhurst E, Dolling H, Erwood M, Frary A, Linger R, Martin JM, Papadia S, Rehnstrom K, Stark H, Allsup D, Austin S, Bakchoul T, Bariana TK, Bolton-Maggs P, Chalmers E, Collins J, Collins P, Erber WN, Everington T, Favier R, Freson K, Furie B, Gattens M, Gebhart J, Gomez K, Greene D, Greinacher A, Gresele P, Hart D, Heemskerk JW, Henskens Y, Kazmi R, Keeling D, Kelly AM, Lambert MP, Lentaigne C, Liesner R, Makris M, Mangles S, Mathias M, Millar CM, Mumford A, Nurden P, Payne J, Pasi J, Peerlinck K, Revel-Vilk S, Richards M, Rondina M, Roughley C, Schulman S, Schulze H, Scully M, Sivapalaratnam S, Stubbs M, Tait RC, Talks K, Thachil J, Toh CH, Turro E, Van Geet C, De Vries M, Warner TQ, Watson H, Westbury S, Furnell A, Mapeta R, Rayner-Matthews P, Simeoni I, Staines S, Stephens J, Watt C, Whitehorn D, Attwood A, Daugherty L, Deevi SV, Halmagyi C, Hu F, Matser V, Meacham S, Megy K, Shamardina O, Titterton C, Tuna S, Yu P, von Ziegenweldt J, Astle W, Bleda M, Carss KJ, Gräf S, Haimel M, Lango-Allen H, Richardson S, Calleja P, Rankin S, Turek W, Anderson J, Bryson C, Carmichael J, McJannet C, Stock S, Allen L, Ambegaonkar G, Armstrong R, Arno G, Bitner-Glindzicz M, Brady A, Canham N, Chitre M, Clement E, Clowes V, Deegan P, Deshpande C, Doffinger R, Firth H, Flinter F, French C, Gardham A, Ghali N, Gissen P, Grozeva D, Henderson R, Hensiek A, Holden S, Holder M, Holder S, Hurst J, Josifova D, Krishnakumar D, Kurian MA, Lees M, MacLaren R, Maw A, Mehta S, Michaelides M, Moore A, Murphy E, Park SM, Parker A, Patch C, Paterson J, Rankin J, Reid E, Rosser E, Sanchis-Juan A, Sandford R, Santra S, Scott R, Sohal A, Stein P, Thomas E, Thompson D, Tischkowitz M, Vogt J, Wakeling E, Wassmer E, Webster A, Ali S, Ali S, Boggard HJ, Church C, Coghlan G, Cookson V, Corris PA, Creaser-Myers A, DaCosta R, Dormand N, Eyries M, Gall H, Ghataorhe PK, Ghio S, Ghofrani A, Gibbs JSR, Girerd B, Greenhalgh A, Hadinnapola C, Houweling AC, Humbert M, in’t Veld AH, Kennedy F, Kiely DG, Kovacs G, Lawrie A, Ross RVM, Machado R, Masati L, Meehan S, Moledina S, Montani D, Othman S, Peacock AJ, Pepke-Zaba J, Pollock V, Polwarth G, Ranganathan L, Rhodes CJ, Rue-Albrecht K, Schotte G, Shipley D, Soubrier F, Southgate L, Scelsi L, Suntharalingam J, Tan Y, Toshner M, Treacy CM, Trembath R, Vonk Noordegraaf A, Walker S, Wanjiku I, Wharton J, Wilkins M, Wort SJ, Yates K, Alachkar H, Antrobus R, Arumugakani G, Bacchelli C, Baxendale H, Bethune C, Bibi S, Booth C, Browning M, Burns S, Chandra A, Cooper N, Davies S, Devlin L, Drewe E, Edgar D, Egner W, Ghurye R, Gilmour K, Goddard S, Gordins P, Grigoriadou S, Hackett S, Hague R, Harper L, Hayman G, Herwadkar A, Huissoon A, Jolles S, Kelleher P, Kumararatne D, Lear S, Longhurst H, Lorenzo L, Maimaris J, Manson A, McDermott E, Murng S, Nejentsev S, Noorani S, Oksenhendler E, Ponsford M, Qasim W, Quinti I, Richter A, Samarghitean C, Sargur R, Savic S, Seneviratne S, Sewell C, Staples E, Stauss H, Thaventhiran J, Thomas M, Welch S, Willcocks L, Yeatman N, Yong P, Ancliff P, Babbs C, Layton M, Louka E, McGowan S, Mead A, Roy N, Chambers J, Dixon P, Estiu C, Hague B, Marschall HU, Simpson M, Chong S, Emmerson I, Ginsberg L, Gosal D, Hadden R, Horvath R, Mahdi-Rogers M, Manzur A, Marshall A, Matthews E, McCarthy M, Reilly M, Renton T, Rice A, Themistocleous A, Vale T, Van Zuydam N, Walker S, Ormondroyd L, Hudson G, Wei W, Yu Wai Man P, Whitworth J, Afzal M, Colby E, Saleem M, Alavijeh OS, Cook HT, Johnson S, Levine AP, Wong EK, Tan R, Boycott KM, MacKenzie A, Majewski J, Brudno M, Bulman D, Dyment D. De Novo Truncating Mutations in WASF1 Cause Intellectual Disability with Seizures. Am J Hum Genet 2018; 103:144-153. [PMID: 29961568 PMCID: PMC6037130 DOI: 10.1016/j.ajhg.2018.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/04/2018] [Indexed: 10/28/2022] Open
Abstract
Next-generation sequencing has been invaluable in the elucidation of the genetic etiology of many subtypes of intellectual disability in recent years. Here, using exome sequencing and whole-genome sequencing, we identified three de novo truncating mutations in WAS protein family member 1 (WASF1) in five unrelated individuals with moderate to profound intellectual disability with autistic features and seizures. WASF1, also known as WAVE1, is part of the WAVE complex and acts as a mediator between Rac-GTPase and actin to induce actin polymerization. The three mutations connected by Matchmaker Exchange were c.1516C>T (p.Arg506Ter), which occurs in three unrelated individuals, c.1558C>T (p.Gln520Ter), and c.1482delinsGCCAGG (p.Ile494MetfsTer23). All three variants are predicted to partially or fully disrupt the C-terminal actin-binding WCA domain. Functional studies using fibroblast cells from two affected individuals with the c.1516C>T mutation showed a truncated WASF1 and a defect in actin remodeling. This study provides evidence that de novo heterozygous mutations in WASF1 cause a rare form of intellectual disability.
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66
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Larizza L, Finelli P. Developmental disorders with intellectual disability driven by chromatin dysregulation: Clinical overlaps and molecular mechanisms. Clin Genet 2018; 95:231-240. [DOI: 10.1111/cge.13365] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/28/2018] [Accepted: 04/14/2018] [Indexed: 12/30/2022]
Affiliation(s)
- L. Larizza
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
| | - P. Finelli
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
- Department of Medical Biotechnology and Translational Medicine; Università degli Studi di Milano; Milan Italy
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67
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Ye B, Liu B, Yang L, Zhu X, Zhang D, Wu W, Zhu P, Wang Y, Wang S, Xia P, Du Y, Meng S, Huang G, Wu J, Chen R, Tian Y, Fan Z. LncKdm2b controls self-renewal of embryonic stem cells via activating expression of transcription factor Zbtb3. EMBO J 2018. [PMID: 29535137 DOI: 10.15252/embj.201797174] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Divergent long noncoding RNAs (lncRNAs) represent a major lncRNA biotype in mouse and human genomes. The biological and molecular functions of the divergent lncRNAs remain largely unknown. Here, we show that lncKdm2b, a divergent lncRNA for Kdm2b gene, is conserved among five mammalian species and highly expressed in embryonic stem cells (ESCs) and early embryos. LncKdm2b knockout impairs ESC self-renewal and causes early embryonic lethality. LncKdm2b can activate Zbtb3 by promoting the assembly and ATPase activity of Snf2-related CREBBP activator protein (SRCAP) complex in trans Zbtb3 potentiates the ESC self-renewal in a Nanog-dependent manner. Finally, Zbtb3 deficiency impairs the ESC self-renewal and early embryonic development. Therefore, our findings reveal that lncRNAs may represent an additional layer of the regulation of ESC self-renewal and early embryogenesis.
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Affiliation(s)
- Buqing Ye
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Benyu Liu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Liuliu Yang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Zhu
- Laboratory Animal Center, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dongdong Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wei Wu
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Pingping Zhu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yanying Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shuo Wang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Pengyan Xia
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ying Du
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shu Meng
- Laboratory Animal Center, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Guanling Huang
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiayi Wu
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yong Tian
- University of Chinese Academy of Sciences, Beijing, China .,Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Zusen Fan
- Key Laboratory of Infection and Immunity of CAS, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China .,University of Chinese Academy of Sciences, Beijing, China
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68
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Moccia A, Martin DM. Nervous system development and disease: A focus on trithorax related proteins and chromatin remodelers. Mol Cell Neurosci 2018; 87:46-54. [PMID: 29196188 PMCID: PMC5828982 DOI: 10.1016/j.mcn.2017.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 11/08/2017] [Accepted: 11/27/2017] [Indexed: 01/12/2023] Open
Abstract
The nervous system comprises many different cell types including neurons, glia, macrophages, and immune cells, each of which is defined by specific patterns of gene expression, morphology, function, and anatomical location. Establishment of these complex and highly regulated cell fates requires spatial and temporal coordination of gene transcription. Open chromatin (euchromatin) allows transcription factors to interact with gene promoters and activate lineage specific genes, whereas closed chromatin (heterochromatin) remains inaccessible to transcriptional activation. Changes in the genome-wide distribution of euchromatin accompany transcriptional plasticity that allows the diversity of mature cell fates to be generated during development. In the past 20years, many new genes and gene families have been identified to participate in regulation of chromatin accessibility. These genes include chromatin remodelers that interact with Trithorax group (TrxG) and Polycomb group (PcG) proteins to activate or repress transcription, respectively. Here we review the role of TrxG proteins in neurodevelopment and disease.
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Affiliation(s)
- Amanda Moccia
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Donna M Martin
- Department of Human Genetics, The University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Pediatrics and Communicable Diseases, The University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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69
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Milani D, Scuvera G, Gatti M, Tolva G, Bonarrigo F, Esposito S, Gervasini C. Perthes disease: A new finding in Floating-Harbor syndrome. Am J Med Genet A 2018; 176:703-706. [PMID: 29383823 DOI: 10.1002/ajmg.a.38605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 10/26/2017] [Accepted: 12/16/2017] [Indexed: 11/11/2022]
Abstract
Floating-Harbor Syndrome (FHS; OMIM #136140) is an ultra-rare autosomal dominant genetic condition characterized by expressive language delay, short stature with delayed bone mineralization, a triangular face with a prominent nose, and deep-set eyes, and hand anomalies. First reported in 1973, FHS is associated with mutations in the SRCAP gene, which encodes SNF2-related CREBBP activator protein. Mutations in the CREBBP gene cause Rubinstein-Taybi Syndrome (RSTS; OMIM #180849, #613684), another rare disease characterized by broad thumbs and halluces, facial dysmorphisms, short stature, and intellectual disability, which has a phenotypic overlap with FHS. We describe a case of FHS associated with a novel SRCAP mutation and characterized by Perthes disease, a skeletal anomaly described in approximately 3% of patients with RSTS. Thus Perthes disease can be added to the list of clinical features that overlap between FHS and RSTS.
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Affiliation(s)
- Donatella Milani
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation University of Milan, Fondazione IRCSS Ca' Granda Ospedale Maggiorte Policlinico, Milan, Italy
| | - Giulietta Scuvera
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation University of Milan, Fondazione IRCSS Ca' Granda Ospedale Maggiorte Policlinico, Milan, Italy
| | - Marta Gatti
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation University of Milan, Fondazione IRCSS Ca' Granda Ospedale Maggiorte Policlinico, Milan, Italy
| | - Gianluca Tolva
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation University of Milan, Fondazione IRCSS Ca' Granda Ospedale Maggiorte Policlinico, Milan, Italy
| | - Francesca Bonarrigo
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation University of Milan, Fondazione IRCSS Ca' Granda Ospedale Maggiorte Policlinico, Milan, Italy
| | - Susanna Esposito
- Pediatric Clinic, Università degli Studi di Perugia, Perugia, Italy
| | - Cristina Gervasini
- Genetica Medica, Dip. Scienze della Salute, Università degli Studi di Milano, Milano, Italy
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70
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Aref-Eshghi E, Rodenhiser DI, Schenkel LC, Lin H, Skinner C, Ainsworth P, Paré G, Hood RL, Bulman DE, Kernohan KD, Boycott KM, Campeau PM, Schwartz C, Sadikovic B, Sadikovic B. Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes. Am J Hum Genet 2018; 102:156-174. [PMID: 29304373 DOI: 10.1016/j.ajhg.2017.12.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/10/2017] [Indexed: 01/23/2023] Open
Abstract
Pediatric developmental syndromes present with systemic, complex, and often overlapping clinical features that are not infrequently a consequence of Mendelian inheritance of mutations in genes involved in DNA methylation, establishment of histone modifications, and chromatin remodeling (the "epigenetic machinery"). The mechanistic cross-talk between histone modification and DNA methylation suggests that these syndromes might be expected to display specific DNA methylation signatures that are a reflection of those primary errors associated with chromatin dysregulation. Given the interrelated functions of these chromatin regulatory proteins, we sought to identify DNA methylation epi-signatures that could provide syndrome-specific biomarkers to complement standard clinical diagnostics. In the present study, we examined peripheral blood samples from a large cohort of individuals encompassing 14 Mendelian disorders displaying mutations in the genes encoding proteins of the epigenetic machinery. We demonstrated that specific but partially overlapping DNA methylation signatures are associated with many of these conditions. The degree of overlap among these epi-signatures is minimal, further suggesting that, consistent with the initial event, the downstream changes are unique to every syndrome. In addition, by combining these epi-signatures, we have demonstrated that a machine learning tool can be built to concurrently screen for multiple syndromes with high sensitivity and specificity, and we highlight the utility of this tool in solving ambiguous case subjects presenting with variants of unknown significance, along with its ability to generate accurate predictions for subjects presenting with the overlapping clinical and molecular features associated with the disruption of the epigenetic machinery.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N6A5C1, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada.
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71
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Quénet D. Histone Variants and Disease. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 335:1-39. [DOI: 10.1016/bs.ircmb.2017.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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72
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Goodwin LR, Picketts DJ. The role of ISWI chromatin remodeling complexes in brain development and neurodevelopmental disorders. Mol Cell Neurosci 2017; 87:55-64. [PMID: 29249292 DOI: 10.1016/j.mcn.2017.10.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/04/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022] Open
Abstract
The mammalian ISWI (Imitation Switch) genes SMARCA1 and SMARCA5 encode the ATP-dependent chromatin remodeling proteins SNF2L and SNF2H. The ISWI proteins interact with BAZ (bromodomain adjacent to PHD zinc finger) domain containing proteins to generate eight distinct remodeling complexes. ISWI complex-mediated nucleosome positioning within genes and gene regulatory elements is proving important for the transition from a committed progenitor state to a differentiated cell state. Genetic studies have implicated the involvement of many ATP-dependent chromatin remodeling proteins in neurodevelopmental disorders (NDDs), including SMARCA1. Here we review the characterization of mice inactivated for ISWI and their interacting proteins, as it pertains to brain development and disease. A better understanding of chromatin dynamics during neural development is a prerequisite to understanding disease pathologies and the development of therapeutics for these complex disorders.
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Affiliation(s)
- Laura R Goodwin
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, 501 Smyth Road, Ottawa, ON K1H 8L6, Canada; Department of Biochemistry, Microbiology & Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Cellular and Molecular Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada; Department of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada.
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73
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Cuvertino S, Stuart HM, Chandler KE, Roberts NA, Armstrong R, Bernardini L, Bhaskar S, Callewaert B, Clayton-Smith J, Davalillo CH, Deshpande C, Devriendt K, Digilio MC, Dixit A, Edwards M, Friedman JM, Gonzalez-Meneses A, Joss S, Kerr B, Lampe AK, Langlois S, Lennon R, Loget P, Ma DY, McGowan R, Des Medt M, O’Sullivan J, Odent S, Parker MJ, Pebrel-Richard C, Petit F, Stark Z, Stockler-Ipsiroglu S, Tinschert S, Vasudevan P, Villa O, White SM, Zahir FR, Woolf AS, Banka S, Banka S. ACTB Loss-of-Function Mutations Result in a Pleiotropic Developmental Disorder. Am J Hum Genet 2017; 101:1021-1033. [PMID: 29220674 PMCID: PMC5812896 DOI: 10.1016/j.ajhg.2017.11.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/13/2017] [Indexed: 10/31/2022] Open
Abstract
ACTB encodes β-actin, an abundant cytoskeletal housekeeping protein. In humans, postulated gain-of-function missense mutations cause Baraitser-Winter syndrome (BRWS), characterized by intellectual disability, cortical malformations, coloboma, sensorineural deafness, and typical facial features. To date, the consequences of loss-of-function ACTB mutations have not been proven conclusively. We describe heterozygous ACTB deletions and nonsense and frameshift mutations in 33 individuals with developmental delay, apparent intellectual disability, increased frequency of internal organ malformations (including those of the heart and the renal tract), growth retardation, and a recognizable facial gestalt (interrupted wavy eyebrows, dense eyelashes, wide nose, wide mouth, and a prominent chin) that is distinct from characteristics of individuals with BRWS. Strikingly, this spectrum overlaps with that of several chromatin-remodeling developmental disorders. In wild-type mouse embryos, β-actin expression was prominent in the kidney, heart, and brain. ACTB mRNA expression levels in lymphoblastic lines and fibroblasts derived from affected individuals were decreased in comparison to those in control cells. Fibroblasts derived from an affected individual and ACTB siRNA knockdown in wild-type fibroblasts showed altered cell shape and migration, consistent with known roles of cytoplasmic β-actin. We also demonstrate that ACTB haploinsufficiency leads to reduced cell proliferation, altered expression of cell-cycle genes, and decreased amounts of nuclear, but not cytoplasmic, β-actin. In conclusion, we show that heterozygous loss-of-function ACTB mutations cause a distinct pleiotropic malformation syndrome with intellectual disability. Our biological studies suggest that a critically reduced amount of this protein alters cell shape, migration, proliferation, and gene expression to the detriment of brain, heart, and kidney development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Siddharth Banka
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine, and Health, The University of Manchester, M13 9PL Manchester, UK; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University Foundation NHS Trust, Health Innovation Manchester, M13 9WL Manchester, UK.
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74
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Singh A, Bhatia HP, Sood S, Sharma N, Mohan A. A novel finding of oligodontia and ankyloglossia in a 14-year-old with Floating-Harbor syndrome. SPECIAL CARE IN DENTISTRY 2017; 37:318-321. [PMID: 29210485 DOI: 10.1111/scd.12257] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Floating-Harbor syndrome (FHS) is a rare genetic condition characterized by distinct facial features, short stature and delayed skeletal development. Here we present case of a 14-year-old boy with short stature, typical facial features, impaired voice quality, clinodactyly, cryptorchidism and unilateral agenesis of kidney. In addition he had oligodontia and ankyloglossia with features suggestive of FHS. Treatment rendered was restoration of caries, application of pit and fissure sealants followed by frenectomy. The purpose of this report is to highlight the oral developmental anomalies and the management of a patient with FHS and to add to the current knowledge of the literature on this syndrome.
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Affiliation(s)
- Akshara Singh
- Assistant Professor, Department of Pedodontics and Preventive Dentistry, Manav Rachna Dental College, Faridabad, Haryana, India
| | - Hind Pal Bhatia
- Professor & Head, Department of Pedodontics and Preventive Dentistry, Manav Rachna Dental College, Faridabad, Haryana, India
| | - Shveta Sood
- Professor, Department of Pedodontics and Preventive Dentistry, Manav Rachna Dental College, Faridabad, Haryana, India
| | - Naresh Sharma
- Reader, Department of Pedodontics and Preventive Dentistry, Manav Rachna Dental College, Faridabad, Haryana, India
| | - Amit Mohan
- Reader, Department of Oral and Maxillofacial Surgery, Manav Rachna Dental College, Faridabad, Haryana, India
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75
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Suppression of SRCAP chromatin remodelling complex and restriction of lymphoid lineage commitment by Pcid2. Nat Commun 2017; 8:1518. [PMID: 29138493 PMCID: PMC5686073 DOI: 10.1038/s41467-017-01788-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 10/16/2017] [Indexed: 12/31/2022] Open
Abstract
Lymphoid lineage commitment is an important process in haematopoiesis, which forms the immune system to protect the host from pathogen invasion. However, how multipotent progenitors (MPP) switch into common lymphoid progenitors (CLP) or common myeloid progenitors (CMP) during this process remains elusive. Here we show that PCI domain-containing protein 2 (Pcid2) is highly expressed in MPPs. Pcid2 deletion in the haematopoietic system causes skewed lymphoid lineage specification. In MPPs, Pcid2 interacts with the Zinc finger HIT-type containing 1 (ZNHIT1) to block Snf2-related CREBBP activator protein (SRCAP) activity and prevents the deposition of histone variant H2A.Z and transcription factor PU.1 to key lymphoid fate regulator genes. Furthermore, Znhit1 deletion also abrogates H2A/H2A.Z exchange in MPPs. Thus Pcid2 controls lymphoid lineage commitment through the regulation of SRCAP remodelling activity.
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76
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Abstract
Short stature is a common and heterogeneous condition that is often genetic in etiology. For most children with genetic short stature, the specific molecular causes remain unknown; but with advances in exome/genome sequencing and bioinformatics approaches, new genetic causes of growth disorders have been identified, contributing to the understanding of the underlying molecular mechanisms of longitudinal bone growth and growth failure. Identifying new genetic causes of growth disorders has the potential to improve diagnosis, prognostic accuracy, and individualized management, and help avoid unnecessary testing for endocrine and other disorders.
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Affiliation(s)
- Youn Hee Jee
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive MSC 1103, Bethesda, MD 20892-1103, USA.
| | - Anenisia C Andrade
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Solnavägen 1, Solna 171 77, Sweden
| | - Jeffrey Baron
- Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, CRC, Room 1-3330, 10 Center Drive MSC 1103, Bethesda, MD 20892-1103, USA
| | - Ola Nilsson
- Division of Pediatric Endocrinology, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Solnavägen 1, Solna 171 77, Sweden; University Hospital, Örebro University, Södra Grev Rosengatan, Örebro 701 85, Sweden
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77
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Haanpää M, Schlecht H, Batra G, Clayton-Smith J, Douzgou S. Interrupted/bipartite clavicle as a diagnostic clue in Kabuki syndrome. Am J Med Genet A 2017; 173:1115-1118. [DOI: 10.1002/ajmg.a.38131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 12/14/2016] [Accepted: 12/24/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Maria Haanpää
- Manchester Center for Genomic Medicine; Central Manchester University Hospitals NHS Foundation Trust; UK Manchester Academic Health Sciences Center; Manchester UK
- Turku University Hospital; Turku Finland
| | - Helena Schlecht
- Manchester Center for Genomic Medicine; Central Manchester University Hospitals NHS Foundation Trust; UK Manchester Academic Health Sciences Center; Manchester UK
| | - Gauri Batra
- Department of Perinatal Histopathology; Central Manchester University Hospitals NHS Foundation Trust; Manchester UK
| | - Jill Clayton-Smith
- Manchester Center for Genomic Medicine; Central Manchester University Hospitals NHS Foundation Trust; UK Manchester Academic Health Sciences Center; Manchester UK
- Faculty of Medical and Human Sciences; Institute of Evolution, Systems and Genomics; University of Manchester; Manchester UK
| | - Sofia Douzgou
- Manchester Center for Genomic Medicine; Central Manchester University Hospitals NHS Foundation Trust; UK Manchester Academic Health Sciences Center; Manchester UK
- Faculty of Medical and Human Sciences; Institute of Evolution, Systems and Genomics; University of Manchester; Manchester UK
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78
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Schenkel LC, Rodenhiser D, Siu V, McCready E, Ainsworth P, Sadikovic B. Constitutional Epi/Genetic Conditions: Genetic, Epigenetic, and Environmental Factors. J Pediatr Genet 2017; 6:30-41. [PMID: 28180025 PMCID: PMC5288004 DOI: 10.1055/s-0036-1593849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
There are more than 4,000 phenotypes for which the molecular basis is at least partly known. Though defects in primary DNA structure constitute a major cause of these disorders, epigenetic disruption is emerging as an important alternative mechanism in the etiology of a broad range of congenital and developmental conditions. These include epigenetic defects caused by either localized (in cis) genetic alterations or more distant (in trans) genetic events but can also include environmental effects. Emerging evidence suggests interplay between genetic and environmental factors in the epigenetic etiology of several constitutional "epi/genetic" conditions. This review summarizes our broadening understanding of how epigenetics contributes to pediatric disease by exploring different classes of epigenomic disorders. It further challenges the simplistic dogma of "DNA encodes RNA encodes protein" to best understand the spectrum of factors that can influence genetic traits in a pediatric population.
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Affiliation(s)
- Laila C. Schenkel
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
| | - David Rodenhiser
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Victoria Siu
- Children's Health Research Institute, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Peter Ainsworth
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- Department of Biochemistry, Western University, London, Ontario, Canada
- Department of Pediatrics, Western University, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
- Department of Oncology, Western University, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- Children's Health Research Institute, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
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79
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The defining DNA methylation signature of Floating-Harbor Syndrome. Sci Rep 2016; 6:38803. [PMID: 27934915 PMCID: PMC5146968 DOI: 10.1038/srep38803] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 11/15/2016] [Indexed: 11/08/2022] Open
Abstract
Floating-Harbor syndrome (FHS) is an autosomal dominant genetic condition characterized by short stature, delayed osseous maturation, expressive language impairment, and unique facial dysmorphology. We previously identified mutations in the chromatin remodeling protein SRCAP (SNF2-related CBP Activator Protein) as the cause of FHS. SRCAP has multiple roles in chromatin and transcriptional regulation; however, specific epigenetic consequences of SRCAP mutations remain to be described. Using high resolution genome-wide DNA methylation analysis, we identified a unique and highly specific DNA methylation "epi-signature" in the peripheral blood of individuals with FHS. Both hyper and hypomethylated loci are distributed across the genome, preferentially occurring in CpG islands. Clonal bisulfite sequencing of two hypermethylated (FIGN and STPG2) and two hypomethylated (MYO1F and RASIP1) genes confirmed these findings. The identification of a unique methylation signature in FHS provides further insight into the biological function of SRCAP and provides a unique biomarker for this disorder.
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80
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Kernohan KD, McBride A, Xi Y, Martin N, Schwartzentruber J, Dyment DA, Majewski J, Blaser S, Boycott KM, Chitayat D. Loss of the arginine methyltranserase PRMT7 causes syndromic intellectual disability with microcephaly and brachydactyly. Clin Genet 2016; 91:708-716. [PMID: 27718516 DOI: 10.1111/cge.12884] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 09/30/2016] [Accepted: 09/30/2016] [Indexed: 01/09/2023]
Abstract
Post-translational protein modifications exponentially expand the functional complement of proteins encoded by the human genome. One such modification is the covalent addition of a methyl group to arginine or lysine residues, which is used to regulate a substantial proportion of the proteome. Arginine and lysine methylation are catalyzed by protein arginine methyltransferase (PRMTs) and protein lysine methyltransferase proteins (PKMTs), respectively; each methyltransferase has a specific set of target substrates. Here, we report a male with severe intellectual disability, facial dysmorphism, microcephaly, short stature, brachydactyly, cryptorchidism and seizures who was found to have a homozygous 15,309 bp deletion encompassing the transcription start site of PRMT7, which we confirmed is functionally a null allele. We show that the patient's cells have decreased levels of protein arginine methylation, and that affected proteins include the essential histones, H2B and H4. Finally, we demonstrate that patient cells have altered Wnt signaling, which may have contributed to the skeletal abnormalities. Our findings confirm the recent disease association of PRMT7, expand the phenotypic manifestations of this disorder and provide insight into the molecular pathogenesis of this new condition.
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Affiliation(s)
- K D Kernohan
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - A McBride
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - Y Xi
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - N Martin
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - J Schwartzentruber
- Genome Quebec Innovation Centre, McGill University, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - J Majewski
- Genome Quebec Innovation Centre, McGill University, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada
| | - S Blaser
- Department of Diagnostic Imaging, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | -
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - D Chitayat
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Canada.,Department of Pediatrics, Division of Clinical and Metabolic Genetics, Hospital for Sick Children, University of Toronto, Toronto, Canada
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81
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Kurzbuch AR, Magdum S. Chiari I malformation as part of the Floating-Harbor syndrome? Eur J Med Genet 2016; 59:615-617. [PMID: 27815143 DOI: 10.1016/j.ejmg.2016.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 10/19/2016] [Accepted: 10/30/2016] [Indexed: 11/26/2022]
Abstract
We report the first case of a patient diagnosed with Floating-Harbor syndrome (FHS) and Chiari I malformation. The 3-year-old girl was of proportional short stature, had delay of language development, conductive hearing loss and a high threshold of pain. Diagnosis of Chiari I malformation may be difficult in FHS patients who present with communication problems. Clinicians following patients with FHS should be aware of a possible relation between FHS and Chiari I malformation.
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Affiliation(s)
- Arthur R Kurzbuch
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Department of Pediatric Neurosurgery, Headley Way, Headington, Oxford OX3 9DU, United Kingdom.
| | - Shailendra Magdum
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Department of Pediatric Neurosurgery, Headley Way, Headington, Oxford OX3 9DU, United Kingdom
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82
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Rubinstein–Taybi syndrome type 2: report of nine new cases that extend the phenotypic and genotypic spectrum. Clin Dysmorphol 2016; 25:135-45. [DOI: 10.1097/mcd.0000000000000143] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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83
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Amita M, Srivastava P, Agarwal D, Phadke SR. Floating Harbor Syndrome. Indian J Pediatr 2016; 83:896-7. [PMID: 27206688 DOI: 10.1007/s12098-016-2153-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 05/09/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Moirangthem Amita
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Priyanka Srivastava
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Divya Agarwal
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India.
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84
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Buske OJ, Schiettecatte F, Hutton B, Dumitriu S, Misyura A, Huang L, Hartley T, Girdea M, Sobreira N, Mungall C, Brudno M. The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles. Hum Mutat 2016; 36:922-7. [PMID: 26255989 DOI: 10.1002/humu.22850] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/24/2015] [Indexed: 01/28/2023]
Abstract
Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis.
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Affiliation(s)
- Orion J Buske
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | | | | | - Sergiu Dumitriu
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Andriy Misyura
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Lijia Huang
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Taila Hartley
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Marta Girdea
- Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chris Mungall
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Michael Brudno
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
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85
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Liu T, Huang J. DNA End Resection: Facts and Mechanisms. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:126-130. [PMID: 27240470 PMCID: PMC4936662 DOI: 10.1016/j.gpb.2016.05.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 05/04/2016] [Accepted: 05/05/2016] [Indexed: 01/05/2023]
Abstract
DNA double-strand breaks (DSBs), which arise following exposure to a number of endogenous and exogenous agents, can be repaired by either the homologous recombination (HR) or non-homologous end-joining (NHEJ) pathways in eukaryotic cells. A vital step in HR repair is DNA end resection, which generates a long 3′ single-stranded DNA (ssDNA) tail that can invade the homologous DNA strand. The generation of 3′ ssDNA is not only essential for HR repair, but also promotes activation of the ataxia telangiectasia and Rad3-related protein (ATR). Multiple factors, including the MRN/X complex, C-terminal-binding protein interacting protein (CtIP)/Sae2, exonuclease 1 (EXO1), Bloom syndrome protein (BLM)/Sgs1, DNA2 nuclease/helicase, and several chromatin remodelers, cooperate to complete the process of end resection. Here we review the basic machinery involved in DNA end resection in eukaryotic cells.
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Affiliation(s)
- Ting Liu
- Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Jun Huang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou 310058, China.
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86
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Messina G, Atterrato MT, Dimitri P. When chromatin organisation floats astray: theSrcapgene and Floating–Harbor syndrome. J Med Genet 2016; 53:793-797. [DOI: 10.1136/jmedgenet-2016-103842] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 02/29/2016] [Accepted: 03/29/2016] [Indexed: 01/19/2023]
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87
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Priest JR, Osoegawa K, Mohammed N, Nanda V, Kundu R, Schultz K, Lammer EJ, Girirajan S, Scheetz T, Waggott D, Haddad F, Reddy S, Bernstein D, Burns T, Steimle JD, Yang XH, Moskowitz IP, Hurles M, Lifton RP, Nickerson D, Bamshad M, Eichler EE, Mital S, Sheffield V, Quertermous T, Gelb BD, Portman M, Ashley EA. De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects. PLoS Genet 2016; 12:e1005963. [PMID: 27058611 PMCID: PMC4825975 DOI: 10.1371/journal.pgen.1005963] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
Congenital heart disease (CHD) has a complex genetic etiology, and recent studies suggest that high penetrance de novo mutations may account for only a small fraction of disease. In a multi-institutional cohort surveyed by exome sequencing, combining analysis of 987 individuals (discovery cohort of 59 affected trios and 59 control trios, and a replication cohort of 100 affected singletons and 533 unaffected singletons) we observe variation at novel and known loci related to a specific cardiac malformation the atrioventricular septal defect (AVSD). In a primary analysis, by combining developmental coexpression networks with inheritance modeling, we identify a de novo mutation in the DNA binding domain of NR1D2 (p.R175W). We show that p.R175W changes the transcriptional activity of Nr1d2 using an in vitro transactivation model in HUVEC cells. Finally, we demonstrate previously unrecognized cardiovascular malformations in the Nr1d2tm1-Dgen knockout mouse. In secondary analyses we map genetic variation to protein-interaction networks suggesting a role for two collagen genes in AVSD, which we corroborate by burden testing in a second replication cohort of 100 AVSDs and 533 controls (p = 8.37e-08). Finally, we apply a rare-disease inheritance model to identify variation in genes previously associated with CHD (ZFPM2, NSD1, NOTCH1, VCAN, and MYH6), cardiac malformations in mouse models (ADAM17, CHRD, IFT140, PTPRJ, RYR1 and ATE1), and hypomorphic alleles of genes causing syndromic CHD (EHMT1, SRCAP, BBS2, NOTCH2, and KMT2D) in 14 of 59 trios, greatly exceeding variation in control trios without CHD (p = 9.60e-06). In total, 32% of trios carried at least one putatively disease-associated variant across 19 loci,suggesting that inherited and de novo variation across a heterogeneous group of loci may contribute to disease risk.
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Affiliation(s)
- James R. Priest
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Kazutoyo Osoegawa
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Nebil Mohammed
- University of California San Francisco Benioff Children’s Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America
| | - Vivek Nanda
- Department of Vascular Surgery, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Ramendra Kundu
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Kathleen Schultz
- University of California San Francisco Benioff Children’s Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America
| | - Edward J. Lammer
- University of California San Francisco Benioff Children’s Hospital Oakland, University of California San Francisco, San Francisco, California, United States of America
| | - Santhosh Girirajan
- Departments of Biochemistry, Molecular Biology, and Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Todd Scheetz
- College of Engineering, University of Iowa, Iowa City, Iowa, United States of America
| | - Daryl Waggott
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Francois Haddad
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Sushma Reddy
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Daniel Bernstein
- Division of Pediatric Cardiology, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Trudy Burns
- College of Public Health, University of Iowa, Iowa City, Iowa, United States of America
| | - Jeffrey D. Steimle
- Department of Pathology, University of Chicago, Chicago, Illinois, United States of America
| | - Xinan H. Yang
- Department of Pathology, University of Chicago, Chicago, Illinois, United States of America
| | - Ivan P. Moskowitz
- Department of Pathology, University of Chicago, Chicago, Illinois, United States of America
| | - Matthew Hurles
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Richard P. Lifton
- Department of Genetics, Yale University, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Debbie Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Evan E. Eichler
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Seema Mital
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Val Sheffield
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- Division of Medical Genetics, University of Iowa Carver College of Medicine, Iowa City, Iowa, United States of America
| | - Thomas Quertermous
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mt. Sinai, New York, New York, United States of America
| | - Michael Portman
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Euan A. Ashley
- Cardiovascular Institute, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford University, Stanford, California, United States of America
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88
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Wit JM, Oostdijk W, Losekoot M, van Duyvenvoorde HA, Ruivenkamp CAL, Kant SG. MECHANISMS IN ENDOCRINOLOGY: Novel genetic causes of short stature. Eur J Endocrinol 2016; 174:R145-73. [PMID: 26578640 DOI: 10.1530/eje-15-0937] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/16/2015] [Indexed: 12/17/2022]
Abstract
The fast technological development, particularly single nucleotide polymorphism array, array-comparative genomic hybridization, and whole exome sequencing, has led to the discovery of many novel genetic causes of growth failure. In this review we discuss a selection of these, according to a diagnostic classification centred on the epiphyseal growth plate. We successively discuss disorders in hormone signalling, paracrine factors, matrix molecules, intracellular pathways, and fundamental cellular processes, followed by chromosomal aberrations including copy number variants (CNVs) and imprinting disorders associated with short stature. Many novel causes of GH deficiency (GHD) as part of combined pituitary hormone deficiency have been uncovered. The most frequent genetic causes of isolated GHD are GH1 and GHRHR defects, but several novel causes have recently been found, such as GHSR, RNPC3, and IFT172 mutations. Besides well-defined causes of GH insensitivity (GHR, STAT5B, IGFALS, IGF1 defects), disorders of NFκB signalling, STAT3 and IGF2 have recently been discovered. Heterozygous IGF1R defects are a relatively frequent cause of prenatal and postnatal growth retardation. TRHA mutations cause a syndromic form of short stature with elevated T3/T4 ratio. Disorders of signalling of various paracrine factors (FGFs, BMPs, WNTs, PTHrP/IHH, and CNP/NPR2) or genetic defects affecting cartilage extracellular matrix usually cause disproportionate short stature. Heterozygous NPR2 or SHOX defects may be found in ∼3% of short children, and also rasopathies (e.g., Noonan syndrome) can be found in children without clear syndromic appearance. Numerous other syndromes associated with short stature are caused by genetic defects in fundamental cellular processes, chromosomal abnormalities, CNVs, and imprinting disorders.
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Affiliation(s)
- Jan M Wit
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilma Oostdijk
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Monique Losekoot
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Hermine A van Duyvenvoorde
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Sarina G Kant
- Departments of PaediatricsClinical GeneticsLeiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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89
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Abstract
'Epigenome' refers to the panoply of chemical modifications borne by DNA and its associated proteins that locally affect genome function. Epigenomic patterns are thought to be determined by external constraints resulting from development, disease and the environment, but DNA sequence is also a potential influence. We propose that domains of relatively uniform DNA base composition may modulate the epigenome through cell type-specific proteins that recognize short, frequent sequence motifs. Differential recruitment of epigenomic modifiers may adjust gene expression in multigene blocks as an alternative to tuning the activity of each gene separately, thus simplifying gene expression programming.
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90
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Yagi H, Takagi M, Narumi S, Hasegawa T, Nishimura G, Hasegawa Y. Stippled calcification in an infant with a recurrent SRCAP gene mutation. Am J Med Genet A 2016; 170A:1088-91. [PMID: 26788936 DOI: 10.1002/ajmg.a.37516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/04/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Hiroko Yagi
- Division of Genetic Research, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan.,Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Masaki Takagi
- Division of Genetic Research, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan.,Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Satoshi Narumi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Tomonobu Hasegawa
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Gen Nishimura
- Division of Radiology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Yukihiro Hasegawa
- Division of Genetic Research, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan.,Division of Endocrinology and Metabolism, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
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91
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Identification of a novel de novo mutation of CREBBP in a patient with Rubinstein-Taybi syndrome by targeted next-generation sequencing: a case report. Hum Pathol 2016; 47:144-9. [DOI: 10.1016/j.humpath.2015.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/24/2015] [Accepted: 09/02/2015] [Indexed: 11/22/2022]
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92
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Dand N, Schulz R, Weale ME, Southgate L, Oakey RJ, Simpson MA, Schlitt T. Network-Informed Gene Ranking Tackles Genetic Heterogeneity in Exome-Sequencing Studies of Monogenic Disease. Hum Mutat 2015; 36:1135-44. [PMID: 26394720 PMCID: PMC4982032 DOI: 10.1002/humu.22906] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 09/09/2015] [Indexed: 11/10/2022]
Abstract
Genetic heterogeneity presents a significant challenge for the identification of monogenic disease genes. Whole-exome sequencing generates a large number of candidate disease-causing variants and typical analyses rely on deleterious variants being observed in the same gene across several unrelated affected individuals. This is less likely to occur for genetically heterogeneous diseases, making more advanced analysis methods necessary. To address this need, we present HetRank, a flexible gene-ranking method that incorporates interaction network data. We first show that different genes underlying the same monogenic disease are frequently connected in protein interaction networks. This motivates the central premise of HetRank: those genes carrying potentially pathogenic variants and whose network neighbors do so in other affected individuals are strong candidates for follow-up study. By simulating 1,000 exome sequencing studies (20,000 exomes in total), we model varying degrees of genetic heterogeneity and show that HetRank consistently prioritizes more disease-causing genes than existing analysis methods. We also demonstrate a proof-of-principle application of the method to prioritize genes causing Adams-Oliver syndrome, a genetically heterogeneous rare disease. An implementation of HetRank in R is available via the Website http://sourceforge.net/p/hetrank/.
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Affiliation(s)
- Nick Dand
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Reiner Schulz
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Michael E Weale
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Laura Southgate
- Division of Genetics and Molecular Medicine, King's College London, London, UK.,Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Rebecca J Oakey
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Michael A Simpson
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | - Thomas Schlitt
- Division of Genetics and Molecular Medicine, King's College London, London, UK.,Institute for Mathematical and Molecular Biomedicine, King's College London, London, UK
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93
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Spena S, Gervasini C, Milani D. Ultra-Rare Syndromes: The Example of Rubinstein-Taybi Syndrome. J Pediatr Genet 2015; 4:177-86. [PMID: 27617129 DOI: 10.1055/s-0035-1564571] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 05/10/2015] [Indexed: 01/08/2023]
Abstract
Rubinstein-Taybi syndrome (RSTS) is a rare, congenital, plurimalformative, and neurodevelopmental disorder. Clinical diagnosis can be complicated by the heterogeneous clinical presentation and the lack of a consensus list of diagnostic criteria, and it is confirmed by molecular tests in approximately 55 to 78% of cases. The etiology is partially known with mutations in two functionally related genes: CREBBP and EP300. Notwithstanding the knowledge on clinical, genetic, and allelic heterogeneity, no clear genotype-phenotype correlation has yet been established. Standardized guidelines for the management of pediatric patients are available and therapy for RSTS patients is currently only symptomatic. In this article, several clinic and genetic aspects of RSTS are critically reviewed.
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Affiliation(s)
- Silvia Spena
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, Milano, Italy
| | - Donatella Milani
- Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore, Policlinico, Milano, Italy
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94
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Lopez-Atalaya JP, Valor LM, Barco A. Epigenetic factors in intellectual disability: the Rubinstein-Taybi syndrome as a paradigm of neurodevelopmental disorder with epigenetic origin. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 128:139-76. [PMID: 25410544 DOI: 10.1016/b978-0-12-800977-2.00006-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The number of genetic syndromes associated with intellectual disability that are caused by mutations in genes encoding chromatin-modifying enzymes has sharply risen in the last decade. We discuss here a neurodevelopmental disorder, the Rubinstein-Taybi syndrome (RSTS), originated by mutations in the genes encoding the lysine acetyltransferases CBP and p300. We first describe clinical and genetic aspects of the syndrome to later focus on the insight provided by the research in animal models of this disease. These studies have not only clarified the molecular etiology of RSTS and helped to dissect the developmental and adult components of the syndrome but also contributed to outline some important connections between epigenetics and cognition. We finally discuss how this body of research has opened new venues for the therapeutic intervention of this currently untreatable disease and present some of the outstanding questions in the field. We believe that the progress in the understanding of this rare disorder also has important implications for other intellectual disability disorders that share an epigenetic origin.
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Affiliation(s)
- Jose P Lopez-Atalaya
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Alicante, Spain
| | - Luis M Valor
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Alicante, Spain
| | - Angel Barco
- Instituto de Neurociencias, Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas, Alicante, Spain
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95
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Au PYB, You J, Caluseriu O, Schwartzentruber J, Majewski J, Bernier FP, Ferguson M, Valle D, Parboosingh JS, Sobreira N, Innes AM, Kline AD. GeneMatcher aids in the identification of a new malformation syndrome with intellectual disability, unique facial dysmorphisms, and skeletal and connective tissue abnormalities caused by de novo variants in HNRNPK. Hum Mutat 2015; 36:1009-1014. [PMID: 26173930 DOI: 10.1002/humu.22837] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 06/29/2015] [Indexed: 12/16/2022]
Abstract
We report a new syndrome due to loss-of-function variants in the heterogeneous nuclear ribonucleoprotein K gene (HNRNPK). We describe two probands: one with a de novo frameshift (NM_002140.3: c.953+1dup), and the other with a de novo splice donor site variant (NM_002140.3: c.257G>A). Both probands have intellectual disability, a shared unique craniofacial phenotype, and connective tissue and skeletal abnormalities. The identification of this syndrome was made possible by a new online tool, GeneMatcher, which facilitates connections between clinicians and researchers based on shared interest in candidate genes. This report demonstrates that new Web-based approaches can be effective in helping investigators solve exome sequencing projects, and also highlights the newer paradigm of "reverse phenotyping," where characterization of syndromic features follows the identification of genetic variants.
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Affiliation(s)
- P Y Billie Au
- Department of Medical Genetics, University of Calgary, Cumming School of Medicine, Alberta, Canada
| | - Jing You
- Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Jeremy Schwartzentruber
- Department of Human Genetics, McGill and Genome Quebec Innovation Center, McGill University, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill and Genome Quebec Innovation Center, McGill University, Quebec, Canada
| | - Francois P Bernier
- Department of Medical Genetics, University of Calgary, Cumming School of Medicine, Alberta, Canada.,Alberta Children's Hospital, Research Institute for Child and Maternal Health, University of Calgary, Alberta, Canada
| | - Marcia Ferguson
- Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD
| | | | - David Valle
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jillian S Parboosingh
- Department of Medical Genetics, University of Calgary, Cumming School of Medicine, Alberta, Canada.,Alberta Children's Hospital, Research Institute for Child and Maternal Health, University of Calgary, Alberta, Canada
| | - Nara Sobreira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - A Micheil Innes
- Department of Medical Genetics, University of Calgary, Cumming School of Medicine, Alberta, Canada.,Alberta Children's Hospital, Research Institute for Child and Maternal Health, University of Calgary, Alberta, Canada
| | - Antonie D Kline
- Harvey Institute for Human Genetics, Department of Pediatrics, Greater Baltimore Medical Center, Baltimore, MD
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96
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Gerundino F, Marseglia G, Pescucci C, Pelo E, Benelli M, Giachini C, Federighi B, Antonelli C, Torricelli F. 16p11.2 de novo microdeletion encompassing SRCAP gene in a patient with speech impairment, global developmental delay and behavioural problems. Eur J Med Genet 2015; 57:649-53. [PMID: 25451714 DOI: 10.1016/j.ejmg.2014.09.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 09/21/2014] [Indexed: 11/28/2022]
Abstract
We describe a patient with speech impairment, global developmental delay, behavioural problems and a 186 kb de novo microdeletion on 16p11.2. There are four OMIM Phenotypes entries partially overlapping with the deleted region and related to recurrent microdeletions/microduplications in 16p11.2. A detailed review of published data shows that microdeletions/microduplications' boundaries do not include genes that are deleted in the case here reported. The deletion encompasses 9 RefSeq genes and includes SRCAP (Snf2-related CREBBP activator protein, OMIM*611421), a disease causing gene. Recently, truncating mutations in the SRCAP gene have been shown to cause Floating-Harbor syndrome (FHS, OMIM#136140), a rare disorder characterized by peculiar facial features, short stature with delayed osseous maturation and speech impairment. The patient reported here shows few subtle phenotypic features resembling that of FHS, but she does not have sufficient signs and symptoms for the clinical diagnosis and a clinical classification based on facial gestalt is not possible. This is the first report of a 16p11.2 deletion completely removing one copy of SRCAP, suggesting that haploinsufficiency of this gene could be associated to speech impairment, global developmental delay, behavioural problems and few subtle phenotypic features resembling FHS. However, further evidence for the putative causative role of SRCAP isolated deletion is needed.
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97
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Fahrner JA, Bjornsson HT. Mendelian disorders of the epigenetic machinery: tipping the balance of chromatin states. Annu Rev Genomics Hum Genet 2015; 15:269-93. [PMID: 25184531 DOI: 10.1146/annurev-genom-090613-094245] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mendelian disorders of the epigenetic machinery are a newly delineated group of multiple congenital anomaly and intellectual disability syndromes resulting from mutations in genes encoding components of the epigenetic machinery. The gene products affected in these inherited conditions act in trans and are expected to have widespread epigenetic consequences. Many of these syndromes demonstrate phenotypic overlap with classical imprinting disorders and with one another. The various writer and eraser systems involve opposing players, which we propose must maintain a balance between open and closed chromatin states in any given cell. An imbalance might lead to disrupted expression of disease-relevant target genes. We suggest that classifying disorders based on predicted effects on this balance would be informative regarding pathogenesis. Furthermore, strategies targeted at restoring this balance might offer novel therapeutic avenues, taking advantage of available agents such as histone deacetylase inhibitors and histone acetylation antagonists.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ,
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98
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Gerhold CB, Hauer MH, Gasser SM. INO80-C and SWR-C: Guardians of the Genome. J Mol Biol 2015; 427:637-51. [DOI: 10.1016/j.jmb.2014.10.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/13/2014] [Accepted: 10/17/2014] [Indexed: 01/01/2023]
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99
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Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios. Genet Med 2015; 17:774-81. [PMID: 25590979 PMCID: PMC4791490 DOI: 10.1038/gim.2014.191] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/19/2014] [Indexed: 12/29/2022] Open
Abstract
Purpose: Despite the recognized clinical value of exome-based diagnostics, methods for comprehensive genomic interpretation remain immature. Diagnoses are based on known or presumed pathogenic variants in genes already associated with a similar phenotype. Here, we extend this paradigm by evaluating novel bioinformatics approaches to aid identification of new gene–disease associations. Genet Med17 10, 774–781. Methods: We analyzed 119 trios to identify both diagnostic genotypes in known genes and candidate genotypes in novel genes. We considered qualifying genotypes based on their population frequency and in silico predicted effects we also characterized the patterns of genotypes enriched among this collection of patients. Genet Med17 10, 774–781. Results: We obtained a genetic diagnosis for 29 (24%) of our patients. We showed that patients carried an excess of damaging de novo mutations in intolerant genes, particularly those shown to be essential in mice (P = 3.4 × 10−8). This enrichment is only partially explained by mutations found in known disease-causing genes. Genet Med17 10, 774–781. Conclusion: This work indicates that the application of appropriate bioinformatics analyses to clinical sequence data can also help implicate novel disease genes and suggest expanded phenotypes for known disease genes. These analyses further suggest that some cases resolved by whole-exome sequencing will have direct therapeutic implications. Genet Med17 10, 774–781.
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100
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Yuan B, Pehlivan D, Karaca E, Patel N, Charng WL, Gambin T, Gonzaga-Jauregui C, Sutton VR, Yesil G, Bozdogan ST, Tos T, Koparir A, Koparir E, Beck CR, Gu S, Aslan H, Yuregir OO, Al Rubeaan K, Alnaqeb D, Alshammari MJ, Bayram Y, Atik MM, Aydin H, Geckinli BB, Seven M, Ulucan H, Fenercioglu E, Ozen M, Jhangiani S, Muzny DM, Boerwinkle E, Tuysuz B, Alkuraya FS, Gibbs RA, Lupski JR. Global transcriptional disturbances underlie Cornelia de Lange syndrome and related phenotypes. J Clin Invest 2015; 125:636-51. [PMID: 25574841 DOI: 10.1172/jci77435] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 12/09/2014] [Indexed: 01/05/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a genetically heterogeneous disorder that presents with extensive phenotypic variability, including facial dysmorphism, developmental delay/intellectual disability (DD/ID), abnormal extremities, and hirsutism. About 65% of patients harbor mutations in genes that encode subunits or regulators of the cohesin complex, including NIPBL, SMC1A, SMC3, RAD21, and HDAC8. Wiedemann-Steiner syndrome (WDSTS), which shares CdLS phenotypic features, is caused by mutations in lysine-specific methyltransferase 2A (KMT2A). Here, we performed whole-exome sequencing (WES) of 2 male siblings clinically diagnosed with WDSTS; this revealed a hemizygous, missense mutation in SMC1A that was predicted to be deleterious. Extensive clinical evaluation and WES of 32 Turkish patients clinically diagnosed with CdLS revealed the presence of a de novo heterozygous nonsense KMT2A mutation in 1 patient without characteristic WDSTS features. We also identified de novo heterozygous mutations in SMC3 or SMC1A that affected RNA splicing in 2 independent patients with combined CdLS and WDSTS features. Furthermore, in families from 2 separate world populations segregating an autosomal-recessive disorder with CdLS-like features, we identified homozygous mutations in TAF6, which encodes a core transcriptional regulatory pathway component. Together, our data, along with recent transcriptome studies, suggest that CdLS and related phenotypes may be "transcriptomopathies" rather than cohesinopathies.
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