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Sun Y, Qian Y, Sun HX, Chen M, Luo Y, Xu X, Yan K, Wang L, Hu J, Dong M. Case Report: De novo DDX3X mutation caused intellectual disability in a female with skewed X-chromosome inactivation on the mutant allele. Front Genet 2022; 13:999442. [PMID: 36299587 PMCID: PMC9589230 DOI: 10.3389/fgene.2022.999442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2023] Open
Abstract
Skewed XCI plays an important role in the phenotypic heterogeneities of many X-linked disorders, even involving in diseases caused by XCI-escaping genes. DDX3X-related intellectual disability is more common in females and less common in males, who usually inherit from unaffected heterozygous mothers. As an X inactivation (XCI) escaping gene, the role of skewed XCI in the phenotype of DDX3X mutant female is unknown. Here we reported a DDX3X: c.694_711dup18 de novo heterozygous mutation in a female with intellectual disability on the maternal X chromosome on the basis of SNPs detected by PCR-sanger sequencing. AR assay revealed that the maternal mutant X chromosome was extremely inactivated in the proband. Using RNA sequencing and whole-exome sequencing, we quantified allelic read counts and allele-specific expression, and confirmed that the mutant X chromosome was inactive. Further, we verified that the mutant DDX3X allele had a lower expression level by RNA sequencing and RT-PCR, and the normal and mutated DDX3X expression accounted for respectively 70% and 30% of total. In conclusion, we found a symptomatic female with extreme skewing XCI in the DDX3X mutant allele. It was discovered that XCI in the mutant allele was insufficient to reverse the phenotype of DDX3X-related neurodevelopmental disorder. It contributed to a better understanding of the role of skewed XCI in phenotypic differences, which can aid in the genetic counseling and prenatal diagnosis of disorders in females with DDX3X defects.
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Affiliation(s)
- Yixi Sun
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yangwen Qian
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hai-Xi Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Min Chen
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuqin Luo
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaojing Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Yan
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liya Wang
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Junjie Hu
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Minyue Dong
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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2
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Cummings CT, Rowley MJ. Implications of Dosage Deficiencies in CTCF and Cohesin on Genome Organization, Gene Expression, and Human Neurodevelopment. Genes (Basel) 2022; 13:583. [PMID: 35456389 PMCID: PMC9030571 DOI: 10.3390/genes13040583] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Properly organizing DNA within the nucleus is critical to ensure normal downstream nuclear functions. CTCF and cohesin act as major architectural proteins, working in concert to generate thousands of high-intensity chromatin loops. Due to their central role in loop formation, a massive research effort has been dedicated to investigating the mechanism by which CTCF and cohesin create these loops. Recent results lead to questioning the direct impact of CTCF loops on gene expression. Additionally, results of controlled depletion experiments in cell lines has indicated that genome architecture may be somewhat resistant to incomplete deficiencies in CTCF or cohesin. However, heterozygous human genetic deficiencies in CTCF and cohesin have illustrated the importance of their dosage in genome architecture, cellular processes, animal behavior, and disease phenotypes. Thus, the importance of considering CTCF or cohesin levels is especially made clear by these heterozygous germline variants that characterize genetic syndromes, which are increasingly recognized in clinical practice. Defined primarily by developmental delay and intellectual disability, the phenotypes of CTCF and cohesin deficiency illustrate the importance of architectural proteins particularly in neurodevelopment. We discuss the distinct roles of CTCF and cohesin in forming chromatin loops, highlight the major role that dosage of each protein plays in the amplitude of observed effects on gene expression, and contrast these results to heterozygous mutation phenotypes in murine models and clinical patients. Insights highlighted by this comparison have implications for future research into these newly emerging genetic syndromes.
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Affiliation(s)
- Christopher T. Cummings
- Munroe-Meyer Institute, Department of Genetic Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - M. Jordan Rowley
- Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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3
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Odanaka Y, Ashida A, Nemoto S, Hamanaka K, Matsumoto N. Severe cardiac defect in Cornelia de Lange syndrome from a novel SMC1A variant. Pediatr Int 2022; 64:e15031. [PMID: 35396801 DOI: 10.1111/ped.15031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/17/2021] [Accepted: 10/12/2021] [Indexed: 01/05/2023]
Affiliation(s)
- Yutaka Odanaka
- Department of Pediatrics, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Akira Ashida
- Department of Pediatrics, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Shintaro Nemoto
- Department of Thoracic and Cardiovascular Surgery, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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4
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Pileggi S, La Vecchia M, Colombo EA, Fontana L, Colapietro P, Rovina D, Morotti A, Tabano S, Porta G, Alcalay M, Gervasini C, Miozzo M, Sirchia SM. Cohesin Mutations Induce Chromatin Conformation Perturbation of the H19/ IGF2 Imprinted Region and Gene Expression Dysregulation in Cornelia de Lange Syndrome Cell Lines. Biomolecules 2021; 11:1622. [PMID: 34827619 PMCID: PMC8615450 DOI: 10.3390/biom11111622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023] Open
Abstract
Traditionally, Cornelia de Lange Syndrome (CdLS) is considered a cohesinopathy caused by constitutive mutations in cohesin complex genes. Cohesin is a major regulator of chromatin architecture, including the formation of chromatin loops at the imprinted IGF2/H19 domain. We used 3C analysis on lymphoblastoid cells from CdLS patients carrying mutations in NIPBL and SMC1A genes to explore 3D chromatin structure of the IGF2/H19 locus and evaluate the influence of cohesin alterations in chromatin architecture. We also assessed quantitative expression of imprinted loci and WNT pathway genes, together with DMR methylation status of the imprinted genes. A general impairment of chromatin architecture and the emergence of new interactions were found. Moreover, imprinting alterations also involved the expression and methylation levels of imprinted genes, suggesting an association among cohesin genetic defects, chromatin architecture impairment, and imprinting network alteration. The WNT pathway resulted dysregulated: canonical WNT, cell cycle, and WNT signal negative regulation were the most significantly affected subpathways. Among the deregulated pathway nodes, the key node of the frizzled receptors was repressed. Our study provides new evidence that mutations in genes of the cohesin complex have effects on the chromatin architecture and epigenetic stability of genes commonly regulated by high order chromatin structure.
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Affiliation(s)
- Silvana Pileggi
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Marta La Vecchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Elisa Adele Colombo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Laura Fontana
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Patrizia Colapietro
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
| | - Davide Rovina
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Annamaria Morotti
- Research Laboratories Coordination Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy;
| | - Silvia Tabano
- Department of Pathophysiology and Transplantation, Medical Genetics, Università degli Studi di Milano, 20122 Milan, Italy; (P.C.); (S.T.)
- Laboratory of Medical Genetics, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giovanni Porta
- Centro di Medicina Genomica, Department of Medicine and Surgery, Università degli Studi dell’Insubria, 21100 Varese, Italy;
| | - Myriam Alcalay
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, 20139 Milan, Italy;
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Cristina Gervasini
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
| | - Monica Miozzo
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
- Unit of Medical Genetics, ASST Santi Paolo e Carlo, 20142 Milano, Italy
| | - Silvia Maria Sirchia
- Medical Genetics, Department of Health Sciences, Università degli Studi di Milano, 20142 Milano, Italy; (S.P.); (M.L.V.); (E.A.C.); (L.F.); (D.R.); (C.G.); (S.M.S.)
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5
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Ayerza-Casas A, Puisac-Uriol B, Pie-Juste J. Cornelia de Lange syndrome: Ventricular size and function in six children without congenital heart defects. Med Clin (Barc) 2020; 154:67-68. [PMID: 30470439 DOI: 10.1016/j.medcli.2018.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/03/2018] [Accepted: 10/04/2018] [Indexed: 10/27/2022]
Affiliation(s)
- Ariadna Ayerza-Casas
- Unidad de Cardiología Pediátrica, Servicio de Pediatría, Hospital Universitario Miguel Servet, Zaragoza, España; Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología, Facultad de Medicina, Universidad de Zaragoza. Instituto de Investigación Sanitaria (IIS)-Aragón, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-GCV02, Zaragoza, España
| | - Beatriz Puisac-Uriol
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología, Facultad de Medicina, Universidad de Zaragoza. Instituto de Investigación Sanitaria (IIS)-Aragón, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-GCV02, Zaragoza, España
| | - Juan Pie-Juste
- Unidad de Genética Clínica y Genómica Funcional, Departamento de Farmacología-Fisiología, Facultad de Medicina, Universidad de Zaragoza. Instituto de Investigación Sanitaria (IIS)-Aragón, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER)-GCV02, Zaragoza, España.
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6
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Ziats CA, Schwartz CE, Gecz J, Shaw M, Field MJ, Stevenson RE, Neri G. X-linked intellectual disability: Phenotypic expression in carrier females. Clin Genet 2019; 97:418-425. [PMID: 31705537 DOI: 10.1111/cge.13667] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/29/2019] [Accepted: 11/01/2019] [Indexed: 12/31/2022]
Abstract
To better understand the landscape of female phenotypic expression in X-linked intellectual disability (XLID), we surveyed the literature for female carriers of XLID gene alterations (n = 1098) and combined this with experience evaluating XLID kindreds at the Greenwood Genetic Center (n = 341) and at the University of Adelaide (n = 157). One-hundred forty-four XLID genes were grouped into nine categories based on the level of female phenotypic expression, ranging from no expression to female only expression. For each gene, the clinical presentation, gene expression in blood, X-inactivation (XI) pattern, biological pathway involved, and whether the gene escapes XI were noted. Among the XLID conditions, 88 (61.1%) exhibited female cognitive phenotypic expression only, while 56 (38.9%) had no female phenotypic expression (n = 45), phenotype expression with normal cognition in females (n = 8), or unknown status for female phenotypic expression (n = 3). In twenty-four (16.6%) XLID genes, XI was consistently skewed in female carriers, in 54 (37.5%) XI showed variable skewing, and in 33 (22.9%) XI was consistently random. The XI pattern was unknown in 33 (22.9%) XLID conditions. Therefore, there is evidence of a female carrier phenotype in the majority of XLID conditions although how exactly XI patterns influence the female phenotype in XLID conditions remains unclear.
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Affiliation(s)
- Catherine A Ziats
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Charles E Schwartz
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Jozef Gecz
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia.,Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Marie Shaw
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | | | - Roger E Stevenson
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Giovanni Neri
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina.,Istituto di Medicina Genomica, Università Cattolica del S. Cuore, Rome, Italy
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7
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Chinen Y, Nakamura S, Kaneshi T, Nakayashiro M, Yanagi K, Kaname T, Naritomi K, Nakanishi K. A novel nonsense SMC1A mutation in a patient with intractable epilepsy and cardiac malformation. Hum Genome Var 2019; 6:23. [PMID: 31098032 PMCID: PMC6513828 DOI: 10.1038/s41439-019-0053-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/20/2019] [Accepted: 03/31/2019] [Indexed: 01/11/2023] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a cohesinopathy caused by genetic variations. We present a female with SMC1A-associated CdLS with a novel SMC1A truncation mutation (p. Arg499Ter), transposition of the great arteries, and periodic intractable seizures from 40 months of age. A review of the literature revealed that a seizure-free period after birth of at least 15 months is required for these patients to be able to walk, irrespective of the epileptic course.
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Affiliation(s)
- Yasutsugu Chinen
- 1Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Sadao Nakamura
- 1Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Takuya Kaneshi
- 1Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Mami Nakayashiro
- Department of Pediatrics, Okinawa Prefectural Nanbu Medical Center Children's Medical Center, Haebaru, Okinawa Japan
| | - Kumiko Yanagi
- 3Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tadashi Kaname
- 3Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kenji Naritomi
- Okinawa Nanbu Habilitation and Medical Center, Naha, Japan
| | - Koichi Nakanishi
- 1Department of Child Health and Welfare (Pediatrics), Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
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8
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Gheldof A, Mackay DJG, Cheong Y, Verpoest W. Genetic diagnosis of subfertility: the impact of meiosis and maternal effects. J Med Genet 2019; 56:271-282. [PMID: 30728173 PMCID: PMC6581078 DOI: 10.1136/jmedgenet-2018-105513] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 12/24/2018] [Accepted: 12/27/2018] [Indexed: 02/06/2023]
Abstract
During reproductive age, approximately one in seven couples are confronted with fertility problems. While the aetiology is diverse, including infections, metabolic diseases, hormonal imbalances and iatrogenic effects, it is becoming increasingly clear that genetic factors have a significant contribution. Due to the complex nature of infertility that often hints at a multifactorial cause, the search for potentially causal gene mutations in idiopathic infertile couples has remained difficult. Idiopathic infertility patients with a suspicion of an underlying genetic cause can be expected to have mutations in genes that do not readily affect general health but are only essential in certain processes connected to fertility. In this review, we specifically focus on genes involved in meiosis and maternal-effect processes, which are of critical importance for reproduction and initial embryonic development. We give an overview of genes that have already been linked to infertility in human, as well as good candidates which have been described in other organisms. Finally, we propose a phenotypic range in which we expect an optimal diagnostic yield of a meiotic/maternal-effect gene panel.
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Affiliation(s)
- Alexander Gheldof
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Brussels, Belgium
- Reproduction and Genetics Department, Vrije Universiteit Brussel, Brussels, Belgium
| | - Deborah J G Mackay
- Faculty of Medicine, University of Southampton, Southampton University Hospital, Southampton, UK
| | - Ying Cheong
- Complete Fertility, Human Development of Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Willem Verpoest
- Reproduction and Genetics Department, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Reproductive Medicine, Universitair Ziekenhuis Brussel, Brussels, Belgium
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9
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Huisman S, Mulder PA, Redeker E, Bader I, Bisgaard AM, Brooks A, Cereda A, Cinca C, Clark D, Cormier-Daire V, Deardorff MA, Diderich K, Elting M, van Essen A, FitzPatrick D, Gervasini C, Gillessen-Kaesbach G, Girisha KM, Hilhorst-Hofstee Y, Hopman S, Horn D, Isrie M, Jansen S, Jespersgaard C, Kaiser FJ, Kaur M, Kleefstra T, Krantz ID, Lakeman P, Landlust A, Lessel D, Michot C, Moss J, Noon SE, Oliver C, Parenti I, Pie J, Ramos FJ, Rieubland C, Russo S, Selicorni A, Tümer Z, Vorstenbosch R, Wenger TL, van Balkom I, Piening S, Wierzba J, Hennekam RC. Phenotypes and genotypes in individuals with SMC1A variants. Am J Med Genet A 2017; 173:2108-2125. [PMID: 28548707 DOI: 10.1002/ajmg.a.38279] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 03/19/2017] [Accepted: 04/13/2017] [Indexed: 11/05/2022]
Abstract
SMC1A encodes one of the proteins of the cohesin complex. SMC1A variants are known to cause a phenotype resembling Cornelia de Lange syndrome (CdLS). Exome sequencing has allowed recognizing SMC1A variants in individuals with encephalopathy with epilepsy who do not resemble CdLS. We performed an international, interdisciplinary study on 51 individuals with SMC1A variants for physical and behavioral characteristics, and compare results to those in 67 individuals with NIPBL variants. For the Netherlands all known individuals with SMC1A variants were studied, both with and without CdLS phenotype. Individuals with SMC1A variants can resemble CdLS, but manifestations are less marked compared to individuals with NIPBL variants: growth is less disturbed, facial signs are less marked (except for periocular signs and thin upper vermillion), there are no major limb anomalies, and they have a higher level of cognitive and adaptive functioning. Self-injurious behavior is more frequent and more severe in the NIPBL group. In the Dutch group 5 of 13 individuals (all females) had a phenotype that shows a remarkable resemblance to Rett syndrome: epileptic encephalopathy, severe or profound intellectual disability, stereotypic movements, and (in some) regression. Their missense, nonsense, and frameshift mutations are evenly spread over the gene. We conclude that SMC1A variants can result in a phenotype resembling CdLS and a phenotype resembling Rett syndrome. Resemblances between the SMC1A group and the NIPBL group suggest that a disturbed cohesin function contributes to the phenotype, but differences between these groups may also be explained by other underlying mechanisms such as moonlighting of the cohesin genes.
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Affiliation(s)
- Sylvia Huisman
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Prinsenstichting Institute, Purmerend, the Netherlands
| | - Paul A Mulder
- Autism Team Northern-Netherlands, Jonx Department of Youth Mental Health and Autism, Lentis Psychiatric Institute, Groningen, the Netherlands
| | - Egbert Redeker
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Ingrid Bader
- Division of Clinical Genetics, Department of Pediatrics, Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Anne-Marie Bisgaard
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Alice Brooks
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Constanza Cinca
- División Genetica, Hospital de Clínicas José de San Martín, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dinah Clark
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Valerie Cormier-Daire
- Department of Medical Genetics, Reference Center for Skeletal Dysplasia, INSERM UMR 1163, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, Paris Descartes-Sorbonne Paris Cité University, AP-HP, Institut Imagine, and Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Matthew A Deardorff
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Karin Diderich
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mariet Elting
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | | | - David FitzPatrick
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Cristina Gervasini
- Department of Health Sciences, Medical Genetics, University of Milan, Milan, Italy
| | | | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal University, Manipal, India
| | | | - Saskia Hopman
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Denise Horn
- Institut für Medizinische Genetik und Humangenetik, Berlin, Germany
| | - Mala Isrie
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Sandra Jansen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cathrine Jespersgaard
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Frank J Kaiser
- Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Maninder Kaur
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ian D Krantz
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Phillis Lakeman
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Annemiek Landlust
- Autism Team Northern-Netherlands, Jonx Department of Youth Mental Health and Autism, Lentis Psychiatric Institute, Groningen, the Netherlands
| | - Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Caroline Michot
- Department of Medical Genetics, Reference Center for Skeletal Dysplasia, INSERM UMR 1163, Laboratory of Molecular and Physiopathological Bases of Osteochondrodysplasia, Paris Descartes-Sorbonne Paris Cité University, AP-HP, Institut Imagine, and Hôpital Universitaire Necker-Enfants Malades, Paris, France
| | - Jo Moss
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, United Kingdom.,Institute of Cognitive Neuroscience, University College London, London, United Kingdom
| | - Sarah E Noon
- Division of Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Chris Oliver
- Cerebra Centre for Neurodevelopmental Disorders, School of Psychology, University of Birmingham, Birmingham, United Kingdom
| | - Ilaria Parenti
- Institut für Humangenetik Lübeck, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany.,Section for Functional Genetics, Institute of Human Genetics, University of Lübeck, Lübeck, Germany
| | - Juan Pie
- Laboratorio de Genética Clínica y Genómica Funcional, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Feliciano J Ramos
- Unidad de Genética Clínica, Servicio de Pediatría, Hospital Clínico Universitario "Lozano Blesa" CIBERER-GCV02 and Departamento de Pediatría, Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain
| | - Claudine Rieubland
- Division of Human Genetics, Department of Pediatrics, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Silvia Russo
- Molecular Biology Laboratory, Istituto Auxologico Italiano, Milan, Italy
| | | | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | | | - Tara L Wenger
- Division of Craniofacial Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Ingrid van Balkom
- Autism Team Northern-Netherlands, Jonx Department of Youth Mental Health and Autism, Lentis Psychiatric Institute, Groningen, the Netherlands
| | - Sigrid Piening
- Autism Team Northern-Netherlands, Jonx Department of Youth Mental Health and Autism, Lentis Psychiatric Institute, Groningen, the Netherlands
| | - Jolanta Wierzba
- Departments of Pediatrics, Hematology, Oncology and Department of General Nursery, Medical University of Gdansk, Gdansk, Poland
| | - Raoul C Hennekam
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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10
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Symonds JD, Joss S, Metcalfe KA, Somarathi S, Cruden J, Devlin AM, Donaldson A, DiDonato N, Fitzpatrick D, Kaiser FJ, Lampe AK, Lees MM, McLellan A, Montgomery T, Mundada V, Nairn L, Sarkar A, Schallner J, Pozojevic J, Parenti I, Tan J, Turnpenny P, Whitehouse WP, Zuberi SM. Heterozygous truncation mutations of the SMC1A gene cause a severe early onset epilepsy with cluster seizures in females: Detailed phenotyping of 10 new cases. Epilepsia 2017; 58:565-575. [PMID: 28166369 DOI: 10.1111/epi.13669] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2016] [Indexed: 12/30/2022]
Abstract
OBJECTIVE The phenotype of seizure clustering with febrile illnesses in infancy/early childhood is well recognized. To date the only genetic epilepsy consistently associated with this phenotype is PCDH19, an X-linked disorder restricted to females, and males with mosaicism. The SMC1A gene, which encodes a structural component of the cohesin complex is also located on the X chromosome. Missense variants and small in-frame deletions of SMC1A cause approximately 5% of Cornelia de Lange Syndrome (CdLS). Recently, protein truncating mutations in SMC1A have been reported in five females, all of whom have been affected by a drug-resistant epilepsy, and severe developmental impairment. Our objective was to further delineate the phenotype of SMC1A truncation. METHOD Female cases with de novo truncation mutations in SMC1A were identified from the Deciphering Developmental Disorders (DDD) study (n = 8), from postmortem testing of an affected twin (n = 1), and from clinical testing with an epilepsy gene panel (n = 1). Detailed information on the phenotype in each case was obtained. RESULTS Ten cases with heterozygous de novo mutations in the SMC1A gene are presented. All 10 mutations identified are predicted to result in premature truncation of the SMC1A protein. All cases are female, and none had a clinical diagnosis of CdLS. They presented with onset of epileptic seizures between <4 weeks and 28 months of age. In the majority of cases, a marked preponderance for seizures to occur in clusters was noted. Seizure clusters were associated with developmental regression. Moderate or severe developmental impairment was apparent in all cases. SIGNIFICANCE Truncation mutations in SMC1A cause a severe epilepsy phenotype with cluster seizures in females. These mutations are likely to be nonviable in males.
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Affiliation(s)
- Joseph D Symonds
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, Queen Elizabeth University Hospitals, Glasgow, United Kingdom.,School of Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Shelagh Joss
- West of Scotland Clinical Genetics Service, Glasgow, United Kingdom
| | - Kay A Metcalfe
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, Manchester, United Kingdom.,Division of Evolution and Genomic sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Suresh Somarathi
- Manchester Centre for Genomic Medicine, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Jamie Cruden
- Department of Paediatrics, Victoria Infirmary, Kirkcaldy, United Kingdom
| | - Anita M Devlin
- Paediatric Neurology, Great North Children's Hospital, Newcastle Acute Hospitals NHS Trust, Newcastle-upon-Tyne, United Kingdom
| | | | | | - David Fitzpatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Frank J Kaiser
- Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany
| | - Anne K Lampe
- South East Scotland Clinical Genetic Service, Edinburgh, United Kingdom
| | - Melissa M Lees
- Clinical Genetics, Great Ormond Street Hospital, London, United Kingdom
| | - Ailsa McLellan
- Department of Paediatric Neurosciences, Royal Hospital for Sick Children, Edinburgh, United Kingdom
| | - Tara Montgomery
- Institute of Genetic Medicine, Newcastle-upon-Tyne, United Kingdom
| | - Vivek Mundada
- Paediatric Neurology Royal London Hospital, London, United Kingdom
| | - Lesley Nairn
- Department of Paediatrics, Royal Alexandra Hospital, Paisley, United Kingdom
| | - Ajoy Sarkar
- Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom
| | - Jens Schallner
- Carl Gustav Carus Hospital, at the TU Dresden, Dresden, Germany
| | - Jelena Pozojevic
- Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany
| | - Ilaria Parenti
- Section for Functional Genetics, Institute for Human Genetics, University of Lübeck, Lübeck, Germany
| | - Jeen Tan
- Paediatric Neurology, Royal Manchester Children's Hospital, Manchester, United Kingdom
| | | | - William P Whitehouse
- Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom.,School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | -
- The Deciphering Developmental Disorders study, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Sameer M Zuberi
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, Queen Elizabeth University Hospitals, Glasgow, United Kingdom.,School of Medicine, University of Glasgow, Glasgow, United Kingdom
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11
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Wenger TL, Chow P, Randle SC, Rosen A, Birgfeld C, Wrede J, Javid P, King D, Manh V, Hing AV, Albers E. Novel findings of left ventricular non-compaction cardiomyopathy, microform cleft lip and poor vision in patient with SMC1A
-associated Cornelia de Lange syndrome. Am J Med Genet A 2016; 173:414-420. [DOI: 10.1002/ajmg.a.38030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 10/03/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Tara L. Wenger
- Division of Craniofacial Medicine; Seattle Children's Hospital; Seattle Washington
| | - Penny Chow
- Division of Genetics; Seattle Children's Hospital; Seattle Washington
| | | | - Anna Rosen
- Division of Craniofacial Medicine; Seattle Children's Hospital; Seattle Washington
| | - Craig Birgfeld
- Division of Craniofacial Medicine; Seattle Children's Hospital; Seattle Washington
| | - Joanna Wrede
- Division of Neurology; Seattle Children's Hospital; Seattle Washington
- Division of Pulmonary and Sleep Medicine; Seattle Children's Hospital; Seattle Washington
| | - Patrick Javid
- Division of Pediatric General and Thoracic Surgery; Seattle Children's Hospital; Seattle Washington
| | - Darcy King
- Division of Craniofacial Medicine; Seattle Children's Hospital; Seattle Washington
- Division of Neurodevelopmental Disabilities; Seattle Children's Hospital; Seattle Washington
| | - Vivian Manh
- Division of Ophthalmology; Seattle Children's Hospital; Seattle Washington
| | - Anne V. Hing
- Division of Craniofacial Medicine; Seattle Children's Hospital; Seattle Washington
| | - Erin Albers
- Division of Cardiology; Seattle Children's Hospital; Seattle Washington
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12
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Fieremans N, Van Esch H, Holvoet M, Van Goethem G, Devriendt K, Rosello M, Mayo S, Martinez F, Jhangiani S, Muzny DM, Gibbs RA, Lupski JR, Vermeesch JR, Marynen P, Froyen G. Identification of Intellectual Disability Genes in Female Patients with a Skewed X-Inactivation Pattern. Hum Mutat 2016; 37:804-11. [PMID: 27159028 DOI: 10.1002/humu.23012] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 12/30/2022]
Abstract
Intellectual disability (ID) is a heterogeneous disorder with an unknown molecular etiology in many cases. Previously, X-linked ID (XLID) studies focused on males because of the hemizygous state of their X chromosome. Carrier females are generally unaffected because of the presence of a second normal allele, or inactivation of the mutant X chromosome in most of their cells (skewing). However, in female ID patients, we hypothesized that the presence of skewing of X-inactivation would be an indicator for an X chromosomal ID cause. We analyzed the X-inactivation patterns of 288 females with ID, and found that 22 (7.6%) had extreme skewing (>90%), which is significantly higher than observed in the general population (3.6%; P = 0.029). Whole-exome sequencing of 19 females with extreme skewing revealed causal variants in six females in the XLID genes DDX3X, NHS, WDR45, MECP2, and SMC1A. Interestingly, variants in genes escaping X-inactivation presumably cause both XLID and skewing of X-inactivation in three of these patients. Moreover, variants likely accounting for skewing only were detected in MED12, HDAC8, and TAF9B. All tested candidate causative variants were de novo events. Hence, extreme skewing is a good indicator for the presence of X-linked variants in female patients.
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Affiliation(s)
- Nathalie Fieremans
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Belgium.,Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Maureen Holvoet
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Gert Van Goethem
- Het GielsBos, Gierle, Belgium and Department of Neurology, University Hospital of Antwerp (UZA), Antwerp, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Monica Rosello
- Genetics Unit, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Sonia Mayo
- Genetics Unit, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Francisco Martinez
- Genetics Unit, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas
| | - Joris R Vermeesch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Belgium
| | - Guy Froyen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Belgium
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13
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Moey C, Hinze SJ, Brueton L, Morton J, McMullan DJ, Kamien B, Barnett CP, Brunetti-Pierri N, Nicholl J, Gecz J, Shoubridge C. Xp11.2 microduplications including IQSEC2, TSPYL2 and KDM5C genes in patients with neurodevelopmental disorders. Eur J Hum Genet 2016; 24:373-80. [PMID: 26059843 PMCID: PMC4757771 DOI: 10.1038/ejhg.2015.123] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/26/2015] [Accepted: 05/06/2015] [Indexed: 01/06/2023] Open
Abstract
Copy number variations are a common cause of intellectual disability (ID). Determining the contribution of copy number variants (CNVs), particularly gains, to disease remains challenging. Here, we report four males with ID with sub-microscopic duplications at Xp11.2 and review the few cases with overlapping duplications reported to date. We established the extent of the duplicated regions in each case encompassing a minimum of three known disease genes TSPYL2, KDM5C and IQSEC2 with one case also duplicating the known disease gene HUWE1. Patients with a duplication encompassing TSPYL2, KDM5C and IQSEC2 without gains of nearby SMC1A and HUWE1 genes have not been reported thus far. All cases presented with ID and significant deficits of speech development. Some patients also manifested behavioral disturbances such as hyperactivity and attention-deficit/hyperactivity disorder. Lymphoblastic cell lines from patients show markedly elevated levels of TSPYL2, KDM5C and SMC1A, transcripts consistent with the extent of their CNVs. The duplicated region in our patients contains several genes known to escape X-inactivation, including KDM5C, IQSEC2 and SMC1A. In silico analysis of expression data in selected gene expression omnibus series indicates that dosage of these genes, especially IQSEC2, is similar in males and females despite the fact they escape from X-inactivation in females. Taken together, the data suggest that gains in Xp11.22 including IQSEC2 cause ID and are associated with hyperactivity and attention-deficit/hyperactivity disorder, and are likely to be dosage-sensitive in males.
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Affiliation(s)
- Ching Moey
- Department of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Susan J Hinze
- Department of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Louise Brueton
- Clinical Genetics unit, Birmingham Women's Hospital, Birmingham, UK
| | - Jenny Morton
- Clinical Genetics unit, Birmingham Women's Hospital, Birmingham, UK
| | | | | | | | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Napoli, Italy
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | | | - Jozef Gecz
- Department of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Cheryl Shoubridge
- Department of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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14
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Jansen S, Kleefstra T, Willemsen MH, de Vries P, Pfundt R, Hehir-Kwa JY, Gilissen C, Veltman JA, de Vries BBA, Vissers LELM. De novo loss-of-function mutations in X-linked SMC1A cause severe ID and therapy-resistant epilepsy in females: expanding the phenotypic spectrum. Clin Genet 2016; 90:413-419. [PMID: 26752331 DOI: 10.1111/cge.12729] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/04/2016] [Accepted: 01/04/2016] [Indexed: 12/30/2022]
Abstract
De novo missense mutations and in-frame coding deletions in the X-linked gene SMC1A (structural maintenance of chromosomes 1A), encoding part of the cohesin complex, are known to cause Cornelia de Lange syndrome in both males and females. For a long time, loss-of-function (LoF) mutations in SMC1A were considered incompatible with life, as such mutations had not been reported in neither male nor female patients. However, recently, the authors and others reported LoF mutations in females with intellectual disability (ID) and epilepsy. Here we present the detailed phenotype of two females with de novo LoF mutations in SMC1A, including a de novo mutation of single base deletion [c.2364del, p.(Asn788Lysfs*10)], predicted to result in a frameshift, and a de novo deletion of exon 16, resulting in an out-of-frame mRNA splice product [p.(Leu808Argfs*6)]. By combining our patients with the other recently reported females carrying SMC1A LoF mutations, we ascertained a phenotypic spectrum of (severe) ID, therapy-resistant epilepsy, absence/delay of speech, hypotonia and small hands and feet. Our data show the existence of a novel phenotypic entity - distinct from CdLS - and caused by de novo SMC1A LoF mutations.
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Affiliation(s)
- S Jansen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - T Kleefstra
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - M H Willemsen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - P de Vries
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - R Pfundt
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - J Y Hehir-Kwa
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - C Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
| | - J A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - B B A de Vries
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - L E L M Vissers
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands
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15
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Goldstein JH, Tim-aroon T, Shieh J, Merrill M, Deeb KK, Zhang S, Bass NE, Bedoyan JK. Novel SMC1A frameshift mutations in children with developmental delay and epilepsy. Eur J Med Genet 2015; 58:562-8. [DOI: 10.1016/j.ejmg.2015.09.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 09/10/2015] [Accepted: 09/15/2015] [Indexed: 11/26/2022]
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16
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Lebrun N, Lebon S, Jeannet PY, Jacquemont S, Billuart P, Bienvenu T. Early-onset encephalopathy with epilepsy associated with a novel splice site mutation in SMC1A. Am J Med Genet A 2015; 167A:3076-81. [PMID: 26358754 DOI: 10.1002/ajmg.a.37364] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/28/2015] [Indexed: 11/07/2022]
Abstract
We report on the clinical and molecular characterization of a female patient with early-onset epileptic encephalopathy, who was found to carry a de novo novel splice site mutation in SMC1A. This girl shared some morphologic and anthropometric traits described in patients with clinical diagnosis of Cornelia de Lange syndrome and with SMC1A mutation but also has severe encephalopathy with early-onset epilepsy. In addition, she had midline hand stereotypies and scoliosis leading to the misdiagnosis of a Rett overlap syndrome. Molecular studies found a novel de novo splice site mutation (c.1911 + 1G > T) in SMC1A. This novel splice mutation was associated with an aberrantly processed mRNA that included intron 11 of the gene. Moreover, quantitative approach by RT-PCR showed a severe reduction of the SMC1A transcript suggesting that this aberrant transcript may be unstable and degraded. Taken together, our data suggest that the phenotype may be due to a loss-of-function of SMC1A in this patient. Our findings suggest that loss-of-function mutations of SMC1A may be associated with early-onset encephalopathy with epilepsy.
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Affiliation(s)
- Nicolas Lebrun
- Inserm, Institut Cochin, Paris, France.,Cnrs, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Sébastien Lebon
- Department of Pediatrics, Pediatric Neurology and Neurorehabilitation Unit, Lausanne University Hospital, Switzerland
| | - Pierre-Yves Jeannet
- Department of Pediatrics, Pediatric Neurology and Neurorehabilitation Unit, Lausanne University Hospital, Switzerland
| | - Sébastien Jacquemont
- Département de Pédiatrie, Faculté de médecine, Université de Montréal, CHU Sainte Justine, Montreal, Canada
| | - Pierre Billuart
- Inserm, Institut Cochin, Paris, France.,Cnrs, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Thierry Bienvenu
- Inserm, Institut Cochin, Paris, France.,Cnrs, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Assistance Publique - Hôpitaux de Paris, Groupe Universitaire Paris Centre, Site Cochin, Laboratoire de Biochimie et Génétique Moléculaire, Paris, France
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17
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Boyle M, Jespersgaard C, Brøndum-Nielsen K, Bisgaard AM, Tümer Z. Cornelia de Lange syndrome. Clin Genet 2014; 88:1-12. [DOI: 10.1111/cge.12499] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/27/2014] [Accepted: 09/07/2014] [Indexed: 12/13/2022]
Affiliation(s)
- M.I. Boyle
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
| | - C. Jespersgaard
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
| | - K. Brøndum-Nielsen
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
| | - A.-M. Bisgaard
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
| | - Z. Tümer
- Applied Human Molecular Genetics, Kennedy Center, Department of Clinical Genetics, Rigshospitalet; University of Copenhagen; Glostrup Denmark
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18
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Parenti I, Rovina D, Masciadri M, Cereda A, Azzollini J, Picinelli C, Limongelli G, Finelli P, Selicorni A, Russo S, Gervasini C, Larizza L. Overall and allele-specific expression of the SMC1A gene in female Cornelia de Lange syndrome patients and healthy controls. Epigenetics 2014; 9:973-9. [PMID: 24756084 DOI: 10.4161/epi.28903] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare multisystem disorder characterized by facial dysmorphisms, limb anomalies, and growth and cognitive deficits. Mutations in genes encoding subunits (SMC1A, SMC3, RAD21) or regulators (NIPBL, HDAC8) of the cohesin complex account for approximately 65% of clinically diagnosed CdLS cases. The SMC1A gene (Xp11.22), responsible for 5% of CdLS cases, partially escapes X chromosome inactivation in humans and the allele on the inactive X chromosome is variably expressed. In this study, we evaluated overall and allele-specific SMC1A expression. Real-time PCR analysis conducted on 17 controls showed that SMC1A expression in females is 50% higher than in males. Immunoblotting experiments confirmed a 44% higher protein level in healthy females than in males, and showed no significant differences in SMC1A protein levels between controls and patients. Pyrosequencing was used to assess the reciprocal level of allelic expression in six female carriers of different SMC1A mutations and 15 controls who were heterozygous at a polymorphic transcribed SMC1A locus. The two alleles were expressed at a 1:1 ratio in the control group and at a 2:1 ratio in favor of the wild type allele in the test group. Since a dominant negative effect is considered the pathogenic mechanism in SMC1A-defective female patients, the level of allelic preferential expression might be one of the factors contributing to the wide phenotypic variability observed in these patients. An extension of this study to a larger cohort containing mild to borderline cases could enhance our understanding of the clinical spectrum of SMC1A-linked CdLS.
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Affiliation(s)
- Ilaria Parenti
- Medical Genetics; Department of Health Sciences; Università degli Studi di Milano; Milan, Italy
| | - Davide Rovina
- Medical Genetics; Department of Health Sciences; Università degli Studi di Milano; Milan, Italy
| | - Maura Masciadri
- Laboratory of Medical Cytogenetics and Molecular Genetics; IRCCS Istituto Auxologico Italiano; Milan, Italy
| | - Anna Cereda
- Department of Pediatrics; Università Milano Bicocca; Fondazione MBBM; Monza, Italy
| | - Jacopo Azzollini
- Medical Genetics; Department of Health Sciences; Università degli Studi di Milano; Milan, Italy
| | - Chiara Picinelli
- Laboratory of Medical Cytogenetics and Molecular Genetics; IRCCS Istituto Auxologico Italiano; Milan, Italy
| | - Giuseppe Limongelli
- Department of Cardiology; Monaldi Hospital; Second University of Naples; Naples, Italy
| | - Palma Finelli
- Laboratory of Medical Cytogenetics and Molecular Genetics; IRCCS Istituto Auxologico Italiano; Milan, Italy; Department of Medical Biotechnology and Translational Medicine; Università degli Studi di Milano; Milan, Italy
| | - Angelo Selicorni
- Department of Pediatrics; Università Milano Bicocca; Fondazione MBBM; Monza, Italy
| | - Silvia Russo
- Laboratory of Medical Cytogenetics and Molecular Genetics; IRCCS Istituto Auxologico Italiano; Milan, Italy
| | - Cristina Gervasini
- Medical Genetics; Department of Health Sciences; Università degli Studi di Milano; Milan, Italy
| | - Lidia Larizza
- Medical Genetics; Department of Health Sciences; Università degli Studi di Milano; Milan, Italy; Laboratory of Medical Cytogenetics and Molecular Genetics; IRCCS Istituto Auxologico Italiano; Milan, Italy
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Gervasini C, Russo S, Cereda A, Parenti I, Masciadri M, Azzollini J, Melis D, Aravena T, Doray B, Ferrarini A, Garavelli L, Selicorni A, Larizza L. Cornelia de Lange individuals with new and recurrent SMC1A mutations enhance delineation of mutation repertoire and phenotypic spectrum. Am J Med Genet A 2013; 161A:2909-19. [PMID: 24124034 DOI: 10.1002/ajmg.a.36252] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/29/2013] [Indexed: 01/11/2023]
Abstract
We report on the clinical and molecular characterization of eight patients, one male and seven females, with clinical diagnosis of Cornelia de Lange syndrome (CdLS), who were found to carry distinct mutations of the SMC1A gene. Five of the eight mutations are novel, with two involving amino acid residues previously described as altered in a different way. The other three have been reported each in a single case. Comparison of pairs of individuals with the same mutation indicates only partial overlap of their clinical phenotypes. The following novel missense mutations, all affecting highly conserved amino acid residues, were found: p.R398G in the N-terminal coiled-coil domain, p.V651M in the C-terminal coiled-coil/hinge junction, p.R693G in the C-terminal coiled-coil, and p.N1166T and p.L1189F in the C-terminal ABC cassette. The latter is localized in the H-loop, and represents the first mutation involving a functional motif of SMC1A protein. The effect of the mutations on SMC1A protein function has been predicted using four bioinformatic tools. All mutations except p.V651M were scored as pathogenic by three or four of the tools. p.V651M was found in the only male individual of our cohort, who presented with the most severe phenotype. This raises the issue of gender effect when addressing mutation-phenotype correlation for genes such as SMC1A, which incompletely escapes X-inactivation. Our clinical and molecular findings expand the total number of characterized SMC1A-mutated patients (from 44 to 52) and the restricted repertoire of SMC1A mutations (from 29 to 34), contributing to the molecular and clinical signature of SMC1A-based CdLS.
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Affiliation(s)
- Cristina Gervasini
- Department of Health Sciences, Medical Genetics, Università degli Studi di Milano, Milan, Italy
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Mannini L, Menga S, Tonelli A, Zanotti S, Bassi MT, Magnani C, Musio A. SMC1A codon 496 mutations affect the cellular response to genotoxic treatments. Am J Med Genet A 2012; 158A:224-8. [PMID: 22140011 DOI: 10.1002/ajmg.a.34384] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 10/24/2011] [Indexed: 01/01/2023]
Abstract
Cornelia de Lange syndrome is a pleiotropic developmental syndrome characterized by growth and cognitive impairment, facial dysmorphic features, limb anomalies, and other malformations. Mutations in core cohesin genes SMC1A and SMC3, and the cohesin regulatory gene, NIPBL, have been identified in Cornelia de Lange syndrome probands. Patients with NIPBL mutations have more severe phenotypes when compared to those with mutations in SMC1A or SMC3. To date, 26 distinct SMC1A mutations have been identified in patients with Cornelia de Lange syndrome. Here, we describe a 3-year-old girl with psychomotor and cognitive impairment, mild facial dysmorphic features but no limb anomaly, heterozygous for a c.1487G>A mutation in SMC1A which predicts p.Arg496His. We show that this mutation leads to an impairment of the cellular response to genotoxic treatments.
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Affiliation(s)
- Linda Mannini
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Pisa, Italy
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Hoppman-Chaney N, Jang JS, Jen J, Babovic-Vuksanovic D, Hodge JC. In-frame multi-exon deletion of SMC1A in a severely affected female with Cornelia de Lange Syndrome. Am J Med Genet A 2011; 158A:193-8. [DOI: 10.1002/ajmg.a.34360] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 10/02/2011] [Indexed: 11/09/2022]
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