1
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Gokce-Samar Z, de Bellescize J, Arzimanoglou A, Putoux A, Chatron N, Lesca G, Portes VD. STAG2 microduplication in a patient with eyelid myoclonia and absences and a review of EMA-related reported genes. Eur J Med Genet 2022; 65:104636. [DOI: 10.1016/j.ejmg.2022.104636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 03/14/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022]
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2
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Aoi H, Lei M, Mizuguchi T, Nishioka N, Goto T, Miyama S, Suzuki T, Iwama K, Uchiyama Y, Mitsuhashi S, Itakura A, Takeda S, Matsumoto N. Nonsense variants of STAG2 result in distinct congenital anomalies. Hum Genome Var 2020; 7:26. [PMID: 33014403 PMCID: PMC7501222 DOI: 10.1038/s41439-020-00114-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/10/2020] [Accepted: 08/12/2020] [Indexed: 12/20/2022] Open
Abstract
Herein, we report two female cases with novel nonsense mutations of STAG2 at Xq25, encoding stromal antigen 2, a component of the cohesion complex. Exome analysis identified c.3097 C>T, p.(Arg1033*) in Case 1 (a fetus with multiple congenital anomalies) and c.2229 G>A, p.(Trp743*) in Case 2 (a 7-year-old girl with white matter hypoplasia and cleft palate). X inactivation was highly skewed in both cases.
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Affiliation(s)
- Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Ming Lei
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuko Nishioka
- Department of Obstetrics and Gynecology, Koshigaya Municipal Hospital, Saitama, Japan
| | - Tomohide Goto
- Department of Neurology, Kanagawa Children’s Medical Center, Kanagawa, Japan
| | - Sahoko Miyama
- Department of Neurology, Tokyo Metropolitan Children’s Medical Center, Fuchu, Tokyo, Japan
| | - Toshifumi Suzuki
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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3
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Frints SGM, Ozanturk A, Rodríguez Criado G, Grasshoff U, de Hoon B, Field M, Manouvrier-Hanu S, E Hickey S, Kammoun M, Gripp KW, Bauer C, Schroeder C, Toutain A, Mihalic Mosher T, Kelly BJ, White P, Dufke A, Rentmeester E, Moon S, Koboldt DC, van Roozendaal KEP, Hu H, Haas SA, Ropers HH, Murray L, Haan E, Shaw M, Carroll R, Friend K, Liebelt J, Hobson L, De Rademaeker M, Geraedts J, Fryns JP, Vermeesch J, Raynaud M, Riess O, Gribnau J, Katsanis N, Devriendt K, Bauer P, Gecz J, Golzio C, Gontan C, Kalscheuer VM. Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder. Mol Psychiatry 2019; 24:1748-1768. [PMID: 29728705 DOI: 10.1038/s41380-018-0065-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/28/2018] [Indexed: 12/25/2022]
Abstract
RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations. In contrast, 44 heterozygous female carriers have normal cognition and behavior, but eight showed mild physical features. All RLIM variants identified are missense changes co-segregating with the phenotype and predicted to affect protein function. Eight of the nine altered amino acids are conserved and lie either within a domain essential for binding interacting proteins or in the C-terminal RING finger catalytic domain. In vitro experiments revealed that these amino acid changes in the RLIM RING finger impaired RLIM ubiquitin ligase activity. In vivo experiments in rlim mutant zebrafish showed that wild type RLIM rescued the zebrafish rlim phenotype, whereas the patient-specific missense RLIM variants failed to rescue the phenotype and thus represent likely severe loss-of-function mutations. In summary, we identified a spectrum of RLIM missense variants causing syndromic XLID and affecting the ubiquitin ligase activity of RLIM, suggesting that enzymatic activity of RLIM is required for normal development, cognition and behavior.
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Affiliation(s)
- Suzanna G M Frints
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands. .,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands.
| | - Aysegul Ozanturk
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | | | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Bas de Hoon
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands.,Department of Gynaecology and Obstetrics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Michael Field
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Sylvie Manouvrier-Hanu
- Clinique de Génétique médicale Guy Fontaine, Centre de référence maladies rares Anomalies du développement Hôpital Jeanne de Flandre, Lille, 59000, France.,EA 7364 RADEME Maladies Rares du Développement et du Métabolisme, Faculté de Médecine, Université de Lille, Lille, 59000, France
| | - Scott E Hickey
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA
| | - Molka Kammoun
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Karen W Gripp
- Alfred I. duPont Hospital for Children Nemours, Wilmington, DE, 19803, USA
| | - Claudia Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Theresa Mihalic Mosher
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Benjamin J Kelly
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Eveline Rentmeester
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Sungjin Moon
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Daniel C Koboldt
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Kees E P van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Lucinda Murray
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Eric Haan
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Renee Carroll
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Lynne Hobson
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Marjan De Rademaeker
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, 1090, Brussels, Belgium
| | - Joep Geraedts
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Jean-Pierre Fryns
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Joris Vermeesch
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Martine Raynaud
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Nicholas Katsanis
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Christelle Golzio
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics; Centre National de la Recherche Scientifique, UMR7104; Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, 67400, Illkirch, France
| | - Cristina Gontan
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany.
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4
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Xq25 microduplication syndrome: a further contribution to its definition. A case report and review of the literature. Clin Dysmorphol 2019; 29:90-96. [PMID: 31609727 DOI: 10.1097/mcd.0000000000000303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Romero-Pérez L, Surdez D, Brunet E, Delattre O, Grünewald TGP. STAG Mutations in Cancer. Trends Cancer 2019; 5:506-520. [PMID: 31421907 DOI: 10.1016/j.trecan.2019.07.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/31/2022]
Abstract
Stromal Antigen 1 and 2 (STAG1/2) are key subunits of the cohesin complex that mediate sister chromatid cohesion, DNA repair, transcriptional regulation, and genome topology. Genetic alterations comprising any of the 11 cohesin-associated genes possibly occur in up to 26% of patients included in The Cancer Genome Atlas (TCGA) studies. STAG2 shows the highest number of putative driver truncating mutations. We provide a comprehensive review of the function of STAG1/2 in human physiology and disease and an integrative analysis of available omics data on STAG alterations in a wide array of cancers, comprising 53 691 patients and 1067 cell lines. Lastly, we discuss opportunities for therapeutic intervention.
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Affiliation(s)
- Laura Romero-Pérez
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, Munich, Germany
| | - Didier Surdez
- INSERM U830, Équipe Labellisé LNCC "Genetics and Biology of Pediatric Cancers", fhna PSL Université, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Erika Brunet
- Institut Imagine, INSERM UMR1163, Équipe Labellisé LNCC, Dynamics of the Genome and Immune System Lab, Paris, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisé LNCC "Genetics and Biology of Pediatric Cancers", fhna PSL Université, SIREDO Oncology Centre, Institut Curie, Paris, France
| | - Thomas G P Grünewald
- Max-Eder Research Group for Pediatric Sarcoma Biology, Institute of Pathology, Faculty of Medicine, LMU, Munich, Germany; Institute of Pathology, Faculty of Medicine, LMU Munich, Munich, Germany; German Cancer Consortium (DKTK), partner site Munich, Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Germany.
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6
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Aoi H, Lei M, Mizuguchi T, Nishioka N, Goto T, Miyama S, Suzuki T, Iwama K, Uchiyama Y, Mitsuhashi S, Itakura A, Takeda S, Matsumoto N. Nonsense variants in STAG2 result in distinct sex-dependent phenotypes. J Hum Genet 2019; 64:487-492. [PMID: 30765867 DOI: 10.1038/s10038-019-0571-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/13/2018] [Accepted: 01/25/2019] [Indexed: 12/14/2022]
Abstract
We herein report two individuals with novel nonsense mutations in STAG2 on Xq25, encoding stromal antigen 2, a component of the cohesion complex. A male fetus (Case 1) clinically presented with holoprosencephaly, cleft palate and lip, blepharophimosis, nasal bone absence, and hypolastic left heart by ultrasonography at 15 gestational weeks. Another female patient (Case 2) showed a distinct phenotype with white matter hypoplasia, cleft palate, developmental delay (DD), and intellectual disability (ID) at 7 years. Whole-exome sequencing identified de novo nonsense mutations in STAG2: c.3097C>T, p.(Arg1033*) in Case 1 and c.2229G>A, p.(Trp743*) in Case 2. X-inactivation was highly skewed in Case 2. To date, only 10 STAG2 pathogenic variants (four nonsense, four missense, and two frameshift) have been reported in patients with multiple congenital anomalies, ID, and DD. Although Case 2 showed similar clinical features to the reported female patients with STAG2 abnormalities, Case 1 showed an extremely severe phenotype, which could be explained by the first detected truncating variant in males.
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Affiliation(s)
- Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Ming Lei
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuko Nishioka
- Department of Obstetrics and Gynecology, Koshigaya Municipal Hospital, Saitama, Japan
| | - Tomohide Goto
- Department of Neurology, Kanagawa Children's Medical Center, Kanagawa, Japan
| | - Sahoko Miyama
- Department of Neurology, Tokyo Metropolitan Children's Medical Center, Fuchu, Tokyo, Japan
| | - Toshifumi Suzuki
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsuo Itakura
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Satoru Takeda
- Department of Obstetrics and Gynecology, Faculty of Medicine, Juntendo University, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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7
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Mullegama SV, Klein SD, Signer RH, Vilain E, Martinez-Agosto JA. Mutations in STAG2 cause an X-linked cohesinopathy associated with undergrowth, developmental delay, and dysmorphia: Expanding the phenotype in males. Mol Genet Genomic Med 2018; 7:e00501. [PMID: 30447054 PMCID: PMC6393687 DOI: 10.1002/mgg3.501] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The cohesin complex is a multi-subunit protein complex which regulates sister chromatid cohesion and separation during cellular division. In addition, this evolutionarily conserved protein complex plays an integral role in DNA replication, DNA repair, and the regulation of transcription. The core complex is composed of four subunits: RAD21, SMC1A, SMC3, and STAG1/2. Mutations in these proteins have been implicated in human developmental disorders collectively termed "cohesinopathies." METHODS Using clinical exome sequencing, we have previously identified three female cases with heterozygous STAG2 mutations and overlapping syndromic phenotypes. Subsequently, a familial missense variant was identified in five male family members. RESULTS We now present the case of a 4-year-old male with developmental delay, failure to thrive, short stature, and polydactyly with a likely pathogenic STAG2 de novo missense hemizygous variant, c.3027A>T, p.Lys1009Asn. Furthermore, we compare the phenotypes of the four previously reported STAG2 variants with our case. CONCLUSION We conclude that mutations in STAG2 cause a novel constellation of sex-specific cohesinopathy-related phenotypes and are furthermore, essential for neurodevelopment, human growth, and behavioral development.
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Affiliation(s)
- Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Steven D Klein
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Rebecca H Signer
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
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- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Eric Vilain
- Department of Genomic and Precision Medicine, Children's National Hospital, Washington, District of Columbia
| | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California.,Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California.,UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
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8
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Lei T, Feng JL, Xie YJ, Xie HN, Zheng J, Lin MF. Chromosomal aneuploidies and copy number variations in posterior fossa abnormalities diagnosed by prenatal ultrasonography. Prenat Diagn 2017; 37:1160-1168. [PMID: 28940600 DOI: 10.1002/pd.5159] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 09/07/2017] [Accepted: 09/13/2017] [Indexed: 01/04/2023]
Abstract
OBJECTIVE To explore the genetic aetiology of fetal posterior fossa abnormalities (PFAs). METHODS This study involved cases of PFAs that were identified by prenatal ultrasonographic screening and confirmed postnatally between January 2012 and January 2016. Conventional cytogenetic analyses and chromosomal microarray analysis were performed, and chromosomal aneuploidies and copy number variations (CNVs) were identified. RESULTS Among 74 cases included in this study, 8 were of Blake's pouch cyst; 7, Dandy-Walker malformation; 11, vermian hypoplasia; 32, enlarged cisterna magna; and 16, cerebellar hypoplasia. The rates of nonbenign chromosomal aberrations (including chromosomal aneuploidies, pathogenic CNVs, and variants of unknown significance) were 2/8 (25.0%), 2/7 (28.5%), 8/11 (72.7%), 7/32 (21.9%), and 6/16 (37.5%), respectively. Cases were also classified as isolated PFAs (30/74), PFAs with other central nervous system (CNS) abnormalities (13/74), or PFAs with extra-CNS structural abnormalities (31/74). No fetuses with isolated PFAs or PFAs accompanied by other CNS abnormalities exhibited chromosomal aneuploidies or pathogenic CNVs. The rate of pathogenic chromosomal aberrations in the remaining fetuses was 17/31 (22.9%). CONCLUSION The combined use of chromosomal microarray analysis and karyotype analysis might assist the prenatal diagnosis and management of PFAs, with extra-CNS structural abnormalities being detected by ultrasonography.
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Affiliation(s)
- Ting Lei
- Department of Ultrasonic Medicine, Fetal Medical Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jie-Ling Feng
- Department of Ultrasonic Medicine, Fetal Medical Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ying-Jun Xie
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Hong-Ning Xie
- Department of Ultrasonic Medicine, Fetal Medical Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ju Zheng
- Department of Ultrasonic Medicine, Fetal Medical Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Mei-Fang Lin
- Department of Ultrasonic Medicine, Fetal Medical Centre, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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9
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Copy number variations independently induce autism spectrum disorder. Biosci Rep 2017; 37:BSR20160570. [PMID: 28533427 PMCID: PMC6434077 DOI: 10.1042/bsr20160570] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/22/2017] [Accepted: 05/22/2017] [Indexed: 12/13/2022] Open
Abstract
The examination of copy number variation (CNV) is critical to understand the etiology of the CNV-related autism spectrum disorders (ASD). DNA samples were obtained from 64 ASD probands, which were genotyped on an Affymetrix CytoScan HD platform. qPCR or FISH were used as a validation for some novel recurrent CNVs. We further compared the clinical phenotypes of the genes in the Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER) database with these overlapping genes. Using vast, readily available databases with previously reported clinically relevant CNVs from human populations, the genes were evaluated using Enrichment Analysis and GO Slim Classification. By using the Ploysearch2 software, we identified the interaction relationship between significant genes and known ASD genes. A total of 29 CNVs, overlapping with 520 genes, including 315 OMIM genes, were identified. Additionally, myocyte enhancer factor 2 family (MEF2C) with two cases of CNV overlapping were also identified. Enrichment analysis showed that the 520 genes are most likely to be related to membrane components with protein-binding functions involved in metabolic processes. In the interaction network of those genes, the known ASD genes are mostly at the core position and the significant genes found in our samples are closely related to the known ASD genes. CNVs should be an independent factor to induce autism. With the strategy of our study, we could find the ASDs candidate genes by CNV data and review certain pathogenesis of this disorder. Those CNVs were associated with ASD and they may contribute to ASD by affecting the ASD-related genes.
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10
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Mullegama SV, Klein S, Mulatinho MV, Senaratne T, Singh K, Nguyen D, Gallant N, Strom S, Ghahremani S, Rao PN, Martinez-Agosto JA. De novo loss-of-function variants in STAG2 are associated with developmental delay, microcephaly, and congenital anomalies. Am J Med Genet A 2017; 173:1319-1327. [PMID: 28296084 PMCID: PMC7033032 DOI: 10.1002/ajmg.a.38207] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 02/09/2017] [Accepted: 02/13/2017] [Indexed: 12/26/2022]
Abstract
The cohesin complex is an evolutionarily conserved multi-subunit protein complex which regulates sister chromatid cohesion during mitosis and meiosis. Additionally, the cohesin complex regulates DNA replication, DNA repair, and transcription. The core of the complex consists of four subunits: SMC1A, SMC3, RAD21, and STAG1/2. Loss-of-function mutations in many of these proteins have been implicated in human developmental disorders collectively termed "cohesinopathies." Through clinical exome sequencing (CES) of an 8-year-old girl with a clinical history of global developmental delay, microcephaly, microtia with hearing loss, language delay, ADHD, and dysmorphic features, we describe a heterozygous de novo variant (c.205C>T; p.(Arg69*)) in the integral cohesin structural protein, STAG2. This variant is associated with decreased STAG2 protein expression. The analyses of metaphase spreads did not exhibit premature sister chromatid separation; however, delayed sister chromatid cohesion was observed. To further support the pathogenicity of STAG2 variants, we identified two additional female cases from the DECIPHER research database with mutations in STAG2 and phenotypes similar to our patient. Interestingly, the clinical features of these three cases are remarkably similar to those observed in other well-established cohesinopathies. Herein, we suggest that STAG2 is a dosage-sensitive gene and that heterozygous loss-of-function variants lead to a cohesinopathy.
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Affiliation(s)
- S. V. Mullegama
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - S. Klein
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - M. V. Mulatinho
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - T.N. Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - K. Singh
- Division of Genetic and Genomic Medicine, University of California, Irvine, California, USA, and Miller Children’s and Women’s Hospital Long Beach, Long Beach, California, USA
| | - UCLA Clinical Genomics Center
- UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - D.C. Nguyen
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - N.M. Gallant
- Division of Genetic and Genomic Medicine, University of California, Irvine, California, USA, and Miller Children’s and Women’s Hospital Long Beach, Long Beach, California, USA
| | - S.P. Strom
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - S. Ghahremani
- Department of Radiology, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - P. N. Rao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - J. A. Martinez-Agosto
- UCLA Clinical Genomics Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
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11
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Kumar R, Corbett MA, Van Bon BWM, Gardner A, Woenig JA, Jolly LA, Douglas E, Friend K, Tan C, Van Esch H, Holvoet M, Raynaud M, Field M, Leffler M, Budny B, Wisniewska M, Badura-Stronka M, Latos-Bieleńska A, Batanian J, Rosenfeld JA, Basel-Vanagaite L, Jensen C, Bienek M, Froyen G, Ullmann R, Hu H, Love MI, Haas SA, Stankiewicz P, Cheung SW, Baxendale A, Nicholl J, Thompson EM, Haan E, Kalscheuer VM, Gecz J. Increased STAG2 dosage defines a novel cohesinopathy with intellectual disability and behavioral problems. Hum Mol Genet 2015; 24:7171-81. [PMID: 26443594 DOI: 10.1093/hmg/ddv414] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 09/28/2015] [Indexed: 11/13/2022] Open
Abstract
Next generation genomic technologies have made a significant contribution to the understanding of the genetic architecture of human neurodevelopmental disorders. Copy number variants (CNVs) play an important role in the genetics of intellectual disability (ID). For many CNVs, and copy number gains in particular, the responsible dosage-sensitive gene(s) have been hard to identify. We have collected 18 different interstitial microduplications and 1 microtriplication of Xq25. There were 15 affected individuals from 6 different families and 13 singleton cases, 28 affected males in total. The critical overlapping region involved the STAG2 gene, which codes for a subunit of the cohesin complex that regulates cohesion of sister chromatids and gene transcription. We demonstrate that STAG2 is the dosage-sensitive gene within these CNVs, as gains of STAG2 mRNA and protein dysregulate disease-relevant neuronal gene networks in cells derived from affected individuals. We also show that STAG2 gains result in increased expression of OPHN1, a known X-chromosome ID gene. Overall, we define a novel cohesinopathy due to copy number gain of Xq25 and STAG2 in particular.
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Affiliation(s)
- Raman Kumar
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Mark A Corbett
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | | | - Alison Gardner
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Joshua A Woenig
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Lachlan A Jolly
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Evelyn Douglas
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Chuan Tan
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Maureen Holvoet
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Martine Raynaud
- Centre Hospitalier Régional Universitaire, Service de Génétique, 37000 Tours, France
| | - Michael Field
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Hunter Genetics, Waratah, NSW 2298, Australia
| | - Bartłomiej Budny
- Department of Endocrinology, Metabolism and Internal Diseases and
| | - Marzena Wisniewska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | | | - Anna Latos-Bieleńska
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan 60-355, Poland
| | | | - Jill A Rosenfeld
- Signature Genomic Laboratories, Spokane, WA 99207, USA, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lina Basel-Vanagaite
- Raphael Recanati Genetic Institute and Felsenstein Medical Research Center, Rabin Medical Center, Beilinson Campus, Petah Tikva 49100, Israel
| | | | | | - Guy Froyen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium and
| | - Reinhard Ullmann
- Department of Human Molecular Genetics and, Bundeswehr Institute of Radiobiology, 80937 Munich, Germany
| | - Hao Hu
- Department of Human Molecular Genetics and
| | - Michael I Love
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne Baxendale
- South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Jillian Nicholl
- Genetics and Molecular Pathology, SA Pathology, North Adelaide, SA 5006, Australia
| | - Elizabeth M Thompson
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia, South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | - Eric Haan
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia, South Australian Clinical Genetics Service, SA Pathology, North Adelaide, SA 5006, Australia
| | | | - Jozef Gecz
- School of Medicine, and the Robinson Research Institute, The University of Adelaide, Adelaide, SA 5000, Australia,
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