1
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Shen L, Ma X, Wang Y, Wang Z, Zhang Y, Pham HQH, Tao X, Cui Y, Wei J, Lin D, Abeywanada T, Hardikar S, Halabelian L, Smith N, Chen T, Barsyte-Lovejoy D, Qiu S, Xing Y, Yang Y. Loss-of-function mutation in PRMT9 causes abnormal synapse development by dysregulation of RNA alternative splicing. Nat Commun 2024; 15:2809. [PMID: 38561334 PMCID: PMC10984984 DOI: 10.1038/s41467-024-47107-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 03/16/2024] [Indexed: 04/04/2024] Open
Abstract
Protein arginine methyltransferase 9 (PRMT9) is a recently identified member of the PRMT family, yet its biological function remains largely unknown. Here, by characterizing an intellectual disability associated PRMT9 mutation (G189R) and establishing a Prmt9 conditional knockout (cKO) mouse model, we uncover an important function of PRMT9 in neuronal development. The G189R mutation abolishes PRMT9 methyltransferase activity and reduces its protein stability. Knockout of Prmt9 in hippocampal neurons causes alternative splicing of ~1900 genes, which likely accounts for the aberrant synapse development and impaired learning and memory in the Prmt9 cKO mice. Mechanistically, we discover a methylation-sensitive protein-RNA interaction between the arginine 508 (R508) of the splicing factor 3B subunit 2 (SF3B2), the site that is exclusively methylated by PRMT9, and the pre-mRNA anchoring site, a cis-regulatory element that is critical for RNA splicing. Additionally, using human and mouse cell lines, as well as an SF3B2 arginine methylation-deficient mouse model, we provide strong evidence that SF3B2 is the primary methylation substrate of PRMT9, thus highlighting the conserved function of the PRMT9/SF3B2 axis in regulating pre-mRNA splicing.
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Affiliation(s)
- Lei Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA, 91010, USA
| | - Xiaokuang Ma
- Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, 85004, USA
| | - Yuanyuan Wang
- Bioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, CA, 90095, USA
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Zhihao Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA, 91010, USA
| | - Yi Zhang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA, 91010, USA
| | - Hoang Quoc Hai Pham
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Xiaoqun Tao
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA, 91010, USA
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Yuehua Cui
- Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, 85004, USA
| | - Jing Wei
- Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, 85004, USA
| | - Dimitri Lin
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA, 91010, USA
| | - Tharindumala Abeywanada
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA, 91010, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Noah Smith
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Shenfeng Qiu
- Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, 85004, USA.
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
| | - Yanzhong Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope Cancer Center, Duarte, CA, 91010, USA.
- Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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2
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Schwartz CE, Louie RJ, Toutain A, Skinner C, Friez MJ, Stevenson RE. X-Linked intellectual disability update 2022. Am J Med Genet A 2023; 191:144-159. [PMID: 36300573 DOI: 10.1002/ajmg.a.63008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/28/2022] [Accepted: 09/29/2022] [Indexed: 12/14/2022]
Abstract
Genes that are involved in the transcription process, mitochondrial function, glycoprotein metabolism, and ubiquitination dominate the list of 21 new genes associated with X-linked intellectual disability since the last update in 2017. The new genes were identified by sequencing of candidate genes (2), the entire X-chromosome (2), the whole exome (15), or the whole genome (2). With these additions, 42 (21%) of the 199 named XLID syndromes and 27 (25%) of the 108 numbered nonsyndromic XLID families remain to be resolved at the molecular level. Although the pace of discovery of new XLID genes has slowed during the past 5 years, the density of genes on the X chromosome that cause intellectual disability still appears to be twice the density of intellectual disability genes on the autosomes.
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Affiliation(s)
| | | | - Annick Toutain
- Department of Medical Genetics, Centre Hospitalier Universitaire, Tours, France
| | - Cindy Skinner
- Greenwood Genetic Center, Greenwood, South Carolina, USA
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3
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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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4
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Pasińska M, Łazarczyk E, Repczyńska A, Sobczyńska-Tomaszewska A, Zimowski J, Runge A, Haus O. Clinical Importance of aCGH in Genetic Counselling of Children with Psychomotor Retardation. Appl Clin Genet 2022; 15:27-38. [PMID: 35603035 PMCID: PMC9116409 DOI: 10.2147/tacg.s357136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/13/2022] [Indexed: 12/02/2022] Open
Abstract
Introduction The X and Y chromosomes are responsible for the determination and differentiation of the gonads, and their numerical and structural abnormalities may cause the abnormal development of secondary sex characteristics. The presence of abnormalities concerning X chromosome can also contribute to many genetically heterogeneous diseases associated with cognitive impairment and intellectual disability. Purpose This study shows the effect of aberrations of the maternal X chromosome on the abnormal development of the child. Patients and Methods Ten women aged 26 to 40 years were consulted in genetic counselling clinic and subsequently subjected to cytogenetic and molecular tests due to abnormal psychomotor development of their children, in whom structural aberrations of the X chromosome had been detected. Results Two women were diagnosed with changes in karyotype: 46,X,der(X)t(X;Y)(p22.3;q11.2) in one and 46,X,inv(X)(p21.2q13). Five women were diagnosed with microduplications in the short arm of the X chromosome; dupXp22.31 in one, and in four women dupXp22.33. The remaining three women were diagnosed with duplication in the long arm of the X chromosome; dupXq25 in one and dupXq26.3 in two women. Conclusion Genetic analysis of the X chromosome, based on cytogenetic and molecular methods of the highest available resolution, is extremely important in women with reproductive failure. These methods allow establishing accurately the breakpoints and rearrangements in chromosomes, and assessment of the copy number variation (CNV) can explain phenotypic variability with apparently similar aberrations. A more precise characterization of the alterations is necessary for the correct genetic diagnosis, as well as determination of the carrier status and genetic risk in family members.
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Affiliation(s)
- Magdalena Pasińska
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Ewelina Łazarczyk
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Anna Repczyńska
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | | | - Janusz Zimowski
- Department of Genetics, Institute of Psychiatry and Neurology, Warszawa, Poland
| | - Agata Runge
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
| | - Olga Haus
- Department of Clinical Genetics, Faculty of Medicine, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Bydgoszcz, Poland
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5
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Freyberger F, Kokotović T, Krnjak G, Frković SH, Nagy V. Expanding the known phenotype of Mullegama-Klein-Martinez syndrome in male patients. Hum Genome Var 2021; 8:37. [PMID: 34580287 PMCID: PMC8476567 DOI: 10.1038/s41439-021-00169-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 02/02/2023] Open
Abstract
Here, we report a novel case of a male patient with a hemizygous missense variant in STAG2 (p.Tyr159His) resulting in Mullegama–Klein–Martinez syndrome (MKMS), a rare X-linked cohesinopathy. He shares distinct clinical features with a previously reported male patient carrying the STAG2 variant p.Tyr159Cys, suggesting that this phenotype is determined by the position of the mutation. Additionally, our patient exhibits symptoms not previously associated with MKMS, expanding the known clinical phenotype of this rare disease.
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Affiliation(s)
- Fiona Freyberger
- Ludwig Boltzmann Institute for Rare and Undiagnosed Disorders, Vienna, Austria.,Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Tomislav Kokotović
- Ludwig Boltzmann Institute for Rare and Undiagnosed Disorders, Vienna, Austria.,Department of Neurology, Medical University of Vienna, Vienna, Austria.,CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Goran Krnjak
- Department of Pediatrics, Varazdin General Hospital, Varazdin, Croatia
| | - Sanda Huljev Frković
- Department of Paediatrics, Division for Genetics and Metabolism, University of Zagreb School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Vanja Nagy
- Ludwig Boltzmann Institute for Rare and Undiagnosed Disorders, Vienna, Austria. .,Department of Neurology, Medical University of Vienna, Vienna, Austria. .,CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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6
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Antony J, Chin CV, Horsfield JA. Cohesin Mutations in Cancer: Emerging Therapeutic Targets. Int J Mol Sci 2021; 22:6788. [PMID: 34202641 PMCID: PMC8269296 DOI: 10.3390/ijms22136788] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/08/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
The cohesin complex is crucial for mediating sister chromatid cohesion and for hierarchal three-dimensional organization of the genome. Mutations in cohesin genes are present in a range of cancers. Extensive research over the last few years has shown that cohesin mutations are key events that contribute to neoplastic transformation. Cohesin is involved in a range of cellular processes; therefore, the impact of cohesin mutations in cancer is complex and can be cell context dependent. Candidate targets with therapeutic potential in cohesin mutant cells are emerging from functional studies. Here, we review emerging targets and pharmacological agents that have therapeutic potential in cohesin mutant cells.
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Affiliation(s)
- Jisha Antony
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Chue Vin Chin
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
| | - Julia A. Horsfield
- Department of Pathology, Otago Medical School, University of Otago, Dunedin 9016, New Zealand;
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
- Genetics Otago Research Centre, University of Otago, Dunedin 9016, New Zealand
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7
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Corrêa T, Santos-Rebouças CB, Mayndra M, Schinzel A, Riegel M. Shared Neurodevelopmental Perturbations Can Lead to Intellectual Disability in Individuals with Distinct Rare Chromosome Duplications. Genes (Basel) 2021; 12:genes12050632. [PMID: 33922640 PMCID: PMC8146713 DOI: 10.3390/genes12050632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 11/16/2022] Open
Abstract
Chromosomal duplications are associated with a large group of human diseases that arise mainly from dosage imbalance of genes within the rearrangements. Phenotypes range widely but are often associated with global development delay, intellectual disability, autism spectrum disorders, and multiple congenital abnormalities. How different contiguous genes from a duplicated genomic region interact and dynamically affect the expression of each other remains unclear in most cases. Here, we report a genomic comparative delineation of genes located in duplicated chromosomal regions 8q24.13q24.3, 18p11.32p11.21, and Xq22.3q27.2 in three patients followed up at our genetics service who has the intellectual disability (ID) as a common phenotype. We integrated several genomic data levels by identification of gene content within the duplications, protein-protein interactions, and functional analysis on specific tissues. We found functional relationships among genes from three different duplicated chromosomal regions, reflecting interactions of protein-coding genes and their involvement in common cellular subnetworks. Furthermore, the sharing of common significant biological processes associated with ID has been demonstrated between proteins from the different chromosomal regions. Finally, we elaborated a shared model of pathways directly or indirectly related to the central nervous system (CNS), which could perturb cognitive function and lead to ID in the three duplication conditions.
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Affiliation(s)
- Thiago Corrêa
- Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul UFRGS, Porto Alegre 91501-970, Brazil;
| | - Cíntia B. Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro 20511-010, Brazil;
| | - Maytza Mayndra
- Children’s Hospital Jeser Amarante Faria, Joinville 89204-310, Brazil;
| | - Albert Schinzel
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland;
| | - Mariluce Riegel
- Department of Genetics, Institute of Biosciences, Federal University of Rio Grande do Sul UFRGS, Porto Alegre 91501-970, Brazil;
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-903, Brazil
- Correspondence:
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8
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Palmer EE, Carroll R, Shaw M, Kumar R, Minoche AE, Leffler M, Murray L, Macintosh R, Wright D, Troedson C, McKenzie F, Townshend S, Ward M, Nawaz U, Ravine A, Runke CK, Thorland EC, Hummel M, Foulds N, Pichon O, Isidor B, Le Caignec C, Demeer B, Andrieux J, Albarazi SH, Bye A, Sachdev R, Kirk EP, Cowley MJ, Field M, Gecz J. RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features. Am J Hum Genet 2020; 107:1157-1169. [PMID: 33159883 PMCID: PMC7820564 DOI: 10.1016/j.ajhg.2020.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Interpretation of the significance of maternally inherited X chromosome variants in males with neurocognitive phenotypes continues to present a challenge to clinical geneticists and diagnostic laboratories. Here we report 14 males from 9 families with duplications at the Xq13.2-q13.3 locus with a common facial phenotype, intellectual disability (ID), distinctive behavioral features, and a seizure disorder in two cases. All tested carrier mothers had normal intelligence. The duplication arose de novo in three mothers where grandparental testing was possible. In one family the duplication segregated with ID across three generations. RLIM is the only gene common to our duplications. However, flanking genes duplicated in some but not all the affected individuals included the brain-expressed genes NEXMIF, SLC16A2, and the long non-coding RNA gene FTX. The contribution of the RLIM-flanking genes to the phenotypes of individuals with different size duplications has not been fully resolved. Missense variants in RLIM have recently been identified to cause X-linked ID in males, with heterozygous females typically having normal intelligence and highly skewed X chromosome inactivation. We detected consistent and significant increase of RLIM mRNA and protein levels in cells derived from seven affected males from five families with the duplication. Subsequent analysis of MDM2, one of the targets of the RLIM E3 ligase activity, showed consistent downregulation in cells from the affected males. All the carrier mothers displayed normal RLIM mRNA levels and had highly skewed X chromosome inactivation. We propose that duplications at Xq13.2-13.3 including RLIM cause a recognizable but mild neurocognitive phenotype in hemizygous males.
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Affiliation(s)
- Elizabeth E Palmer
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia; School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia; Kinghorn Centre for Clinical Genomics, Garvan Institute, Darlinghurst, Sydney, NSW 2010, Australia.
| | - Renee Carroll
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Raman Kumar
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Andre E Minoche
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Lucinda Murray
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | | | - Dale Wright
- Discipline of Genomic Medicine and Discipline of Child & Adolescent Health, University of Sydney, Sydney, NSW 2010, Australia; Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Chris Troedson
- Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Fiona McKenzie
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6009, Australia; Genetic Services of Western Australia, Perth, WA 6008, Australia
| | | | - Michelle Ward
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Urwah Nawaz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Anja Ravine
- Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Pathwest Laboratory Medicine WA, Perth, WA 6008, Australia
| | - Cassandra K Runke
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Marybeth Hummel
- West Virginia University School of Medicine, Department of Pediatrics, Section of Medical Genetics Morgantown, WV 26506-9600, USA
| | - Nicola Foulds
- Wessex Clinical Genetics Services, Southampton SO16 5YA, UK
| | - Olivier Pichon
- Service de génétique médicale - Unité de Génétique Clinique, CHU de Nantes - Hôtel Dieu, Nantes 44093, France
| | - Bertrand Isidor
- Service de génétique médicale - Unité de Génétique Clinique, CHU de Nantes - Hôtel Dieu, Nantes 44093, France
| | - Cédric Le Caignec
- Service de génétique médicale, Institut fédératif de Biologie, CHU Hopital Purpan, Toulouse 31059, France
| | - Bénédicte Demeer
- Center for Human Genetics, CLAD Nord de France, CHU Amiens-Picardie, Amiens 80080, France; CHIMERE EA 7516, University Picardie Jules Verne, Amiens 80025, France
| | - Joris Andrieux
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille 59000, France
| | | | - Ann Bye
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Rani Sachdev
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Edwin P Kirk
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW 2033, Australia
| | - Mike Field
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
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9
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Li L, Fu F, Li R, Xiao W, Yu Q, Wang D, Jing X, Zhang Y, Yang X, Pan M, Liu Z, Liao C. Genetic tests aid in counseling of fetuses with cerebellar vermis defects. Prenat Diagn 2020; 40:1228-1238. [PMID: 32386258 DOI: 10.1002/pd.5732] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/06/2020] [Accepted: 05/06/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVE To assess the value of chromosome microarray analysis (CMA) and whole exome sequencing (WES) in fetuses with cerebellar vermis defects (CVD). METHODS From 2013 to 2019, we performed CMA on 43 fetuses with CVD, who were divided into cerebellar vermis hypoplasia (CVH) group and Dandy-Walker malformation (DWM) group according to morphological subtypes. Subsequently, WES was performed on 19 fetuses with normal CMA results to identify diagnostic genetic variants (DGVs). RESULTS Chromosome aneuploidies and clinically significant copy number variants were identified in 23.3% (10/43) of fetuses, and a significantly higher positive rate was found in fetuses with multiple compared with isolated malformations (36% vs 5.6%, P = .028). STAG2 genes related to Xq25 duplication syndrome was possibly a novel candidate gene for CVD. WES detected eight DGVs in seven genes among the 19 fetuses tested. Autosomal recessive ciliopathies (4/8) caused by TMEM231, CSPP1, and CEP290 mutations, were the most frequent monogenetic diseases, followed by Opitz GBBB syndrome (2/8) caused by MID1 and SPECC1L variants. CONCLUSION The combined use of CMA and WES has the potential to provide genetic diagnoses in 42% (18/43) of fetal CVD. WES should be offered when CMA results are normal.
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Affiliation(s)
- Lushan Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ru Li
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Weiqiang Xiao
- Radiation department, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Qiuxia Yu
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Dan Wang
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiangyi Jing
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yongning Zhang
- Eugenic and Perinatal Institute, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Zequn Liu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
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10
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Abstract
Congenital diaphragmatic hernia (CDH) is a common birth defect that is associated with significant morbidity and mortality, especially when associated with additional congenital anomalies. Both environmental and genetic factors are thought to contribute to CDH. The genetic contributions to CDH are highly heterogeneous and incompletely defined. No one genetic cause accounts for more than 1-2% of CDH cases. In this review, we summarize the known genetic causes of CDH from chromosomal anomalies to individual genes. Both de novo and inherited variants contribute to CDH. Genes causing CDH are increasingly identified from animal models and from genomic strategies including exome and genome sequencing in humans. CDH genes are often transcription factors, genes involved in cell migration or the components of extracellular matrix. We provide clinical genetic testing strategies in the clinical evaluation that can identify a genetic cause in up to ∼30% of patients with non-isolated CDH and can be useful to refine prognosis, identify associated medical and neurodevelopmental issues to address, and inform family planning options.
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Affiliation(s)
- Lan Yu
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Rebecca R. Hernan
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY 10032, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10032, USA; Department of Medicine, Columbia University, New York, NY 10032, USA.
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11
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Piché J, Van Vliet PP, Pucéat M, Andelfinger G. The expanding phenotypes of cohesinopathies: one ring to rule them all! Cell Cycle 2019; 18:2828-2848. [PMID: 31516082 PMCID: PMC6791706 DOI: 10.1080/15384101.2019.1658476] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/13/2019] [Accepted: 08/17/2019] [Indexed: 12/13/2022] Open
Abstract
Preservation and development of life depend on the adequate segregation of sister chromatids during mitosis and meiosis. This process is ensured by the cohesin multi-subunit complex. Mutations in this complex have been associated with an increasing number of diseases, termed cohesinopathies. The best characterized cohesinopathy is Cornelia de Lange syndrome (CdLS), in which intellectual and growth retardations are the main phenotypic manifestations. Despite some overlap, the clinical manifestations of cohesinopathies vary considerably. Novel roles of the cohesin complex have emerged during the past decades, suggesting that important cell cycle regulators exert important biological effects through non-cohesion-related functions and broadening the potential pathomechanisms involved in cohesinopathies. This review focuses on non-cohesion-related functions of the cohesin complex, gene dosage effect, epigenetic regulation and TGF-β in cohesinopathy context, especially in comparison to Chronic Atrial and Intestinal Dysrhythmia (CAID) syndrome, a very distinct cohesinopathy caused by a homozygous Shugoshin-1 (SGO1) mutation (K23E) and characterized by pacemaker failure in both heart (sick sinus syndrome followed by atrial flutter) and gut (chronic intestinal pseudo-obstruction) with no intellectual or growth delay. We discuss the possible impact of SGO1 alterations in human pathologies and the potential impact of the SGO1 K23E mutation in the sinus node and gut development and functions. We suggest that the human phenotypes observed in CdLS, CAID syndrome and other cohesinopathies can inform future studies into the less well-known non-cohesion-related functions of cohesin complex genes. Abbreviations: AD: Alzheimer Disease; AFF4: AF4/FMR2 Family Member 4; ANKRD11: Ankyrin Repeat Domain 11; APC: Anaphase Promoter Complex; ASD: Atrial Septal Defect; ATRX: ATRX Chromatin Remodeler; ATRX: Alpha Thalassemia X-linked intellectual disability syndrome; BIRC5: Baculoviral IAP Repeat Containing 5; BMP: Bone Morphogenetic Protein; BRD4: Bromodomain Containing 4; BUB1: BUB1 Mitotic Checkpoint Serine/Threonine Kinase; CAID: Chronic Atrial and Intestinal Dysrhythmia; CDK1: Cyclin Dependent Kinase 1; CdLS: Cornelia de Lange Syndrome; CHD: Congenital Heart Disease; CHOPS: Cognitive impairment, coarse facies, Heart defects, Obesity, Pulmonary involvement, Short stature, and skeletal dysplasia; CIPO: Chronic Intestinal Pseudo-Obstruction; c-kit: KIT Proto-Oncogene Receptor Tyrosine Kinase; CoATs: Cohesin Acetyltransferases; CTCF: CCCTC-Binding Factor; DDX11: DEAD/H-Box Helicase 11; ERG: Transcriptional Regulator ERG; ESCO2: Establishment of Sister Chromatid Cohesion N-Acetyltransferase 2; GJC1: Gap Junction Protein Gamma 1; H2A: Histone H2A; H3K4: Histone H3 Lysine 4; H3K9: Histone H3 Lysine 9; HCN4: Hyperpolarization Activated Cyclic Nucleotide Gated Potassium and Sodium Channel 4;p HDAC8: Histone deacetylases 8; HP1: Heterochromatin Protein 1; ICC: Interstitial Cells of Cajal; ICC-MP: Myenteric Plexus Interstitial cells of Cajal; ICC-DMP: Deep Muscular Plexus Interstitial cells of Cajal; If: Pacemaker Funny Current; IP3: Inositol trisphosphate; JNK: C-Jun N-Terminal Kinase; LDS: Loeys-Dietz Syndrome; LOAD: Late-Onset Alzheimer Disease; MAPK: Mitogen-Activated Protein Kinase; MAU: MAU Sister Chromatid Cohesion Factor; MFS: Marfan Syndrome; NIPBL: NIPBL, Cohesin Loading Factor; OCT4: Octamer-Binding Protein 4; P38: P38 MAP Kinase; PDA: Patent Ductus Arteriosus; PDS5: PDS5 Cohesin Associated Factor; P-H3: Phospho Histone H3; PLK1: Polo Like Kinase 1; POPDC1: Popeye Domain Containing 1; POPDC2: Popeye Domain Containing 2; PP2A: Protein Phosphatase 2; RAD21: RAD21 Cohesin Complex Component; RBS: Roberts Syndrome; REC8: REC8 Meiotic Recombination Protein; RNAP2: RNA polymerase II; SAN: Sinoatrial node; SCN5A: Sodium Voltage-Gated Channel Alpha Subunit 5; SEC: Super Elongation Complex; SGO1: Shogoshin-1; SMAD: SMAD Family Member; SMC1A: Structural Maintenance of Chromosomes 1A; SMC3: Structural Maintenance of Chromosomes 3; SNV: Single Nucleotide Variant; SOX2: SRY-Box 2; SOX17: SRY-Box 17; SSS: Sick Sinus Syndrome; STAG2: Cohesin Subunit SA-2; TADs: Topology Associated Domains; TBX: T-box transcription factors; TGF-β: Transforming Growth Factor β; TGFBR: Transforming Growth Factor β receptor; TOF: Tetralogy of Fallot; TREK1: TREK-1 K(+) Channel Subunit; VSD: Ventricular Septal Defect; WABS: Warsaw Breakage Syndrome; WAPL: WAPL Cohesin Release Factor.
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Affiliation(s)
- Jessica Piché
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montréal, QC, Canada
| | - Patrick Piet Van Vliet
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montréal, QC, Canada
- LIA (International Associated Laboratory), CHU Sainte-Justine, Montréal, QC, Canada
- LIA (International Associated Laboratory), INSERM, Marseille, U1251-13885, France
| | - Michel Pucéat
- LIA (International Associated Laboratory), CHU Sainte-Justine, Montréal, QC, Canada
- LIA (International Associated Laboratory), INSERM, Marseille, U1251-13885, France
- INSERM U-1251, MMG,Aix-Marseille University, Marseille, 13885, France
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, CHU Sainte-Justine, Montréal, QC, Canada
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12
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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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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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14
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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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15
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Gudmundsson S, Wilbe M, Filipek-Górniok B, Molin AM, Ekvall S, Johansson J, Allalou A, Gylje H, Kalscheuer VM, Ledin J, Annerén G, Bondeson ML. TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish. Sci Rep 2019; 9:10730. [PMID: 31341187 PMCID: PMC6656882 DOI: 10.1038/s41598-019-46632-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 07/01/2019] [Indexed: 11/22/2022] Open
Abstract
The TATA-box binding protein associated factor 1 (TAF1) protein is a key unit of the transcription factor II D complex that serves a vital function during transcription initiation. Variants of TAF1 have been associated with neurodevelopmental disorders, but TAF1's molecular functions remain elusive. In this study, we present a five-generation family affected with X-linked intellectual disability that co-segregated with a TAF1 c.3568C>T, p.(Arg1190Cys) variant. All affected males presented with intellectual disability and dysmorphic features, while heterozygous females were asymptomatic and had completely skewed X-chromosome inactivation. We investigated the role of TAF1 and its association to neurodevelopment by creating the first complete knockout model of the TAF1 orthologue in zebrafish. A crucial function of human TAF1 during embryogenesis can be inferred from the model, demonstrating that intact taf1 is essential for embryonic development. Transcriptome analysis of taf1 zebrafish knockout revealed enrichment for genes associated with neurodevelopmental processes. In conclusion, we propose that functional TAF1 is essential for embryonic development and specifically neurodevelopmental processes.
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Affiliation(s)
- Sanna Gudmundsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, 751 08, Sweden.
| | - Maria Wilbe
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, 751 08, Sweden
| | - Beata Filipek-Górniok
- Department of Organismal Biology, Genome Engineering Zebrafish, Science for Life Laboratory, Uppsala University, Uppsala, 752 36, Sweden
| | - Anna-Maja Molin
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, 751 08, Sweden
| | - Sara Ekvall
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, 751 08, Sweden
| | - Josefin Johansson
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, 751 08, Sweden
| | - Amin Allalou
- Department of Information Technology, Uppsala University, Sweden and Science for Life Laboratory, Uppsala, 751 05, Sweden
| | - Hans Gylje
- Department of Paediatrics, Central Hospital, Västerås, 721 89, Sweden
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, 141 95, Germany
| | - Johan Ledin
- Department of Organismal Biology, Genome Engineering Zebrafish, Science for Life Laboratory, Uppsala University, Uppsala, 752 36, Sweden
| | - Göran Annerén
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, 751 08, Sweden.
| | - Marie-Louise Bondeson
- Department of Immunology, Genetics and Pathology, Uppsala University, Science for Life Laboratory, Uppsala, 751 08, Sweden.
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16
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Yuan B, Neira J, Pehlivan D, Santiago-Sim T, Song X, Rosenfeld J, Posey JE, Patel V, Jin W, Adam MP, Baple EL, Dean J, Fong CT, Hickey SE, Hudgins L, Leon E, Madan-Khetarpal S, Rawlins L, Rustad CF, Stray-Pedersen A, Tveten K, Wenger O, Diaz J, Jenkins L, Martin L, McGuire M, Pietryga M, Ramsdell L, Slattery L, Abid F, Bertuch AA, Grange D, Immken L, Schaaf CP, Van Esch H, Bi W, Cheung SW, Breman AM, Smith JL, Shaw C, Crosby AH, Eng C, Yang Y, Lupski JR, Xiao R, Liu P. Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies. Genet Med 2019; 21:663-675. [PMID: 30158690 PMCID: PMC6395558 DOI: 10.1038/s41436-018-0085-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 06/01/2018] [Indexed: 01/09/2023] Open
Abstract
PURPOSE Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective. METHODS We retrospectively studied patients referred for clinical exome sequencing (CES, N = 10,698). Patients with causative variants in novel or recently described cohesinopathy genes were enrolled for phenotypic characterization. RESULTS Pathogenic or likely pathogenic single-nucleotide and insertion/deletion variants (SNVs/indels) were identified in established disease genes including NIPBL (N = 5), SMC1A (N = 14), SMC3 (N = 4), RAD21 (N = 2), and HDAC8 (N = 8). The phenotypes in this genetically defined cohort skew towards the mild end of CdLS spectrum as compared with phenotype-driven cohorts. Candidate or recently reported cohesinopathy genes were supported by de novo SNVs/indels in STAG1 (N = 3), STAG2 (N = 5), PDS5A (N = 1), and WAPL (N = 1), and one inherited SNV in PDS5A. We also identified copy-number deletions affecting STAG1 (two de novo, one of unknown inheritance) and STAG2 (one of unknown inheritance). Patients with STAG1 and STAG2 variants presented with overlapping features yet without characteristic facial features of CdLS. CONCLUSION CES effectively identified disease-causing alleles at the mild end of the cohensinopathy spectrum and enabled characterization of candidate disease genes.
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Affiliation(s)
- Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Juanita Neira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Teresa Santiago-Sim
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | | | - Margaret P Adam
- Seattle Children's Hospital, Seattle, Washington, 98105, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, 98105, USA
| | - Emma L Baple
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, EX1 2ED, UK
| | - John Dean
- Clinical Genetics Service, NHS Grampian, Aberdeen, AB25 2ZA, Scotland
| | - Chin-To Fong
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642, USA
| | - Scott E Hickey
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, Ohio, 43205, USA
| | - Louanne Hudgins
- Division of Medical Genetics, Stanford University, Stanford, California, 94305, USA
| | - Eyby Leon
- Rare Disease Institute, Children's National Health System, Washington, DC, 20010, USA
| | | | - Lettie Rawlins
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital, Gladstone Road, Exeter, EX1 2ED, UK
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, 0424, Oslo, Norway
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, 0424, Oslo, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710, Skien, Norway
| | - Olivia Wenger
- New Leaf Center, Clinic for Special Children, Mt. Eaton, Ohio, 44659, USA
| | - Jullianne Diaz
- Rare Disease Institute, Children's National Health System, Washington, DC, 20010, USA
| | - Laura Jenkins
- Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, 15224, USA
| | - Laura Martin
- Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, 14642, USA
| | - Marianne McGuire
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Marguerite Pietryga
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Linda Ramsdell
- Seattle Children's Hospital, Seattle, Washington, 98105, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, 98105, USA
| | - Leah Slattery
- Division of Medical Genetics, Stanford University, Stanford, California, 94305, USA
| | - Farida Abid
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Section of Child Neurology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alison A Bertuch
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Dorothy Grange
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - LaDonna Immken
- Dell Children's Medical Center of Central Texas, Austin, Texas, 78723, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Institute of Human Genetics, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Center for Rare Diseases, University Hospital Cologne, Cologne, Germany
| | - Hilde Van Esch
- Center for Human Genetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Chad Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Andrew H Crosby
- University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon & Exeter NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, UK
| | - Christine Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children's Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Rui Xiao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Baylor Genetics, Houston, Texas, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA.
- Baylor Genetics, Houston, Texas, 77021, USA.
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17
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Herriges JC, Arch EM, Burgio PA, Baldwin EE, LaGrave D, Lamb AN, Toydemir RM. Delineating the Clinical Spectrum Associated With Xq25q26.2 Duplications: Report of 2 Families and Review of the Literature. J Child Neurol 2019; 34:86-93. [PMID: 30458662 DOI: 10.1177/0883073818811454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To date, 13 patients with interstitial microduplications involving Xq25q26.2 have been reported. Here, we report 6 additional patients from 2 families with duplications involving Xq25q26.2. Family I carries a 5.3-Mb duplication involving 26 genes. This duplication was identified in 3 patients and was associated with microcephaly, growth failure, developmental delay, and dysmorphic features. Family II carries an overlapping 791-kb duplication that involves 3 genes. This duplication was identified in 3 patients and was associated with learning disability and speech delay. The size and gene content of published overlapping Xq25q26.2 duplications vary, making it difficult to define a critical region or establish a genotype-phenotype correlation. However, patients with overlapping duplications have been found to share common clinical features including microcephaly, growth failure, intellectual disability, learning difficulties, and dysmorphic features. The 2 families presented here provide additional insight into the phenotypic spectrum and clinical significance of duplications in this region.
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Affiliation(s)
- John C Herriges
- 1 Department of Pathology, University of Utah, Salt Lake City, UT, USA.,2 ARUP Laboratories, Salt Lake City, UT, USA
| | - Ellen M Arch
- 3 Genetics and Developmental Medicine, Dixie Regional Medical Center, St George, UT, USA
| | - Pamela A Burgio
- 4 Pediatrics Medical Group, Renown Regional Medical Center, Reno, NV, USA
| | | | | | - Allen N Lamb
- 1 Department of Pathology, University of Utah, Salt Lake City, UT, USA.,2 ARUP Laboratories, Salt Lake City, UT, USA
| | - Reha M Toydemir
- 1 Department of Pathology, University of Utah, Salt Lake City, UT, USA.,2 ARUP Laboratories, Salt Lake City, UT, USA.,5 Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
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18
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Wang T, Glover B, Hadwiger G, Miller CA, di Martino O, Welch JS. Smc3 is required for mouse embryonic and adult hematopoiesis. Exp Hematol 2018; 70:70-84.e6. [PMID: 30553776 DOI: 10.1016/j.exphem.2018.11.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 11/28/2018] [Indexed: 10/27/2022]
Abstract
SMC3 encodes a subunit of the cohesin complex that has canonical roles in regulating sister chromatids segregation during mitosis and meiosis. Recurrent heterozygous mutations in SMC3 have been reported in acute myeloid leukemia (AML) and other myeloid malignancies. In this study, we investigated whether the missense mutations in SMC3 might have dominant-negative effects or phenocopy loss-of-function effects by comparing the consequences of Smc3-deficient and -haploinsufficient mouse models. We found that homozygous deletion of Smc3 during embryogenesis or in adult mice led to hematopoietic failure, suggesting that SMC3 missense mutations are unlikely to be associated with simple dominant-negative phenotypes. In contrast, haploinsufficiency was tolerated during embryonic and adult hematopoiesis. Under steady-state conditions, Smc3 haploinsufficiency did not alter colony forming in methylcellulose, only modestly decreased mature myeloid cell populations, and led to limited expression changes and chromatin alteration in Lin-cKit+ bone marrow cells. However, following transplantation, engraftment, and subsequent deletion, we observed a hematopoietic competitive disadvantage across myeloid and lymphoid lineages and within the stem/progenitor compartments. This disadvantage was not affected by hematopoietic stresses, but was partially abrogated by concurrent Dnmt3a haploinsufficiency, suggesting that antecedent mutations may be required to optimize the leukemogenic potential of Smc3 mutations.
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Affiliation(s)
- Tianjiao Wang
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Brandi Glover
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Gayla Hadwiger
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Miller
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Orsola di Martino
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - John S Welch
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
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19
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Qi H, Yu L, Zhou X, Wynn J, Zhao H, Guo Y, Zhu N, Kitaygorodsky A, Hernan R, Aspelund G, Lim FY, Crombleholme T, Cusick R, Azarow K, Danko ME, Chung D, Warner BW, Mychaliska GB, Potoka D, Wagner AJ, ElFiky M, Wilson JM, Nickerson D, Bamshad M, High FA, Longoni M, Donahoe PK, Chung WK, Shen Y. De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders. PLoS Genet 2018; 14:e1007822. [PMID: 30532227 PMCID: PMC6301721 DOI: 10.1371/journal.pgen.1007822] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 12/20/2018] [Accepted: 11/08/2018] [Indexed: 12/24/2022] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a severe birth defect that is often accompanied by other congenital anomalies. Previous exome sequencing studies for CDH have supported a role of de novo damaging variants but did not identify any recurrently mutated genes. To investigate further the genetics of CDH, we analyzed de novo coding variants in 362 proband-parent trios including 271 new trios reported in this study. We identified four unrelated individuals with damaging de novo variants in MYRF (P = 5.3x10(-8)), including one likely gene-disrupting (LGD) and three deleterious missense (D-mis) variants. Eight additional individuals with de novo LGD or missense variants were identified from our other genetic studies or from the literature. Common phenotypes of MYRF de novo variant carriers include CDH, congenital heart disease and genitourinary abnormalities, suggesting that it represents a novel syndrome. MYRF is a membrane associated transcriptional factor highly expressed in developing diaphragm and is depleted of LGD variants in the general population. All de novo missense variants aggregated in two functional protein domains. Analyzing the transcriptome of patient-derived diaphragm fibroblast cells suggest that disease associated variants abolish the transcription factor activity. Furthermore, we showed that the remaining genes with damaging variants in CDH significantly overlap with genes implicated in other developmental disorders. Gene expression patterns and patient phenotypes support pleiotropic effects of damaging variants in these genes on CDH and other developmental disorders. Finally, functional enrichment analysis implicates the disruption of regulation of gene expression, kinase activities, intra-cellular signaling, and cytoskeleton organization as pathogenic mechanisms in CDH.
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Affiliation(s)
- Hongjian Qi
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Applied Mathematics and Applied Physics, Columbia University, New York, New York, United States of America
| | - Lan Yu
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Xueya Zhou
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Julia Wynn
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Haoquan Zhao
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
| | - Yicheng Guo
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
| | - Na Zhu
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Alexander Kitaygorodsky
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
| | - Rebecca Hernan
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
| | - Gudrun Aspelund
- Department of Surgery, Columbia University Medical Center, New York, New York, United States of America
| | - Foong-Yen Lim
- Cincinnati Children's Hospital, Cincinnati, Ohio, United States of America
| | | | - Robert Cusick
- Children's Hospital & Medical Center of Omaha, University of Nebraska College of Medicine, Omaha, Nebraska, United States of America
| | - Kenneth Azarow
- Department of Surgery, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Melissa E Danko
- Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Dai Chung
- Monroe Carell Jr. Children's Hospital, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Brad W Warner
- Washington University, St. Louis Children's Hospital, St. Louis, Missouri, United States of America
| | - George B Mychaliska
- University of Michigan, CS Mott Children's Hospital, Ann Arbor, Michigan, United States of America
| | - Douglas Potoka
- Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Amy J Wagner
- Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Mahmoud ElFiky
- Department of Pediatric Surgery, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Jay M Wilson
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Debbie Nickerson
- University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- University of Washington, Seattle, Washington, United States of America
| | - Frances A High
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, United States of America
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mauro Longoni
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Patricia K Donahoe
- Department of Surgery, Harvard Medical School, Boston, Massachusetts, United States of America
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Wendy K Chung
- Department of Pediatrics Medical Center, Columbia University, New York, New York, United States of America
- Department of Medicine, Columbia University, New York, New York, United States of America
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, United States of America
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, New York, United States of America
- Department of Biomedical Informatics, Columbia University Medical Center, New York, New York, United States of America
- JP Sulzberger Columbia Genome Center, Columbia University Medical Center, New York, New York, United States of America
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20
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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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21
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Rao CV, Farooqui M, Asch AS, Yamada HY. Critical role of mitosis in spontaneous late-onset Alzheimer's disease; from a Shugoshin 1 cohesinopathy mouse model. Cell Cycle 2018; 17:2321-2334. [PMID: 30231670 DOI: 10.1080/15384101.2018.1515554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
From early-onset Alzheimer's disease (EOAD) studies, the amyloid-beta hypothesis emerged as the foremost theory of the pathological causes of AD. However, how amyloid-beta accumulation is triggered and progresses toward senile plaques in spontaneous late-onset Alzheimer's disease (LOAD) in humans remains unanswered. Various LOAD facilitators have been proposed, and LOAD is currently considered a complex disease with multiple causes. Mice do not normally develop LOAD. Possibly due to the multiple causes, proposed LOAD facilitators have not been able to replicate spontaneous LOAD in mice, representing a disease modeling issue. Recently, we reported spontaneous late-onset development of amyloid-beta accumulation in brains of Shugoshin 1 (Sgo1) haploinsufficient mice, a cohesinopathy-mediated chromosome instability model. The result for the first time expands disease relevance of mitosis studies to a major disease other than cancers. Reverse-engineering of the model would shed light on the process of late-onset amyloid-beta accumulation in the brain and spontaneous LOAD development, and contribute to development of interventions for LOAD. This review will discuss the Sgo1 model, our current "three-hit hypothesis" regarding LOAD development with an emphasis on critical role of prolonged mitosis in amyloid-beta accumulation, and implications for human LOAD intervention and treatment. Abbreviations: Alzheimer's disease (AD); Late-onset Alzheimer's disease (LOAD); Early-onset Alzheimer's disease (EOAD); Shugoshin-1 (Sgo1); Chromosome Instability (CIN); apolipoprotein (Apoe); Central nervous system (CNS); Amyloid precursor protein (APP); N-methyl-d-aspartate (NMDA); Hazard ratio (HR); Cyclin-dependent kinase (CDK); Chronic Atrial Intestinal Dysrhythmia (CAID); beta-secretase 1 (BACE); phosphor-Histone H3 (p-H3); Research and development (R&D); Non-steroidal anti-inflammatory drugs (NSAIDs); Brain blood barrier (BBB).
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Affiliation(s)
- Chinthalapally V Rao
- a Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section , University of Oklahoma Health Sciences Center (OUHSC) , Oklahoma City , OK , USA
| | - Mudassir Farooqui
- a Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section , University of Oklahoma Health Sciences Center (OUHSC) , Oklahoma City , OK , USA
| | - Adam S Asch
- b Stephenson Cancer Center, Department of Medicine, Hematology/Oncology Section , University of Oklahoma Health Sciences Center (OUHSC) , Oklahoma City , OK , USA
| | - Hiroshi Y Yamada
- a Center for Cancer Prevention and Drug Development, Department of Medicine, Hematology/Oncology Section , University of Oklahoma Health Sciences Center (OUHSC) , Oklahoma City , OK , USA
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22
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Rao CV, Farooqui M, Zhang Y, Asch AS, Yamada HY. Spontaneous development of Alzheimer's disease-associated brain pathology in a Shugoshin-1 mouse cohesinopathy model. Aging Cell 2018; 17:e12797. [PMID: 29943428 PMCID: PMC6052391 DOI: 10.1111/acel.12797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 05/04/2018] [Accepted: 05/27/2018] [Indexed: 12/14/2022] Open
Abstract
Spontaneous late-onset Alzheimer's disease (LOAD) accounts for more than 95% of all human AD. As mice do not normally develop AD and as understanding on molecular processes leading to spontaneous LOAD has been insufficient to successfully model LOAD in mouse, no mouse model for LOAD has been available. Existing mouse AD models are all early-onset AD (EOAD) models that rely on forcible expression of AD-associated protein(s), which may not recapitulate prerequisites for spontaneous LOAD. This limitation in AD modeling may contribute to the high failure rate of AD drugs in clinical trials. In this study, we hypothesized that genomic instability facilitates development of LOAD and tested two genomic instability mice models in the brain pathology at the old age. Shugoshin-1 (Sgo1) haploinsufficient (∓) mice, a model of chromosome instability (CIN) with chromosomal and centrosomal cohesinopathy, spontaneously exhibited a major feature of AD pathology; amyloid beta accumulation that colocalized with phosphorylated Tau, beta-secretase 1 (BACE), and mitotic marker phospho-Histone H3 (p-H3) in the brain. Another CIN model, spindle checkpoint-defective BubR1-/+ haploinsufficient mice, did not exhibit the pathology at the same age, suggesting the prolonged mitosis-origin of the AD pathology. RNA-seq identified ten differentially expressed genes, among which seven genes have indicated association with AD pathology or neuronal functions (e.g., ARC, EBF3). Thus, the model represents a novel model that recapitulates spontaneous LOAD pathology in mouse. The Sgo1-/+ mouse may serve as a novel tool for investigating mechanisms of spontaneous progression of LOAD pathology, for early diagnosis markers, and for drug development.
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Affiliation(s)
- Chinthalapally V. Rao
- Center for Cancer Prevention and Drug DevelopmentDepartment of MedicineHematology/Oncology SectionUniversity of Oklahoma Health Sciences Center (OUHSC)Oklahoma CityOklahoma
| | - Mudassir Farooqui
- Center for Cancer Prevention and Drug DevelopmentDepartment of MedicineHematology/Oncology SectionUniversity of Oklahoma Health Sciences Center (OUHSC)Oklahoma CityOklahoma
| | - Yuting Zhang
- Center for Cancer Prevention and Drug DevelopmentDepartment of MedicineHematology/Oncology SectionUniversity of Oklahoma Health Sciences Center (OUHSC)Oklahoma CityOklahoma
| | - Adam S. Asch
- Stephenson Cancer CenterDepartment of MedicineHematology/Oncology SectionUniversity of Oklahoma Health Sciences Center (OUHSC)Oklahoma CityOklahoma
| | - Hiroshi Y. Yamada
- Center for Cancer Prevention and Drug DevelopmentDepartment of MedicineHematology/Oncology SectionUniversity of Oklahoma Health Sciences Center (OUHSC)Oklahoma CityOklahoma
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23
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Larizza L, Finelli P. Developmental disorders with intellectual disability driven by chromatin dysregulation: Clinical overlaps and molecular mechanisms. Clin Genet 2018; 95:231-240. [DOI: 10.1111/cge.13365] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/28/2018] [Accepted: 04/14/2018] [Indexed: 12/30/2022]
Affiliation(s)
- L. Larizza
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
| | - P. Finelli
- Laboratory of Cytogenetics and Molecular Genetics; Istituto Auxologico Italiano; Milan Italy
- Department of Medical Biotechnology and Translational Medicine; Università degli Studi di Milano; Milan Italy
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24
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Neri G, Schwartz CE, Lubs HA, Stevenson RE. X-linked intellectual disability update 2017. Am J Med Genet A 2018; 176:1375-1388. [PMID: 29696803 DOI: 10.1002/ajmg.a.38710] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/23/2018] [Accepted: 03/23/2018] [Indexed: 12/28/2022]
Abstract
The X-chromosome comprises only about 5% of the human genome but accounts for about 15% of the genes currently known to be associated with intellectual disability. The early progress in identifying the X-linked intellectual disability (XLID)-associated genes through linkage analysis and candidate gene sequencing has been accelerated with the use of high-throughput technologies. In the 10 years since the last update, the number of genes associated with XLID has increased by 96% from 72 to 141 and duplications of all 141 XLID genes have been described, primarily through the application of high-resolution microarrays and next generation sequencing. The progress in identifying genetic and genomic alterations associated with XLID has not been matched with insights that improve the clinician's ability to form differential diagnoses, that bring into view the possibility of curative therapies for patients, or that inform scientists of the impact of the genetic alterations on cell organization and function.
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Affiliation(s)
- 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
| | - Charles E Schwartz
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Herbert A Lubs
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Roger E Stevenson
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
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25
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Lehalle D, Mosca-Boidron AL, Begtrup A, Boute-Benejean O, Charles P, Cho MT, Clarkson A, Devinsky O, Duffourd Y, Duplomb-Jego L, Gérard B, Jacquette A, Kuentz P, Masurel-Paulet A, McDougall C, Moutton S, Olivié H, Park SM, Rauch A, Revencu N, Rivière JB, Rubin K, Simonic I, Shears DJ, Smol T, Taylor Tavares AL, Terhal P, Thevenon J, Van Gassen K, Vincent-Delorme C, Willemsen MH, Wilson GN, Zackai E, Zweier C, Callier P, Thauvin-Robinet C, Faivre L. STAG1 mutations cause a novel cohesinopathy characterised by unspecific syndromic intellectual disability. J Med Genet 2017; 54:479-488. [PMID: 28119487 DOI: 10.1136/jmedgenet-2016-104468] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 12/26/2016] [Accepted: 12/27/2016] [Indexed: 11/04/2022]
Abstract
BACKGROUND Cohesinopathies are rare neurodevelopmental disorders arising from a dysfunction in the cohesin pathway, which enables chromosome segregation and regulates gene transcription. So far, eight genes from this pathway have been reported in human disease. STAG1 belongs to the STAG subunit of the core cohesin complex, along with five other subunits. This work aimed to identify the phenotype ascribed to STAG1 mutations. METHODS Among patients referred for intellectual disability (ID) in genetics departments worldwide, array-comparative genomic hybridisation (CGH), gene panel, whole-exome sequencing or whole-genome sequencing were performed following the local diagnostic standards. RESULTS A mutation in STAG1 was identified in 17 individuals from 16 families, 9 males and 8 females aged 2-33 years. Four individuals harboured a small microdeletion encompassing STAG1; three individuals from two families had an intragenic STAG1 deletion. Six deletions were identified by array-CGH, one by whole-exome sequencing. Whole-exome sequencing found de novo heterozygous missense or frameshift STAG1 variants in eight patients, a panel of genes involved in ID identified a missense and a frameshift variant in two individuals. The 17 patients shared common facial features, with wide mouth and deep-set eyes. Four individuals had mild microcephaly, seven had epilepsy. CONCLUSIONS We report an international series of 17 individuals from 16 families presenting with syndromic unspecific ID that could be attributed to a STAG1 deletion or point mutation. This first series reporting the phenotype ascribed to mutation in STAG1 highlights the importance of data sharing in the field of rare disorders.
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Affiliation(s)
- Daphné Lehalle
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Anne-Laure Mosca-Boidron
- Laboratoire de Cytogénétique, Centre Hospitalier Universitaire Dijon, Dijon, France
- Equipe GAD, EA4271, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Amber Begtrup
- GeneDx, 207 Perry Parkway, Gaithersburg, Maryland, USA
| | | | - Perrine Charles
- Genetic Department, University Hospital La Pitié Salpêtrière, Paris, France
| | - Megan T Cho
- GeneDx, 207 Perry Parkway, Gaithersburg, Maryland, USA
| | - Amanda Clarkson
- Department of Clinical Genetics, Cambridge University Hospitals, Cambridge, UK
| | - Orrin Devinsky
- Epilepsy Center, NYU Langone Medical Center, New York, New York, USA
| | - Yannis Duffourd
- Equipe GAD, EA4271, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Laurence Duplomb-Jego
- Laboratoire de Cytogénétique, Centre Hospitalier Universitaire Dijon, Dijon, France
- Equipe GAD, EA4271, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Bénédicte Gérard
- Laboratoire de biologie moléculaire, CHU Strasbourg, Strasbourg, France
| | - Aurélia Jacquette
- Genetic Department, University Hospital La Pitié Salpêtrière, Paris, France
| | - Paul Kuentz
- Laboratoire de Cytogénétique, Centre Hospitalier Universitaire Dijon, Dijon, France
- Equipe GAD, EA4271, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Alice Masurel-Paulet
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
| | - Carey McDougall
- Clinical Genetics Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Hilde Olivié
- Department of Human Genetics and Centre for Developmental Disabilities, KU University Hospital Leuven, Leuven, Belgium
| | - Soo-Mi Park
- Department of Clinical Genetics, Cambridge University Hospitals, Cambridge, UK
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schwerzenbach-Zurich, Switzerland
| | - Nicole Revencu
- Centre for Human Genetics, Cliniques universitaires Saint-Luc, Université catholique de Louvain, Brussels, Belgium
| | - Jean-Baptiste Rivière
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
- Laboratoire de Cytogénétique, Centre Hospitalier Universitaire Dijon, Dijon, France
- Equipe GAD, EA4271, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Karol Rubin
- University of Minnesota Children's Hospital, Minneapolis, Minnesota, USA
| | - Ingrid Simonic
- Department of Clinical Genetics, Cambridge University Hospitals, Cambridge, UK
| | - Deborah J Shears
- Oxford Centre for Genomic Medicine Nuffield Orthopaedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE
| | - Thomas Smol
- Service de génétique clinique, CHU Lille, Lille, France
- Univ. Lille, RADEME (Research team on rare developmental and metabolic diseases), Lille, France
| | | | - Paulien Terhal
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Julien Thevenon
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
- Equipe GAD, EA4271, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Koen Van Gassen
- Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Marjolein H Willemsen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences and Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Golder N Wilson
- Department of Pediatrics, Texas Tech University Health Science Center, Lubbock, Texas, USA
| | | | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universitat Erlangen-Nurnberg, Erlangen, Germany
| | - Patrick Callier
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
- Laboratoire de Cytogénétique, Centre Hospitalier Universitaire Dijon, Dijon, France
- Equipe GAD, EA4271, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Christel Thauvin-Robinet
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
- Equipe GAD, EA4271, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
| | - Laurence Faivre
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Centre Hospitalier Universitaire Dijon, Dijon, France
- Equipe GAD, EA4271, Faculté de Médecine, Université de Bourgogne Franche-Comté, Dijon, France
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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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27
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Familial STAG2 germline mutation defines a new human cohesinopathy. NPJ Genom Med 2017; 2:7. [PMID: 29263825 PMCID: PMC5677968 DOI: 10.1038/s41525-017-0009-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 02/07/2017] [Accepted: 02/17/2017] [Indexed: 01/03/2023] Open
Abstract
We characterize a novel human cohesinopathy originated from a familial germline mutation of the gene encoding the cohesin subunit STAG2, which we propose to call STAG2-related X-linked Intellectual Deficiency. Five individuals carry a STAG2 p.Ser327Asn (c.980 G > A) variant that perfectly cosegregates with a phenotype of syndromic mental retardation in a characteristic X-linked recessive pattern. Although patient-derived cells did not show overt sister-chromatid cohesion defects, they exhibited altered cell cycle profiles and gene expression patterns that were consistent with cohesin deficiency. The protein level of STAG2 in patient cells was normal. Interestingly, STAG2 S327 is located at a conserved site crucial for binding to SCC1 and cohesin regulators. When expressed in human cells, the STAG2 p.Ser327Asn mutant is defective in binding to SCC1 and other cohesin subunits and regulators. Thus, decreased amount of intact cohesin likely underlies the phenotypes of STAG2-SXLID. Intriguingly, recombinant STAG2 p.Ser327Asn binds normally to SCC1, WAPL, and SGO1 in vitro, suggesting the existence of unknown in vivo mechanisms that regulate the interaction between STAG2 and SCC1. A newly discovered developmental disease is characterized by mutations in a subunit of the cohesin protein involved in cell division. A team led by Sérgio Pena from GENE—Núcleo de Genética Médica, Brazil, and Hongtao Yu from the University of Texas Southwestern Medical Center, USA, describe a Brazilian family with five male relatives, all with intellectual deficiency, short stature, and other abnormalities. The family tree pointed toward an X-linked pattern of inheritance, so the researchers performed a network analysis of 24 genes on the X chromosome known to contribute to mental retardation. They found that all five individuals had a mutation in a gene called STAG2, which encodes a subunit of cohesin. The mutant STAG2 did not bind properly to other cohesin subunits in human cells, and patient-derived cells exhibited altered cell cycle profiles. The researchers propose calling the disease “STAG2-related X-linked intellectual deficiency”.
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28
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Hill VK, Kim JS, Waldman T. Cohesin mutations in human cancer. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1866:1-11. [PMID: 27207471 PMCID: PMC4980180 DOI: 10.1016/j.bbcan.2016.05.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/12/2016] [Accepted: 05/14/2016] [Indexed: 12/19/2022]
Abstract
Cohesin is a highly-conserved protein complex that plays important roles in sister chromatid cohesion, chromatin structure, gene expression, and DNA repair. In humans, cohesin is a ubiquitously expressed, multi-subunit protein complex composed of core subunits SMC1A, SMC3, RAD21, STAG1/2 and regulatory subunits WAPL, PDS5A/B, CDCA5, NIPBL, and MAU2. Recent studies have demonstrated that genes encoding cohesin subunits are somatically mutated in a wide range of human cancers. STAG2 is the most commonly mutated subunit, and in a recent analysis was identified as one of only 12 genes that are significantly mutated in four or more cancer types. In this review we summarize the findings reported to date and comment on potential functional implications of cohesin mutation in the pathogenesis of human cancer.
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Affiliation(s)
- Victoria K Hill
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road, NW, NRB E304, Washington, DC 20057, USA
| | - Jung-Sik Kim
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road, NW, NRB E304, Washington, DC 20057, USA
| | - Todd Waldman
- Lombardi Comprehensive Cancer Center, Georgetown University School of Medicine, 3970 Reservoir Road, NW, NRB E304, Washington, DC 20057, USA
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