1
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Wei C, Gao Y, Li P. THOC6 is a novel biomarker of glioma and a target of anti-glioma drugs: An analysis based on bioinformatics and molecular docking. Medicine (Baltimore) 2024; 103:e37999. [PMID: 38728502 PMCID: PMC11081617 DOI: 10.1097/md.0000000000037999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/03/2024] [Indexed: 05/12/2024] Open
Abstract
Glioma is a typical malignant tumor of the nervous system. It is of great significance to identify new biomarkers for accurate diagnosis of glioma. In this context, THOC6 has been studied as a highly diagnostic prognostic biomarker, which contributes to improve the dilemma in diagnosing gliomas. We used online databases and a variety of statistical methods, such as Wilcoxon rank sum test, Dunn test and t test. We analyzed the mutation, location and expression profile of THOC6, revealing the network of THOC6 interaction with disease. Wilcoxon rank sum test showed that THOC6 is highly expressed in gliomas (P < 0.001). Dunn test, Wilcoxon rank sum test and t test showed that THOC6 expression was correlated with multiple clinical features. Logistic regression analysis further confirmed that THOC6 gene expression was a categorical dependent variable related to clinical features of poor prognosis. Kaplan-Meier survival analysis showed that the overall survival (OS) of glioma patients with high expression of THOC6 was poor (P < 0.001). Both univariate (P < 0.001) and multivariate (P = 0.04) Cox analysis confirmed that THOC6 gene expression was an independent risk factor for OS in patients with glioma. ROC curve analysis showed that THOC6 had a high diagnostic value in glioma (AUC = 0.915). Based on this, we constructed a nomogram to predict patient survival. Enrichment analysis showed that THOC6 expression was associated with multiple signal pathways. Immuno-infiltration analysis showed that the expression of THOC6 in glioma was closely related to the infiltration level of multiple immune cells. Molecular docking results showed that THOC6 might be the target of anti-glioma drugs. THOC6 is a novel diagnostic factor and prognostic biomarker of glioma.
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Affiliation(s)
- Chuang Wei
- Institute for Translational Medicine, Qingdao University, Qingdao, China
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yijun Gao
- School of Medicine, Shanghai University, Shanghai, China
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao, China
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2
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Werren EA, LaForce GR, Srivastava A, Perillo DR, Li S, Johnson K, Baris S, Berger B, Regan SL, Pfennig CD, de Munnik S, Pfundt R, Hebbar M, Jimenez-Heredia R, Karakoc-Aydiner E, Ozen A, Dmytrus J, Krolo A, Corning K, Prijoles EJ, Louie RJ, Lebel RR, Le TL, Amiel J, Gordon CT, Boztug K, Girisha KM, Shukla A, Bielas SL, Schaffer AE. TREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome. Nat Commun 2024; 15:1640. [PMID: 38388531 PMCID: PMC10884030 DOI: 10.1038/s41467-024-45948-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 02/07/2024] [Indexed: 02/24/2024] Open
Abstract
THOC6 variants are the genetic basis of autosomal recessive THOC6 Intellectual Disability Syndrome (TIDS). THOC6 is critical for mammalian Transcription Export complex (TREX) tetramer formation, which is composed of four six-subunit THO monomers. The TREX tetramer facilitates mammalian RNA processing, in addition to the nuclear mRNA export functions of the TREX dimer conserved through yeast. Human and mouse TIDS model systems revealed novel THOC6-dependent, species-specific TREX tetramer functions. Germline biallelic Thoc6 loss-of-function (LOF) variants result in mouse embryonic lethality. Biallelic THOC6 LOF variants reduce the binding affinity of ALYREF to THOC5 without affecting the protein expression of TREX members, implicating impaired TREX tetramer formation. Defects in RNA nuclear export functions were not detected in biallelic THOC6 LOF human neural cells. Instead, mis-splicing was detected in human and mouse neural tissue, revealing novel THOC6-mediated TREX coordination of mRNA processing. We demonstrate that THOC6 is required for key signaling pathways known to regulate the transition from proliferative to neurogenic divisions during human corticogenesis. Together, these findings implicate altered RNA processing in the developmental biology of TIDS neuropathology.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Geneva R LaForce
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Anshika Srivastava
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Delia R Perillo
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Shaokun Li
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Katherine Johnson
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Safa Baris
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Brandon Berger
- Advanced Precision Medicine Laboratory, The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Samantha L Regan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Christian D Pfennig
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Sonja de Munnik
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Centre Nijmegen, Nijmegen, 6524, the Netherlands
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, 98195, Seattle, WA, USA
| | - Raúl Jimenez-Heredia
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Elif Karakoc-Aydiner
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Ahmet Ozen
- Division of Pediatric Allergy and Immunology, School of Medicine, Marmara University, Istanbul Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, The Isil Berat Barlan Center for Translational Medicine, Istanbul, 34722, Turkey
| | - Jasmin Dmytrus
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
| | - Ana Krolo
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
| | - Ken Corning
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - E J Prijoles
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | | | - Robert Roger Lebel
- Section of Medical Genetics, SUNY Upstate Medical University, Syracuse, NY, 13210, USA
| | - Thuy-Linh Le
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
| | - Jeanne Amiel
- Imagine Institute, INSERM U1163, Paris Cité University, Paris, 75015, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, 75015, France
| | | | - Kaan Boztug
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, 1090, Austria
- Research Centre for Molecular Medicine of the Austrian Academy of Sciences, Vienna, 1090, Austria
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, 1090, Austria
- St. Anna Children's Hospital and Children's Cancer Research Institute, Department of Pediatrics, Medical University of Vienna, Vienna, 1090, Austria
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Anju Shukla
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Ashleigh E Schaffer
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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3
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Ruaud L, Roux N, Boutaud L, Bessières B, Ageorges F, Achaiaa A, Bole C, Nitschke P, Masson C, Vekemans M, Verloes A, Attie‐Bitach T. Biallelic
THOC6
pathogenic variants: Prenatal phenotype and review of the literature. Birth Defects Res 2022; 114:499-504. [DOI: 10.1002/bdr2.2011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 01/20/2023]
Affiliation(s)
- Lyse Ruaud
- INSERM UMR 1141, Neurodiderot Université de Paris Paris France
- Département de Génétique APHp.Nord, Hopital Universitaire Robert‐Debré Paris France
| | - Nathalie Roux
- APHp.Centre, Hopital Necker‐Enfants Malades, Service de Médecine Génomique des Maladies Rares Paris France
- Université de Paris Paris France
| | - Lucile Boutaud
- APHp.Centre, Hopital Necker‐Enfants Malades, Service de Médecine Génomique des Maladies Rares Paris France
- Institut Imagine, INSERM U1163 Paris France
| | - Bettina Bessières
- APHp.Centre, Hopital Necker‐Enfants Malades, Service de Médecine Génomique des Maladies Rares Paris France
| | - Faustine Ageorges
- Département de Génétique APHp.Nord, Hopital Universitaire Robert‐Debré Paris France
| | - Amale Achaiaa
- APHp.Centre, Hopital Necker‐Enfants Malades, Service de Médecine Génomique des Maladies Rares Paris France
| | | | - Patrick Nitschke
- Université de Paris Paris France
- Institut Imagine, Plateforme de Génomique Paris France
| | - Cécile Masson
- Institut Imagine, Plateforme de Génomique Paris France
| | - Michel Vekemans
- APHp.Centre, Hopital Necker‐Enfants Malades, Service de Médecine Génomique des Maladies Rares Paris France
- Université de Paris Paris France
- Institut Imagine, INSERM U1163 Paris France
| | - Alain Verloes
- INSERM UMR 1141, Neurodiderot Université de Paris Paris France
- Département de Génétique APHp.Nord, Hopital Universitaire Robert‐Debré Paris France
| | - Tania Attie‐Bitach
- APHp.Centre, Hopital Necker‐Enfants Malades, Service de Médecine Génomique des Maladies Rares Paris France
- Université de Paris Paris France
- Institut Imagine, INSERM U1163 Paris France
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4
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Pühringer T, Hohmann U, Fin L, Pacheco-Fiallos B, Schellhaas U, Brennecke J, Plaschka C. Structure of the human core transcription-export complex reveals a hub for multivalent interactions. eLife 2020; 9:e61503. [PMID: 33191911 PMCID: PMC7744094 DOI: 10.7554/elife.61503] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022] Open
Abstract
The export of mRNA from nucleus to cytoplasm requires the conserved and essential transcription and export (TREX) complex (THO-UAP56/DDX39B-ALYREF). TREX selectively binds mRNA maturation marks and licenses mRNA for nuclear export by loading the export factor NXF1-NXT1. How TREX integrates these marks and achieves high selectivity for mature mRNA is poorly understood. Here, we report the cryo-electron microscopy structure of the human THO-UAP56/DDX39B complex at 3.3 Å resolution. The seven-subunit THO-UAP56/DDX39B complex multimerizes into a 28-subunit tetrameric assembly, suggesting that selective recognition of mature mRNA is facilitated by the simultaneous sensing of multiple, spatially distant mRNA regions and maturation marks. Two UAP56/DDX39B RNA helicases are juxtaposed at each end of the tetramer, which would allow one bivalent ALYREF protein to bridge adjacent helicases and regulate the TREX-mRNA interaction. Our structural and biochemical results suggest a conserved model for TREX complex function that depends on multivalent interactions between proteins and mRNA.
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Affiliation(s)
- Thomas Pühringer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Ulrich Hohmann
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)ViennaAustria
| | - Laura Fin
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Belén Pacheco-Fiallos
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Ulla Schellhaas
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)ViennaAustria
| | - Clemens Plaschka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC)ViennaAustria
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5
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Zhang Q, Chen S, Qin Z, Zheng H, Fan X. The first reported case of Beaulieu-Boycott-Innes syndrome caused by two novel mutations in THOC6 gene in a Chinese infant. Medicine (Baltimore) 2020; 99:e19751. [PMID: 32282736 PMCID: PMC7220430 DOI: 10.1097/md.0000000000019751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE This case report expands the mutation and phenotypic spectra of Beaulieu-Boycott-Innes syndrome (BBIS), and will be valuable for mutation-based pre- and post-natal screening of BBIS when conducting a genetic diagnosis. PATIENT CONCERNS A 4-year old boy from Guilin City, Guangxi Zhuang Autonomous Region, China, was referred to our clinic for clarification of his diagnosis because he showed moderate intellectual disability. DIAGNOSIS Two novel compound heterozygous mutations of THOC6, c.664T>C (p.Trp222Arg) and c.945+1 G>A were identified in this patient by whole exome sequencing. The two mutations were evaluated as pathogenic and likely pathogenic respectively according to the American College of Medical Genetics guidelines. This is the first case displaying the BBIS phenotype reported in the Chinese population. These two mutations have not been reported previously. INTERVENTIONS Symptomatic treatment and rehabilitation training for patients. OUTCOMES The genetic cause of the disease was identified. The family received scientific genetic counseling. LESSONS BBIS is a rare syndromic autosomal recessive disease with intellectual disability and it is normally difficult for clinicians to recognize it. Whole exome sequencing is an efficient way to identify the gene which causes a particular disease in patients.
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Affiliation(s)
- Qiang Zhang
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi
| | - Shaoke Chen
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zailong Qin
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi
| | - Haiyang Zheng
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi
| | - Xin Fan
- Laboratory of Genetic and Metabolism, Department of Paediatric Endocrine and Metabolism, Maternal and Child Health Hospital of Guangxi
- Department of Pediatrics, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
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6
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Mattioli F, Isidor B, Abdul-Rahman O, Gunter A, Huang L, Kumar R, Beaulieu C, Gecz J, Innes M, Mandel JL, Piton A. Clinical and functional characterization of recurrent missense variants implicated in THOC6-related intellectual disability. Hum Mol Genet 2020; 28:952-960. [PMID: 30476144 DOI: 10.1093/hmg/ddy391] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/11/2018] [Accepted: 08/11/2018] [Indexed: 01/08/2023] Open
Abstract
THOC6 encodes a subunit of the THO complex that is part of a highly conserved transcription and export complex known to have roles in mRNA processing and export. Few homozygous or compound heterozygous variants have been identified in the THOC6 gene in patients with a syndromic form of intellectual disability [Beaulieu-Boycott-Innes syndrome (BBIS); MIM: 613680]. Here we report two additional individuals affected with BBIS originating from the north of Europe and sharing a haplotype composed of three very rare missense changes in the THOC6 gene-Trp100Arg, Val234Leu, Gly275Asp. The first individual is a boy who is homozygous for the three-variant haplotype due to a maternal uniparental disomy event. The second is a girl who is compound heterozygous for this haplotype and a previously reported Gly190Glu missense variant. We analyzed the impact of these different amino acid changes on THOC6 protein expression, cellular localization and interaction with the other THO complex subunits. We show that the different THOC6 variants alter the physiological nuclear localizationof the protein and its interaction with at least two THO subunits, THOC1 and THOC5. Two amino acid changes from the three-variant haplotype alone have specific effects and might contribute to the pathogenicity of the haplotype. Overall, we expanded the cohort of currently known individuals with BBIS by reporting two individuals carrying the same recurrent European haplotype composed of three amino acid changes, affecting THOC6 localization and interaction with THO protein partners.
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Affiliation(s)
- Francesca Mattioli
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch-Graffenstaden, France.,Centre National de la Recherche Scientifique, UMR7104, 75016 Paris, France.,Institut National de la Santé et de la Recherche Médicale, U964, 75654 Paris, France.,Université de Strasbourg, 67081 Strasbourg, France
| | - Bertrand Isidor
- Service de Génétique Médicale, Centre Hospitalier Universitaire (CHU) de Nantes, 44093 Nantes, France
| | - Omar Abdul-Rahman
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Andrew Gunter
- Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lijia Huang
- Department of Genetics, Children's Hospital of Eastern Ontario (CHEO), 401 Smyth Road, Ottawa, ON K1H 8L1, Canada
| | - Raman Kumar
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Chandree Beaulieu
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Jean-Louis Mandel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch-Graffenstaden, France.,Centre National de la Recherche Scientifique, UMR7104, 75016 Paris, France.,Institut National de la Santé et de la Recherche Médicale, U964, 75654 Paris, France.,Université de Strasbourg, 67081 Strasbourg, France.,Institute for Advanced Studies, University of Strasbourg, 67083 Strasbourg, France
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch-Graffenstaden, France.,Centre National de la Recherche Scientifique, UMR7104, 75016 Paris, France.,Institut National de la Santé et de la Recherche Médicale, U964, 75654 Paris, France.,Université de Strasbourg, 67081 Strasbourg, France.,Unite de Genetique Moleculaire, Hopitaux Universitaires de Strasbourg, 67091 Strasbourg, France Institute for Advanced Studies, University of Strasbourg, 67083 Strasbourg, France
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7
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Gupta N, Yadav S, Gurramkonda VB, Vl R, Sg T, Kabra M. First report of THOC6 related intellectual disability (Beaulieu Boycott Innes syndrome) in two siblings from India. Eur J Med Genet 2019; 63:103742. [PMID: 31421288 DOI: 10.1016/j.ejmg.2019.103742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/08/2019] [Accepted: 08/13/2019] [Indexed: 01/02/2023]
Abstract
THOC6 is a newly described causal gene for an autosomal recessive intellectual disability (ID) - Beaulieu Boycott Innes syndrome (BBIS) (OMIM # 613680). It is characterized by ID with dysmorphic facies, genitourinary, cardiac anomalies, and dentition problems. Here, we report the first two siblings of BBIS from the Indian subcontinent with previously unreported skeletal anomalies such as Sprengel shoulder, calcaneo valgus deformity, radioulnar dysostosis, and overlapping toes. Whole exome sequencing (WES) identified previously reported three missense variants (p.Trp100Arg, p.Val234Leu, p.Gly275Asp) in THOC6. THOC6 is a subunit of TRanscription and EXport (TREX) complex involved in mRNA transcription, processing, and nuclear export of spliced mRNAs and has a potential role in neurodevelopment. Till date, only 12 patients with BBIS have been reported. This report reviews the phenotypic and genetic data of known BBIS cases in addition to the new phenotypic features, thereby expanding the phenotype of this rare syndrome.
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Affiliation(s)
- Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Genetics, New Delhi, India.
| | - Sakshi Yadav
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Genetics, New Delhi, India
| | - Venkatesh Babu Gurramkonda
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Genetics, New Delhi, India
| | - Ramprasad Vl
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, India
| | - Thenral Sg
- Medgenome Laboratory Private Limited, 3rd Floor, 258/A, Narayana Health City, Hosur Road, Bommasandra, Bengaluru, India
| | - Madhulika Kabra
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Genetics, New Delhi, India
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8
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Accogli A, Scala M, Calcagno A, Castello R, Torella A, Musacchia F, Allegri AME, Mancardi MM, Maghnie M, Severino M, Nigro V, Capra V. Novel CNS malformations and skeletal anomalies in a patient with Beaulieu-boycott-Innes syndrome. Am J Med Genet A 2018; 176:2835-2840. [PMID: 30238602 DOI: 10.1002/ajmg.a.40534] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022]
Abstract
THO/TREX (transcription/export) is a conserved eukaryotic complex that plays a crucial role in gene expression and prevents DNA damage during mitosis and meiosis. In mammals, TREX is essential during embryogenesis, determining stem cell fate specification by regulating posttranscriptional self-renewal and differentiation in several tissues. It is composed of a core called THO, consisting of THOC1, 2, 5, 6, 7, and additional proteins. Bi-allelic mutations in THOC6 have been associated to Beaulieu-Boycott-Innes syndrome (BBIS), a syndromic form of intellectual disability (ID). To date, nine patients harbouring homozygous or compound heterozygous mutations in THOC6 have been reported. Despite the clinical heterogenity and subtle dysmorphic features in some individuals, distinctive facial features are tall forehead, short and upslanting palpebral fissures, deep set eyes, flat philtrum, and malocclusion. Nonlife threatening congenital anomalies are common, including cardiac and renal malformations, anteriorly displaced anus, cryptorchidism in males, submucous cleft palate, and corpus callosum dysgenesis. Affected patients usually have short stature, mild microcephaly, and mild to moderate ID. Here, we describe an Italian patient with BBIS, carrying two compound heterozygous loss-of-function (LoF) variants in THOC6 (c.577C > T, p.R193* and c.792_793delCA, p.V264Vfs*48). In addition to the common phenotype, she displays cerebellar hypoplasia with severe vermian dysgenesis and hydrocephalus due to aqueductal stenosis, multiple skeletal anomalies and hypergonadotropic hypogonadism. Thus, we review the previous cases and discuss the phenotypic spectrum of BBIS, providing further evidence regarding the pivotal role of TREX complex in human development.
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Affiliation(s)
- Andrea Accogli
- UOC Neurochirurgia, Istituto Giannina Gaslini, Genoa, Italy.,Università degli studi di Genova, Italy
| | - Marcello Scala
- UOC Neurochirurgia, Istituto Giannina Gaslini, Genoa, Italy.,Università degli studi di Genova, Italy
| | - Annalisa Calcagno
- UOC Clinica Pediatrica, Istituto Giannina Gaslini, Università di Genova, Genoa, Italy
| | | | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Anna M E Allegri
- UOC Clinica Pediatrica, Istituto Giannina Gaslini, Università di Genova, Genoa, Italy
| | - Maria M Mancardi
- UOC Neuropsichiatria Infantile-Centro Epilessia, Istituto Giannina Gaslini, Genoa, Italy
| | - Mohamad Maghnie
- UOC Clinica Pediatrica, Istituto Giannina Gaslini, Università di Genova, Genoa, Italy
| | | | | | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy.,Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Valeria Capra
- UOC Neurochirurgia, Istituto Giannina Gaslini, Genoa, Italy
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9
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Anazi S, Maddirevula S, Salpietro V, Asi YT, Alsahli S, Alhashem A, Shamseldin HE, AlZahrani F, Patel N, Ibrahim N, Abdulwahab FM, Hashem M, Alhashmi N, Al Murshedi F, Al Kindy A, Alshaer A, Rumayyan A, Al Tala S, Kurdi W, Alsaman A, Alasmari A, Banu S, Sultan T, Saleh MM, Alkuraya H, Salih MA, Aldhalaan H, Ben-Omran T, Al Musafri F, Ali R, Suleiman J, Tabarki B, El-Hattab AW, Bupp C, Alfadhel M, Al Tassan N, Monies D, Arold ST, Abouelhoda M, Lashley T, Houlden H, Faqeih E, Alkuraya FS. Expanding the genetic heterogeneity of intellectual disability. Hum Genet 2017; 136:1419-1429. [PMID: 28940097 DOI: 10.1007/s00439-017-1843-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/15/2017] [Indexed: 11/30/2022]
Abstract
Intellectual disability (ID) is a common morbid condition with a wide range of etiologies. The list of monogenic forms of ID has increased rapidly in recent years thanks to the implementation of genomic sequencing techniques. In this study, we describe the phenotypic and genetic findings of 68 families (105 patients) all with novel ID-related variants. In addition to established ID genes, including ones for which we describe unusual mutational mechanism, some of these variants represent the first confirmatory disease-gene links following previous reports (TRAK1, GTF3C3, SPTBN4 and NKX6-2), some of which were based on single families. Furthermore, we describe novel variants in 14 genes that we propose as novel candidates (ANKHD1, ASTN2, ATP13A1, FMO4, MADD, MFSD11, NCKAP1, NFASC, PCDHGA10, PPP1R21, SLC12A2, SLK, STK32C and ZFAT). We highlight MADD and PCDHGA10 as particularly compelling candidates in which we identified biallelic likely deleterious variants in two independent ID families each. We also highlight NCKAP1 as another compelling candidate in a large family with autosomal dominant mild intellectual disability that fully segregates with a heterozygous truncating variant. The candidacy of NCKAP1 is further supported by its biological function, and our demonstration of relevant expression in human brain. Our study expands the locus and allelic heterogeneity of ID and demonstrates the power of positional mapping to reveal unusual mutational mechanisms.
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Affiliation(s)
- Shams Anazi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Vincenzo Salpietro
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Yasmine T Asi
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Saud Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amal Alhashem
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Hanan E Shamseldin
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Fatema AlZahrani
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous M Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nadia Alhashmi
- Department of Genetics, College of Medicine, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Fathiya Al Murshedi
- Department of Genetics, College of Medicine, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Adila Al Kindy
- Department of Genetics, College of Medicine, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Ahmad Alshaer
- Pediatric Neurology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ahmed Rumayyan
- King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Neurology Division, Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Saeed Al Tala
- Department of Pediatrics and Genetic Unit, Armed Forces Hospital, Khamis Mushayt, Saudi Arabia
| | - Wesam Kurdi
- Department of Obstetrics and Gynecology, King Faisal Specialist Hospital, Riyadh, Saudi Arabia
| | - Abdulaziz Alsaman
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Ali Alasmari
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Selina Banu
- Department of Pediatric Neurology, ICH and SSF Hospital Mirpur, Dhaka, 1216, Bangladesh
| | - Tipu Sultan
- Department of Pediatric Neurology, Institute of Child Health and The Children's Hospital Lahore, 381-D/2, Lahore, Pakistan
| | - Mohammed M Saleh
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Hisham Alkuraya
- Department of Ophthalmology, Specialized Medical Center Hospital, Riyadh, Saudi Arabia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, King Khalid University Hospital and College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Hesham Aldhalaan
- Pediatric Neurology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tawfeg Ben-Omran
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Fatima Al Musafri
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Rehab Ali
- Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
| | - Jehan Suleiman
- Division of Neurology, Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Brahim Tabarki
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Ayman W El-Hattab
- Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, Al-Ain, United Arab Emirates
| | - Caleb Bupp
- Spectrum Health Genetics, Grand Rapids, MI, USA
| | - Majid Alfadhel
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | - Nada Al Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Dorota Monies
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Stefan T Arold
- Division of Biological and Environmental Sciences and Engineering (BESE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Tammaryn Lashley
- Queen Square Brain Bank for Neurological Disorders, Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Eissa Faqeih
- Department of Pediatric Subspecialties, Children's Hospital, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia. .,Spectrum Health Genetics, Grand Rapids, MI, USA. .,Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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10
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Beaulieu-Boycott-Innes syndrome: an intellectual disability syndrome with characteristic facies. Clin Dysmorphol 2017; 25:146-51. [PMID: 27295358 DOI: 10.1097/mcd.0000000000000134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report a female child from an Irish Traveller family presenting with severe intellectual disability, dysmorphic features, renal anomalies, dental caries and cyclical vomiting. Current health issues include global developmental delay, mild concentric left ventricular hypertrophy, dental malocclusion and caries and a single duplex left kidney. The proband and her mother also have multiple epiphyseal dysplasia. Whole-exome sequencing was performed to identify the underlying genetic cause. DNA from the proband was enriched with the Agilent Sure Select v5 Exon array and sequenced on an Illumina HiSeq. Rare homozygous variants were prioritized. Whole-exome sequencing identified three linked homozygous missense variants in THOC6 (c.298T>A, p.Trp100Arg; c.700G>C, p.Val234Leu; c.824G>A, p.Gly275Asp) as the likely cause of this child's intellectual disability syndrome, resulting in a molecular diagnosis of Beaulieu-Boycott-Innes syndrome (BBIS). This is the first report of BBIS in Europe. BBIS has been reported previously in two Hutterite families and one Saudi family. A review of all patients to date shows a relatively homogenous phenotype. Core clinical features include low birth weight with subsequent growth failure, short stature, intellectual disability with language delay, characteristic facies, renal anomalies and dental malocclusion with caries. Some patients also have cardiac defects. All patients show characteristic dysmorphic facial features including a tall forehead with high anterior hairline and deep-set eyes with upslanting palpebral fissures. The coexistence of intellectual disability together with these characteristic facies should provide a diagnostic clue for BBIS during patient evaluation.
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11
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Amos JS, Huang L, Thevenon J, Kariminedjad A, Beaulieu CL, Masurel-Paulet A, Najmabadi H, Fattahi Z, Beheshtian M, Tonekaboni SH, Tang S, Helbig KL, Alcaraz W, Rivière JB, Faivre L, Innes AM, Lebel RR, Boycott KM. Autosomal recessive mutations in THOC6 cause intellectual disability: syndrome delineation requiring forward and reverse phenotyping. Clin Genet 2016; 91:92-99. [PMID: 27102954 DOI: 10.1111/cge.12793] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 01/21/2023]
Abstract
THOC6 is a part of the THO complex, which is involved in coordinating mRNA processing with export. The THO complex interacts with additional components to form the larger TREX complex (transcription export complex). Previously, a homozygous missense mutation in THOC6 in the Hutterite population was reported in association with syndromic intellectual disability. Using exome sequencing, we identified three unrelated patients with bi-allelic mutations in THOC6 associated with intellectual disability and additional clinical features. Two of the patients were compound heterozygous for a stop and a missense mutation, and the third was homozygous for a missense mutation; the missense mutations were predicted to be pathogenic by in silico analysis and modeling. Clinical features of the three newly identified patients and those previously reported are reviewed; intellectual disability is moderate to severe, and malformations are variable including renal and heart defects, cleft palate, microcephaly, and corpus callosum dysgenesis. Facial features are variable and include tall forehead, short upslanting palpebral fissures +/- deep set eyes, and a long nose with overhanging columella. These subtle facial features render the diagnosis difficult to make in isolation with certainty. Our results expand the mutational and clinical spectrum of this rare disease, confirm that THOC6 is an intellectual disability causing gene, while providing insight into the importance of the THO complex in neurodevelopment.
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Affiliation(s)
- J S Amos
- Medical Genetics Section, SUNY Upstate Medical University, Syracuse, NY, USA
| | - L Huang
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - J Thevenon
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,EA4271-Génétique des Anomalies du développement, Université de Bourgogne, Dijon, France
| | - A Kariminedjad
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran
| | - C L Beaulieu
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - A Masurel-Paulet
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,EA4271-Génétique des Anomalies du développement, Université de Bourgogne, Dijon, France
| | - H Najmabadi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.,Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Z Fattahi
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.,Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - M Beheshtian
- Kariminejad-Najmabadi Pathology & Genetics Center, Tehran, Iran.,Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - S Tang
- Ambry Genetics Corporation, Aliso Viejo, CA, USA
| | - K L Helbig
- Ambry Genetics Corporation, Aliso Viejo, CA, USA
| | - W Alcaraz
- Ambry Genetics Corporation, Aliso Viejo, CA, USA
| | - J-B Rivière
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,EA4271-Génétique des Anomalies du développement, Université de Bourgogne, Dijon, France
| | - L Faivre
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon, Dijon, France.,EA4271-Génétique des Anomalies du développement, Université de Bourgogne, Dijon, France
| | - A M Innes
- Department of Medical Genetics, University of Calgary, Calgary, Alberta, Canada
| | - R R Lebel
- Medical Genetics Section, SUNY Upstate Medical University, Syracuse, NY, USA
| | - K M Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
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