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Qin Y, Yao Y, Liu N, Wang B, Liu L, Li H, Gao T, Xu R, Wang X, Zhang F, Song J. Prenatal whole-exome sequencing for fetal structural anomalies: a retrospective analysis of 145 Chinese cases. BMC Med Genomics 2023; 16:262. [PMID: 37880672 PMCID: PMC10601195 DOI: 10.1186/s12920-023-01697-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Whole-exome sequencing (WES) significantly improves the diagnosis of the etiology of fetal structural anomalies. This study aims to evaluate the diagnostic value of prenatal WES and to investigate the pathogenic variants in structurally abnormal fetuses. METHODS We recruited 144 fetuses with structural anomalies between 14 and 2020 and 15 December 2021 in the study. Genetic screening was performed by WES combined with karyotyping and chromosomal microarray analysis. The molecular diagnostic yield of prenatal WES for each type of fetal structural anomaly and the identified pathogenic genes and mutations were reported. RESULTS In this study, we retrospectively analyzed the clinical and genetic data of 145 structurally anomalous fetuses. These cases were classified into 9 phenotypic classes based on antenatal ultrasound findings. Thirty-eight pathogenic variants in 24 genes were identified in 35 of the 145 cases, including 14 novel variants in 13 genes (EP300, MYH3, TSC2, MMP9, CPLANE1, INVS, COL1A1, EYA1, TTC21B, MKS1, COL11A2, PDHA1 and L1CAM). Five additional pathogenic variants were classified as incidental findings. Our study showed that the overall diagnosis rate of WES was 28.1% (27/96) in the parent-fetus trio cases and 16.3% (8/49) in the proband-only cases. Fetuses with musculoskeletal anomalies had the highest diagnostic yield (51.4%, 19/37). In addition, FGFR3 and COL1A1 were the most common pathogenic genes. CONCLUSIONS Our work expands the mutation spectrum of the genes associated with fetal structural anomalies and provides valuable information for future parental genetic counselling and pregnancy management of the structurally anomalous fetuses.
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Affiliation(s)
- Yayun Qin
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Yanyi Yao
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Nian Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Bo Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Lijun Liu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Hui Li
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Tangxinzi Gao
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Runhong Xu
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Xiaoyan Wang
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China
| | - Fanglian Zhang
- Honghu Hospital of Traditional Chinese Medicine, Jingzhou, 433200, Hubei Province, China
| | - Jieping Song
- Medical Genetics Center, Maternal and Child Health Hospital of Hubei Province, Wuhan, 430070, Hubei Province, China.
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2
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Keyan KS, Salim S, Gowda S, Abdelrahman D, Amir SS, Islam Z, Vargas C, Bengoechea-Alonso MT, Alwa A, Dahal S, Kolatkar PR, Da'as S, Torrisani J, Ericsson J, Mohammad F, Khan OM. Control of TGFβ signalling by ubiquitination independent function of E3 ubiquitin ligase TRIP12. Cell Death Dis 2023; 14:692. [PMID: 37863914 PMCID: PMC10589240 DOI: 10.1038/s41419-023-06215-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: 06/19/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023]
Abstract
Transforming growth factor β (TGFβ) pathway is a master regulator of cell proliferation, differentiation, and death. Deregulation of TGFβ signalling is well established in several human diseases including autoimmune disorders and cancer. Thus, understanding molecular pathways governing TGFβ signalling may help better understand the underlying causes of some of those conditions. Here, we show that a HECT domain E3 ubiquitin ligase TRIP12 controls TGFβ signalling in multiple models. Interestingly, TRIP12 control of TGFβ signalling is completely independent of its E3 ubiquitin ligase activity. Instead, TRIP12 recruits SMURF2 to SMAD4, which is most likely responsible for inhibitory monoubiquitination of SMAD4, since SMAD4 monoubiquitination and its interaction with SMURF2 were dramatically downregulated in TRIP12-/- cells. Additionally, genetic inhibition of TRIP12 in human and murine cells leads to robust activation of TGFβ signalling which was rescued by re-introducing wildtype TRIP12 or a catalytically inactive C1959A mutant. Importantly, TRIP12 control of TGFβ signalling is evolutionary conserved. Indeed, genetic inhibition of Drosophila TRIP12 orthologue, ctrip, in gut leads to a reduced number of intestinal stem cells which was compensated by the increase in differentiated enteroendocrine cells. These effects were completely normalised in Drosophila strain where ctrip was co-inhibited together with Drosophila SMAD4 orthologue, Medea. Similarly, in murine 3D intestinal organoids, CRISPR/Cas9 mediated genetic targeting of Trip12 enhances TGFβ mediated proliferation arrest and cell death. Finally, CRISPR/Cas9 mediated genetic targeting of TRIP12 in MDA-MB-231 breast cancer cells enhances the TGFβ induced migratory capacity of these cells which was rescued to the wildtype level by re-introducing wildtype TRIP12. Our work establishes TRIP12 as an evolutionary conserved modulator of TGFβ signalling in health and disease.
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Affiliation(s)
- Kripa S Keyan
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Safa Salim
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Swetha Gowda
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Syeda Sakina Amir
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Zeyaul Islam
- Qatar Biomedical Research Institute, Doha, Qatar
| | - Claire Vargas
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | | | - Amira Alwa
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Subrat Dahal
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Sahar Da'as
- Department of Research, Sidra Medicine, Doha, Qatar
| | - Jerome Torrisani
- Centre de Recherches en Cancérologie de Toulouse, Université de Toulouse, Inserm, CNRS, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Johan Ericsson
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Farhan Mohammad
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Omar M Khan
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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3
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Wu CS, Tsai TH, Chen WL, Tsai HJ, Chien YL. Ophthalmologic diagnoses in youths with autism spectrum disorder: Prevalence and clinical correlates. Autism Res 2023; 16:2008-2020. [PMID: 37632715 DOI: 10.1002/aur.3019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/10/2023] [Indexed: 08/28/2023]
Abstract
Autism spectrum disorder (ASD) is associated with a high prevalence of visual dysfunction. This study aimed to investigate the rates of amblyopia, refractive errors, and strabismus, as well as their clinical correlates in ASD. This population-based matched-cohort study used data from the Taiwan National Health Insurance Research Database. A total of 3,551 youths with ASD and 35,510 non-autistic control participants matched by age and sex were included. All the participants were followed-up until they were 18 years old. The prevalence of amblyopia, refractive errors, and strabismus was compared between the ASD and control groups. Effect modifiers, including sex, ASD subgroup, and co-diagnosis of intelligence disability, were examined. Compared to the control group, youths with ASD had a significantly increased risk of amblyopia (adjusted odds ratio [aOR] = 1.75), anisometropia (aOR = 1.66), astigmatism (aOR = 1.51), hypermetropia (aOR = 2.08), exotropia (aOR = 2.86), and esotropia (aOR = 2.63), but a comparable likelihood of myopia according to age. Males with ASD had a significantly lower likelihood of exotropia, but a higher likelihood of myopia than females with ASD. The autism subgroup had a higher OR for hypermetropia, but a lower OR for myopia than the other ASD subgroups. ASD youths with intelligence disabilities demonstrated significantly higher ORs for amblyopia, hypermetropia, and all types of strabismus and lower OR for myopia than those without intelligence disabilities. In conclusion, the rates of amblyopia, refractive errors, and strabismus were higher in youths with ASD. Ocular abnormalities in youths with ASD require a comprehensive assessment and management.
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Affiliation(s)
- Chi-Shin Wu
- National Center for Geriatrics and Welfare Research, National Health Research Institutes, Yunlin, Taiwan
- Department of Psychiatry, National Taiwan University Hospital, Yunlin Branch, Yunlin, Taiwan
| | - Tzu-Hsun Tsai
- Department of Ophthalmology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
| | - Wei-Li Chen
- Department of Ophthalmology, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
- Advanced Ocular Surface and Corneal Nerve Regeneration Center, National Taiwan University Hospital, Taipei, Taiwan
| | - Hui-Ju Tsai
- Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Yi-Ling Chien
- Department of Psychiatry, National Taiwan University Hospital and College of Medicine, Taipei, Taiwan
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4
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Mitrakos A, Kosma K, Makrythanasis P, Tzetis M. Prenatal Chromosomal Microarray Analysis: Does Increased Resolution Equal Increased Yield? Genes (Basel) 2023; 14:1519. [PMID: 37628571 PMCID: PMC10454647 DOI: 10.3390/genes14081519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Chromosomal microarray analysis (CMA) is considered a first-tier test for patients with developmental disabilities and congenital anomalies and is also routinely applied in prenatal diagnosis. The current consensus size cut-off for reporting copy number variants (CNVs) in the prenatal setting ranges from 200 Kb to 400 Kb, with the intention of minimizing the impact of variants of uncertain significance (VUS). Very limited data are currently available on the application of higher resolution platforms prenatally. The aim of this study is to investigate the feasibility and impact of applying high-resolution CMA in the prenatal setting. To that end, we report on the outcomes of applying CMA with a size cut-off of 20 Kb in 250 prenatal samples and discuss the findings and diagnostic yield and also provide follow-up for cases with variants of uncertain significance. Overall, 19.6% (49) showed one or more chromosomal abnormalities, with the findings classified as Pathogenic (P) or Likely Pathogenic (LP) in 15.6% and as VUS in 4%. When excluding the cases with known familial aberrations, the diagnostic yield was 12%. The smallest aberration detected was a 32 Kb duplication of the 16p11.2 region. In conclusion, this study demonstrates that prenatal diagnosis with a high-resolution aCGH platform can reliably detect smaller CNVs that are often associated with neurodevelopmental phenotypes while providing an increased diagnostic yield, regardless of the indication for testing, with only a marginal increase in the VUS incidence. Thus, it can be an important tool in the prenatal setting.
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Affiliation(s)
- Anastasios Mitrakos
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (K.K.); (P.M.)
| | | | | | - Maria Tzetis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, St. Sophia’s Children’s Hospital, 11527 Athens, Greece; (K.K.); (P.M.)
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5
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Aerden M, Denommé-Pichon AS, Bonneau D, Bruel AL, Delanne J, Gérard B, Mazel B, Philippe C, Pinson L, Prouteau C, Putoux A, Tran Mau-Them F, Viora-Dupont É, Vitobello A, Ziegler A, Piton A, Isidor B, Francannet C, Maillard PY, Julia S, Philippe A, Schaefer E, Koene S, Ruivenkamp C, Hoffer M, Legius E, Theunis M, Keren B, Buratti J, Charles P, Courtin T, Misra-Isrie M, van Haelst M, Waisfisz Q, Wieczorek D, Schmetz A, Herget T, Kortüm F, Lisfeld J, Debray FG, Bramswig NC, Atallah I, Fodstad H, Jouret G, Almoguera B, Tahsin-Swafiri S, Santos-Simarro F, Palomares-Bralo M, López-González V, Kibaek M, Tørring PM, Renieri A, Bruno LP, Õunap K, Wojcik M, Hsieh TC, Krawitz P, Van Esch H. The neurodevelopmental and facial phenotype in individuals with a TRIP12 variant. Eur J Hum Genet 2023; 31:461-468. [PMID: 36747006 PMCID: PMC10133310 DOI: 10.1038/s41431-023-01307-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/22/2022] [Accepted: 01/27/2023] [Indexed: 02/08/2023] Open
Abstract
Haploinsufficiency of TRIP12 causes a neurodevelopmental disorder characterized by intellectual disability associated with epilepsy, autism spectrum disorder and dysmorphic features, also named Clark-Baraitser syndrome. Only a limited number of cases have been reported to date. We aimed to further delineate the TRIP12-associated phenotype and objectify characteristic facial traits through GestaltMatcher image analysis based on deep-learning algorithms in order to establish a TRIP12 gestalt. 38 individuals between 3 and 66 years (F = 20, M = 18) - 1 previously published and 37 novel individuals - were recruited through an ERN ITHACA call for collaboration. 35 TRIP12 variants were identified, including frameshift (n = 15) and nonsense (n = 6) variants, as well as missense (n = 5) and splice (n = 3) variants, intragenic deletions (n = 4) and two multigene deletions disrupting TRIP12. Though variable in severity, global developmental delay was noted in all individuals, with language deficit most pronounced. About half showed autistic features and susceptibility to obesity seemed inherent to this disorder. A more severe expression was noted in individuals with a missense variant. Facial analysis showed a clear gestalt including deep-set eyes with narrow palpebral fissures and fullness of the upper eyelids, downturned corners of the mouth and large, often low-set ears with prominent earlobes. We report the largest cohort to date of individuals with TRIP12 variants, further delineating the associated phenotype and introducing a facial gestalt. These findings will improve future counseling and patient guidance.
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Affiliation(s)
- Mio Aerden
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium.
| | - Anne-Sophie Denommé-Pichon
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS 6015-INSERM 1083, Angers, France
| | - Ange-Line Bruel
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Julian Delanne
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Bénédicte Gérard
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Benoît Mazel
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Lucile Pinson
- Service de génétique - Centre de Référence Anomalies du Développement CLAD Sud Est, Groupement Hospitalier Est, Hospices Civils de Lyon, Bron, France
| | - Clément Prouteau
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS 6015-INSERM 1083, Angers, France
| | - Audrey Putoux
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs Centre Est, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Tran Mau-Them
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Éléonore Viora-Dupont
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, FHU TRANSLAD, Hôpital d'Enfants, CHU Dijon, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France
| | - Alban Ziegler
- Department of Biochemistry and Genetics, Angers University Hospital and UMR CNRS 6015-INSERM 1083, Angers, France
| | - Amélie Piton
- Hôpitaux Universitaires de Strasbourg, Laboratoire de Diagnostic Génétique, Strasbourg, France
| | - Bertrand Isidor
- Service de Genetique Medicale, CHU de Nantes & Inserm, CNRS, Universite de Nantes, l'institut du thorax, Nantes, France
| | - Christine Francannet
- Service de Genetique Medicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - Pierre-Yves Maillard
- Service de Genetique Medicale, IGMA, Hopitaux Universitaires de Strasbourg, Strasbourg, France
| | - Sophie Julia
- Service de Génétique Clinique, CHU Toulouse, Toulouse, France
| | - Anais Philippe
- Service de Genetique Medicale, IGMA, Hopitaux Universitaires de Strasbourg, Strasbourg, France
| | - Elise Schaefer
- Service de Genetique Medicale, IGMA, Hopitaux Universitaires de Strasbourg, Strasbourg, France
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Mariette Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric Legius
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Miel Theunis
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Boris Keren
- Genetic Department, Pitié-Salpêtrière Hospital, AP-HP.Sorbonne Université, Paris, France
| | - Julien Buratti
- Genetic Department, Pitié-Salpêtrière Hospital, AP-HP.Sorbonne Université, Paris, France
| | - Perrine Charles
- Genetic Department, Pitié-Salpêtrière Hospital, AP-HP.Sorbonne Université, Paris, France
| | - Thomas Courtin
- Genetic Department, Pitié-Salpêtrière Hospital, AP-HP.Sorbonne Université, Paris, France
| | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam University Medical Centers, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mieke van Haelst
- Department of Human Genetics, Amsterdam University Medical Centers, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam University Medical Centers, Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dagmar Wieczorek
- Heinrich-Heine-Universität, Institut für Humangenetik, Düsseldorf, Germany
| | - Ariane Schmetz
- Heinrich-Heine-Universität, Institut für Humangenetik, Düsseldorf, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jasmin Lisfeld
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Nuria C Bramswig
- Heinrich-Heine-Universität, Institut für Humangenetik, Düsseldorf, Germany
| | - Isis Atallah
- Lausanne University Hospital, Division of Genetic Medicine, Lausanne, Switzerland
| | - Heidi Fodstad
- Lausanne University Hospital, Division of Genetic Medicine, Lausanne, Switzerland
| | - Guillaume Jouret
- National Center of Genetics (NCG), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Berta Almoguera
- Fundación Jiménez Díaz Hospital, Department of Genetics and Genomics, Madrid, Spain
| | - Saoud Tahsin-Swafiri
- Fundación Jiménez Díaz Hospital, Department of Genetics and Genomics, Madrid, Spain
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
- Molecular Diagnostics and Clinical Genetics Unit (UDMGC), Hospital Universitari Son Espses, IdISBa, Palma, Spain
| | - Maria Palomares-Bralo
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Vanesa López-González
- Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Sección de Genética Médica, Servicio de Pediatría, Murcia, Spain
| | - Maria Kibaek
- Pediatric Department, Odense University Hospital, Odense, Denmark
| | - Pernille M Tørring
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Lucia Pia Bruno
- Medical Genetics, University of Siena, Siena, Italy
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Katrin Õunap
- Tartu University Hospital, Genetic and Personalized Medicine Clinic, Department of Clinical Genetics, Tartu, Estonia
- University of Tartu, Institute of Clinical Medicine, Tartu, Estonia
| | - Monica Wojcik
- Department of Pediatrics, Boston Children's Hospital, Divisions of Newborn Medicine and Genetics and Genomics, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium.
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6
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Amici DR, Cingoz H, Alasady MJ, Alhayek S, Phoumyvong CM, Sahni N, Yi SS, Mendillo ML. The HAPSTR2 retrogene buffers stress signaling and resilience in mammals. Nat Commun 2023; 14:152. [PMID: 36631436 PMCID: PMC9834230 DOI: 10.1038/s41467-022-35697-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
We recently identified HAPSTR1 (C16orf72) as a key component in a novel pathway which regulates the cellular response to molecular stressors, such as DNA damage, nutrient scarcity, and protein misfolding. Here, we identify a functional paralog to HAPSTR1: HAPSTR2. HAPSTR2 formed early in mammalian evolution, via genomic integration of a reverse transcribed HAPSTR1 transcript, and has since been preserved under purifying selection. HAPSTR2, expressed primarily in neural and germline tissues and a subset of cancers, retains established biochemical features of HAPSTR1 to achieve two functions. In normal physiology, HAPSTR2 directly interacts with HAPSTR1, markedly augmenting HAPSTR1 protein stability in a manner independent from HAPSTR1's canonical E3 ligase, HUWE1. Alternatively, in the context of HAPSTR1 loss, HAPSTR2 expression is sufficient to buffer stress signaling and resilience. Thus, we discover a mammalian retrogene which safeguards fitness.
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Affiliation(s)
- David R Amici
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Harun Cingoz
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Milad J Alasady
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Sammy Alhayek
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Claire M Phoumyvong
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, and Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - S Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, and Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
- Interdisciplinary Life Sciences Graduate Programs (ILSGP), and Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, 78712, USA
| | - Marc L Mendillo
- Dept. of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA.
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60610, USA.
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van der Laan L, Rooney K, Alders M, Relator R, McConkey H, Kerkhof J, Levy MA, Lauffer P, Aerden M, Theunis M, Legius E, Tedder ML, Vissers LELM, Koene S, Ruivenkamp C, Hoffer MJV, Wieczorek D, Bramswig NC, Herget T, González VL, Santos-Simarro F, Tørring PM, Denomme-Pichon AS, Isidor B, Keren B, Julia S, Schaefer E, Francannet C, Maillard PY, Misra-Isrie M, Van Esch H, Mannens MMAM, Sadikovic B, van Haelst MM, Henneman P. Episignature Mapping of TRIP12 Provides Functional Insight into Clark-Baraitser Syndrome. Int J Mol Sci 2022; 23:ijms232213664. [PMID: 36430143 PMCID: PMC9690904 DOI: 10.3390/ijms232213664] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/09/2022] Open
Abstract
Clark-Baraitser syndrome is a rare autosomal dominant intellectual disability syndrome caused by pathogenic variants in the TRIP12 (Thyroid Hormone Receptor Interactor 12) gene. TRIP12 encodes an E3 ligase in the ubiquitin pathway. The ubiquitin pathway includes activating E1, conjugating E2 and ligating E3 enzymes which regulate the breakdown and sorting of proteins. This enzymatic pathway is crucial for physiological processes. A significant proportion of TRIP12 variants are currently classified as variants of unknown significance (VUS). Episignatures have been shown to represent a powerful diagnostic tool to resolve inconclusive genetic findings for Mendelian disorders and to re-classify VUSs. Here, we show the results of DNA methylation episignature analysis in 32 individuals with pathogenic, likely pathogenic and VUS variants in TRIP12. We identified a specific and sensitive DNA methylation (DNAm) episignature associated with pathogenic TRIP12 variants, establishing its utility as a clinical biomarker for Clark-Baraitser syndrome. In addition, we performed analysis of differentially methylated regions as well as functional correlation of the TRIP12 genome-wide methylation profile with the profiles of 56 additional neurodevelopmental disorders.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Kathleen Rooney
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Michael A. Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
| | - Peter Lauffer
- Department of Pediatric Endocrinology, Emma Children’s Hospital, Amsterdam Gastroenterology, Endocrinology & Metabolism, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Mio Aerden
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Miel Theunis
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Eric Legius
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | | | - Lisenka E. L. M. Vissers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Mariette J. V. Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Nuria C. Bramswig
- Institute of Human Genetics, Medical Faculty, Heinrich-Heine-University, 40225 Düsseldorf, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Vanesa López González
- Sección Genética Médica, Servicio de Pediatría, Hospital Clínico Universitario Virgen de la Arrixaca, IMIB-Arrixaca, CIBERER, 30120 Murcia, Spain
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, 28029 Madrid, Spain
| | - Pernille M. Tørring
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | - Anne-Sophie Denomme-Pichon
- UF6254 Innovation en Diagnostic Genomique des Maladies Rares, 21070 Dijon, France
- Équipe Génétique des Anomalies du Développement (GAD), CHU Dijon-Bourgogne, 21000 Dijon, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, 44000 Nantes, France
| | - Boris Keren
- Department of Medical Genetics, Pitié-Salpêtrière Hospital, AP-HP, Sorbonne Université, 75013 Paris, France
| | - Sophie Julia
- Service de Génétique Clinique, CHU Toulouse, 31300 Toulouse, France
| | - Elise Schaefer
- Service de Génétique Clinique, CHU Toulouse, 31300 Toulouse, France
| | - Christine Francannet
- Service de Genetique Medicale, CHU de Clermont-Ferrand, 63000 Clermont-Ferrand, France
| | | | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Hilde Van Esch
- Centre for Human Genetics, University Hospitals Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Marcel M. A. M. Mannens
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON N6A 5W9, Canada
- Correspondence: (B.S.); (P.H.)
| | - Mieke M. van Haelst
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
- Correspondence: (B.S.); (P.H.)
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8
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Bustos F, Mathur S, Espejo-Serrano C, Toth R, Hastie CJ, Virdee S, Findlay GM. Activity-based probe profiling of RNF12 E3 ubiquitin ligase function in Tonne-Kalscheuer syndrome. Life Sci Alliance 2022; 5:5/11/e202101248. [PMID: 35764390 PMCID: PMC9240097 DOI: 10.26508/lsa.202101248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Ubiquitylation enzymes are involved in all aspects of eukaryotic biology and are frequently disrupted in disease. One example is the E3 ubiquitin ligase RNF12/RLIM, which is mutated in the developmental disorder Tønne-Kalscheuer syndrome (TOKAS). RNF12 TOKAS variants largely disrupt catalytic E3 ubiquitin ligase activity, which presents a pressing need to develop approaches to assess the impact of variants on RNF12 activity in patients. Here, we use photocrosslinking activity-based probes (photoABPs) to monitor RNF12 RING E3 ubiquitin ligase activity in normal and pathogenic contexts. We demonstrate that photoABPs undergo UV-induced labelling of RNF12 that is consistent with its RING E3 ligase activity. Furthermore, photoABPs robustly report the impact of RNF12 TOKAS variants on E3 activity, including variants within the RING domain and distal non-RING regulatory elements. Finally, we show that this technology can be rapidly deployed in human pluripotent stem cells. In summary, photoABPs are versatile tools that can directly identify disruptions to RING E3 ubiquitin ligase activity in human disease, thereby providing new insight into pathogenic mechanisms.
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Affiliation(s)
- Francisco Bustos
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Sunil Mathur
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Carmen Espejo-Serrano
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Rachel Toth
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - C James Hastie
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Satpal Virdee
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Greg M Findlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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9
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Kane E, Beasley S, Schafer J, Bohl J, Lee Y, Rich K, Bosia E, Spratt D. Redefining the catalytic HECT domain boundaries for the HECT E3 ubiquitin ligase family. Biosci Rep 2022; 42:BSR20221036. [PMID: 36111624 PMCID: PMC9547173 DOI: 10.1042/bsr20221036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
There are 28 unique human members of the homologous to E6AP C-terminus (HECT) E3 ubiquitin ligase family. Each member of the HECT E3 ubiquitin ligases contains a conserved bilobal HECT domain of approximately 350 residues found near their C-termini that is responsible for their respective ubiquitylation activities. Recent studies have begun to elucidate specific roles that each HECT E3 ubiquitin ligase has in various cancers, age-induced neurodegeneration, and neurological disorders. New structural models have been recently released for some of the HECT E3 ubiquitin ligases, but many HECT domain structures have yet to be examined due to chronic insolubility and/or protein folding issues. Building on these recently published structural studies coupled with our in-house experiments discussed in the present study, we suggest that the addition of ∼50 conserved residues preceding the N-terminal to the current UniProt defined boundaries of the HECT domain are required for isolating soluble, stable, and active HECT domains. We show using in silico bioinformatic analyses coupled with secondary structural prediction software that this predicted N-terminal α-helix found in all 28 human HECT E3 ubiquitin ligases forms an obligate amphipathic α-helix that binds to a hydrophobic pocket found within the HECT N-terminal lobe. The present study brings forth the proposal to redefine the residue boundaries of the HECT domain to include this N-terminal extension that will likely be critical for future biochemical, structural, and therapeutic studies on the HECT E3 ubiquitin ligase family.
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Affiliation(s)
- Emma I. Kane
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, U.S.A
| | - Steven A. Beasley
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, U.S.A
| | - Johanna M. Schafer
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, U.S.A
| | - Justine E. Bohl
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, U.S.A
| | - Young Sun Lee
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, U.S.A
| | - Kayla J. Rich
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, U.S.A
| | - Elizabeth F. Bosia
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, U.S.A
| | - Donald E. Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, MA 01610, U.S.A
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10
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Yi S, Chen F, Qin Z, Yi S, Huang L, Huang L, Feng Y, Wei H, Yang Q, Zhang Q, Luo J. Novel Synonymous and Frameshift Variants in the TRIP12 Gene Identified in 2 Chinese Patients With Intellectual Disability. NEUROLOGY GENETICS 2022; 8:e200025. [PMID: 36275919 PMCID: PMC9585485 DOI: 10.1212/nxg.0000000000200025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/20/2022] [Indexed: 11/15/2022]
Abstract
Background and Objectives Clark-Baraitser syndrome is characterized by intellectual disability with or without autism spectrum disorders, speech delay, motor delay, behavioral abnormalities, and facial dysmorphism. It is caused by a heterozygous pathogenic variant in the thyroid hormone receptor interactor 12 (TRIP12) gene. However, loss of function and haploinsufficiency are the pathogenic mechanisms behind the TRIP12-related disorder. Methods We conducted an exome sequencing analysis for 2 unrelated patients with moderate intellectual disability, speech delay, and motor delay. Results We identified 2 de novo TRIP12 mutations in these 2 patients. One patient had a frameshift duplication, whereas the other had a synonymous variant. Both patients presented with common features of the syndrome, but clinical heterogeneity has been also observed between them. For the synonymous variant, reverse transcription PCR in RNA extracted from leukocytes demonstrated the presence of a truncated messenger RNA (mRNA) transcript that skipped exon 12. This transcript escapes degradation at the mRNA level. To assess the effect of the synonymous substitute on TRIP12 proteolytic activity, the expression of 9 known responsive genes at the mRNA level was measured, of which 3 genes were upregulated at least 2-fold in the patient. Discussion We reported 2 patients with Clark-Baraitser syndrome caused by novel synonymous and frameshift variants in the TRIP12 gene, and our study expands the mutation spectrum of the TRIP12 gene. This study will help to improve our understanding of variable phenotypic presentations in TRIP12-related disorders.
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11
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Lindstrand A, Ek M, Kvarnung M, Anderlid BM, Björck E, Carlsten J, Eisfeldt J, Grigelioniene G, Gustavsson P, Hammarsjö A, Helgadóttir HT, Hellström-Pigg M, Kuchinskaya E, Lagerstedt-Robinson K, Levin LÅ, Lieden A, Lindelöf H, Malmgren H, Nilsson D, Svensson E, Paucar M, Sahlin E, Tesi B, Tham E, Winberg J, Winerdal M, Wincent J, Johansson Soller M, Pettersson M, Nordgren A. Genome sequencing is a sensitive first-line test to diagnose individuals with intellectual disability. Genet Med 2022; 24:2296-2307. [PMID: 36066546 DOI: 10.1016/j.gim.2022.07.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 10/14/2022] Open
Abstract
PURPOSE Individuals with intellectual disability (ID) and/or neurodevelopment disorders (NDDs) are currently investigated with several different approaches in clinical genetic diagnostics. METHODS We compared the results from 3 diagnostic pipelines in patients with ID/NDD: genome sequencing (GS) first (N = 100), GS as a secondary test (N = 129), or chromosomal microarray (CMA) with or without FMR1 analysis (N = 421). RESULTS The diagnostic yield was 35% (GS-first), 26% (GS as a secondary test), and 11% (CMA/FMR1). Notably, the age of diagnosis was delayed by 1 year when GS was performed as a secondary test and the cost per diagnosed individual was 36% lower with GS first than with CMA/FMR1. Furthermore, 91% of those with a negative result after CMA/FMR1 analysis (338 individuals) have not yet been referred for additional genetic testing and remain undiagnosed. CONCLUSION Our findings strongly suggest that genome analysis outperforms other testing strategies and should replace traditional CMA and FMR1 analysis as a first-line genetic test in individuals with ID/NDD. GS is a sensitive, time- and cost-effective method that results in a confirmed molecular diagnosis in 35% of all referred patients.
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Affiliation(s)
- Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
| | - Marlene Ek
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Björck
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jonas Carlsten
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Sweden
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hafdís T Helgadóttir
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maritta Hellström-Pigg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ekaterina Kuchinskaya
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Lars-Åke Levin
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Agne Lieden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Hillevi Lindelöf
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Solna, Sweden
| | - Eva Svensson
- Department of Pediatric Neurology, Karolinska University Hospital, Huddinge, Sweden
| | - Martin Paucar
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Johanna Winberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Max Winerdal
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Johansson Soller
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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12
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Complex Diagnostics of Non-Specific Intellectual Developmental Disorder. Int J Mol Sci 2022; 23:ijms23147764. [PMID: 35887114 PMCID: PMC9323143 DOI: 10.3390/ijms23147764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Intellectual development disorder (IDD) is characterized by a general deficit in intellectual and adaptive functioning. In recent years, there has been a growing interest in studying the genetic structure of IDD. Of particular difficulty are patients with non-specific IDD, for whom it is impossible to establish a clinical diagnosis without complex genetic diagnostics. We examined 198 patients with non-specific IDD from 171 families using whole-exome sequencing and chromosome microarray analysis. Hereditary forms of IDD account for at least 35.7% of non-specific IDD, of which 26.9% are monogenic forms. Variants in the genes associated with the BAF (SWI/SNF) complex were the most frequently identified. We were unable to identify phenotypic features that would allow differential diagnosis of monogenic and microstructural chromosomal rearrangements in non-specific IDD at the stage of clinical examination, but due to its higher efficiency, exome sequencing should be the diagnostic method of the highest priority study after the standard examination of patients with NIDD in Russia.
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13
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Liu Y, Lv Y, Zarrei M, Dong R, Yang X, Higginbotham EJ, Li Y, Zhao D, Song F, Yang Y, Zhang H, Wang Y, Scherer SW, Gai Z. Chromosomal microarray analysis of 410 Han Chinese patients with autism spectrum disorder or unexplained intellectual disability and developmental delay. NPJ Genom Med 2022; 7:1. [PMID: 35022430 PMCID: PMC8755789 DOI: 10.1038/s41525-021-00271-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
Copy number variants (CNVs) are recognized as a crucial genetic cause of neurodevelopmental disorders (NDDs). Chromosomal microarray analysis (CMA), the first-tier diagnostic test for individuals with NDDs, has been utilized to detect CNVs in clinical practice, but most reports are still from populations of European ancestry. To contribute more worldwide clinical genomics data, we investigated the genetic etiology of 410 Han Chinese patients with NDDs (151 with autism and 259 with unexplained intellectual disability (ID) and developmental delay (DD)) using CMA (Affymetrix) after G-banding karyotyping. Among all the NDD patients, 109 (26.6%) carried clinically relevant CNVs or uniparental disomies (UPDs), and 8 (2.0%) had aneuploidies (6 with trisomy 21 syndrome, 1 with 47,XXY, 1 with 47,XYY). In total, we found 129 clinically relevant CNVs and UPDs, including 32 CNVs in 30 ASD patients, and 92 CNVs and 5 UPDs in 79 ID/DD cases. When excluding the eight patients with aneuploidies, the diagnostic yield of pathogenic and likely pathogenic CNVs and UPDs was 20.9% for all NDDs (84/402), 3.3% in ASD (5/151), and 31.5% in ID/DD (79/251). When aneuploidies were included, the diagnostic yield increased to 22.4% for all NDDs (92/410), and 33.6% for ID/DD (87/259). We identified a de novo CNV in 14.9% (60/402) of subjects with NDDs. Interestingly, a higher diagnostic yield was observed in females (31.3%, 40/128) compared to males (16.1%, 44/274) for all NDDs (P = 4.8 × 10-4), suggesting that a female protective mechanism exists for deleterious CNVs and UPDs.
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Affiliation(s)
- Yi Liu
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Yuqiang Lv
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Rui Dong
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Edward J Higginbotham
- The Centre for Applied Genomics and Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Yue Li
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Dongmei Zhao
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Fengling Song
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Yali Yang
- Rehabilitation Center, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Haiyan Zhang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Ying Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China
| | - Stephen W Scherer
- The Centre for Applied Genomics and Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada. .,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A1, Canada.
| | - Zhongtao Gai
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, 250022, China.
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14
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Kehinde TA, Bhatia A, Olarewaju B, Shoaib MZ, Mousa J, Osundiji MA. Syndromic obesity with neurodevelopmental delay: Opportunities for targeted interventions. Eur J Med Genet 2022; 65:104443. [DOI: 10.1016/j.ejmg.2022.104443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/09/2022] [Accepted: 01/22/2022] [Indexed: 01/01/2023]
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15
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Özaslan A, Kayhan G, İşeri E, Ergün MA, Güney E, Perçin FE. Identification of copy number variants in children and adolescents with autism spectrum disorder: a study from Turkey. Mol Biol Rep 2021; 48:7371-7378. [PMID: 34637094 DOI: 10.1007/s11033-021-06745-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Copy number variants (CNVs) play a key role in the etiology of autism spectrum disorder (ASD). Therefore, recent guidelines recommend chromosomal microarrays (CMAs) as first-tier genetic tests. This study's first aim was to determine the clinical usefulness of CMAs in children diagnosed with ASD in a Turkish population. The second aim was to describe the CNVs and clinical phenotypes of children with ASD. METHODS AND RESULTS This was a single-center retrospective cross-sectional study. Data were obtained from the medical records of children with ASD followed at Gazi University Hospital, (Ankara, Turkey). The sample consisted of 47 ASD cases (mean age: 60.34 ± 25.60 months; 82.9% boys). The diagnostic yield of the CMAs was 8.5%. Four pathogenic CNVs were identified: 9p24.3p24.2 deletion, 15q11-q13 duplication, 16p11.2 deletion, and 22q13.3 deletion. Also, four variants were found at 2q36.3, 10p11.21, 15q11.2, and Xp11.22, which were classified as variants of uncertain significance (VUS). CONCLUSIONS The TRAP12 and PARD3 genes in CNVs classified as VUS may be worth investigating for autism. The initial identification of both clinical and biological markers can facilitate monitoring, early intervention, or prevention and advance our understanding of the neurobiology underlying ASD.
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Affiliation(s)
- Ahmet Özaslan
- Child and Adolescent Psychiatry Department, Gazi University Medical Faculty, Emniyet Mahallesi, Bandırma Caddesi No. 6/1, Yenimahalle, Ankara, Turkey.
| | - Gülsüm Kayhan
- Medical Genetics Department, Gazi University Medical Faculty, Ankara, Turkey
| | - Elvan İşeri
- Child and Adolescent Psychiatry Department, Gazi University Medical Faculty, Emniyet Mahallesi, Bandırma Caddesi No. 6/1, Yenimahalle, Ankara, Turkey
| | - Mehmet Ali Ergün
- Medical Genetics Department, Gazi University Medical Faculty, Ankara, Turkey
| | - Esra Güney
- Child and Adolescent Psychiatry Department, Gazi University Medical Faculty, Emniyet Mahallesi, Bandırma Caddesi No. 6/1, Yenimahalle, Ankara, Turkey
| | - Ferda Emriye Perçin
- Medical Genetics Department, Gazi University Medical Faculty, Ankara, Turkey
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16
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Seo BA, Kim D, Hwang H, Kim MS, Ma SX, Kwon SH, Kweon SH, Wang H, Yoo JM, Choi S, Kwon SH, Kang SU, Kam TI, Kim K, Karuppagounder SS, Kang BG, Lee S, Park H, Kim S, Yan W, Li YS, Kuo SH, Redding-Ochoa J, Pletnikova O, Troncoso JC, Lee G, Mao X, Dawson VL, Dawson TM, Ko HS. TRIP12 ubiquitination of glucocerebrosidase contributes to neurodegeneration in Parkinson's disease. Neuron 2021; 109:3758-3774.e11. [PMID: 34644545 DOI: 10.1016/j.neuron.2021.09.031] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 06/09/2021] [Accepted: 09/14/2021] [Indexed: 11/25/2022]
Abstract
Impairment in glucocerebrosidase (GCase) is strongly associated with the development of Parkinson's disease (PD), yet the regulators responsible for its impairment remain elusive. In this paper, we identify the E3 ligase Thyroid Hormone Receptor Interacting Protein 12 (TRIP12) as a key regulator of GCase. TRIP12 interacts with and ubiquitinates GCase at lysine 293 to control its degradation via ubiquitin proteasomal degradation. Ubiquitinated GCase by TRIP12 leads to its functional impairment through premature degradation and subsequent accumulation of α-synuclein. TRIP12 overexpression causes mitochondrial dysfunction, which is ameliorated by GCase overexpression. Further, conditional TRIP12 knockout in vitro and knockdown in vivo promotes the expression of GCase, which blocks α-synuclein preformed fibrils (α-syn PFFs)-provoked dopaminergic neurodegeneration. Moreover, TRIP12 accumulates in human PD brain and α-synuclein-based mouse models. The identification of TRIP12 as a regulator of GCase provides a new perspective on the molecular mechanisms underlying dysfunctional GCase-driven neurodegeneration in PD.
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Affiliation(s)
- Bo Am Seo
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Donghoon Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pharmacology, Peripheral Neuropathy Research Center (PNRC), Dong-A University College of Medicine, Busan, Republic of Korea.
| | - Heehong Hwang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Min Seong Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shi-Xun Ma
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Seung-Hwan Kwon
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sin Ho Kweon
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hu Wang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Je Min Yoo
- Department of Chemistry, Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD, USA; Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea
| | - Seulah Choi
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sang Ho Kwon
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sung-Ung Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Tae-In Kam
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
| | - Kwangsoo Kim
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Senthilkumar S Karuppagounder
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bong Gu Kang
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Saebom Lee
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Hyejin Park
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA
| | - Sangjune Kim
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Biology, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Wei Yan
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yong-Shi Li
- Department of Neurology, Columbia University, New York, NY, USA
| | - Sheng-Han Kuo
- Department of Neurology, Columbia University, New York, NY, USA
| | - Javier Redding-Ochoa
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Juan C Troncoso
- Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gabsang Lee
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xiaobo Mao
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Physiology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA.
| | - Han Seok Ko
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Department of Neurology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA; Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA; Diana Helis Henry Medical Research Foundation, New Orleans, LA, USA.
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17
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Genetic risk factors for autism-spectrum disorders: a systematic review based on systematic reviews and meta-analysis. J Neural Transm (Vienna) 2021; 128:717-734. [PMID: 34115189 DOI: 10.1007/s00702-021-02360-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/28/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Based on recent evidence, more than 200 susceptibility genes have been identified to be associated with autism until now. Correspondingly, cytogenetic abnormalities have been reported for almost every chromosome. While the results of multiple genes associated with risk factors for autism are still incomplete, this paper systematically reviews published meta-analyses and systematic reviews of evidence related to autism occurrence. METHOD Literature search was conducted in the PubMed system, and the publication dates were limited between January 2000 and July 2020. We included a meta-analysis and systematic review that assessed the impact of related gene variants on the development of autism. After screening, this comprehensive literature search identified 31 meta-analyses and ten systematic reviews. We arranged the genes related to autism in the published studies according to the order of the chromosomes, and based on the results of a meta-analysis and systematic review, we selected 6 candidate genes related to ASD, namely MTHFR C677T, SLC25A12, OXTR, RELN, 5-HTTLPR, SHANK, including basic features and functions. In addition to these typical genes, we have also listed candidate genes that may exist on almost every chromosome that are related to autism. RESULTS We found that the results of several literature reviews included in this study showed that the MTHFR C667T variant was a risk factor for the occurrence of ASD, and the results were consistent. The results of studies on SLC25A12 variation (rs2056202 and rs2292813) and ASD risk were inconsistent but statistically significant. No association of 5-HTTLPR was found with autism, but when subgroup analysis was performed according to ethnicity, the association was statistically significant. RELN variants (rs362691 and rs736707) were consistent with ASD risk studies, but some of the results were not statistically significant. CONCLUSION This review summarized the well-known ASD candidate genes and listed some new genes that need further study in larger sample sets to improve our understanding of the genetic basis of ASD, but sample size and heterogeneity remain major limiting factors in some genome-wide association studies. We also found that common genetic variants in some genes may be co-risk factors for autism or other neuropsychiatric disorders when we collated these results. It is worth considering screening for these mutations in clinical applications.
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18
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Li Z, Zhang P, Feng F, Zhang Q. Screening and Interaction Analysis of Key Genes in miR-542-3p Over- Expressed Osteosarcoma Cells by Bioinformatics. Comb Chem High Throughput Screen 2021; 23:411-418. [PMID: 32233998 DOI: 10.2174/1386207323666200401103353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/19/2020] [Accepted: 03/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Osteosarcoma is one of the most serious primary malignant bone tumors that threaten the lives of children and adolescents. However, the mechanism underlying and how to prevent or treat the disease have not been well understood. AIMS AND OBJECTIVE This aim of the present study was to identify the key genes and explore novel insights into the molecular mechanism of miR-542-3p over-expressed Osteosarcoma. MATERIALS AND METHODS Gene expression profile data GDS5367 was downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were screened using GEO2R, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the DAVID database. And protein-protein interaction (PPI) network was constructed by the STRING database. In addition, the most highly connected module was screened by plugin MCODE and hub genes by plugin CytoHubba. Furthermore, UALCAN and The Cancer Genome Atlas were performed for survival analysis. RESULT In total, 1421 DEGs were identified, including 598 genes were up-regulated and 823 genes were down-regulated. GO analysis showed that DEGs were classified into three groups and DEGs mainly enriched in Steroid biosynthesis, Ubiquitin mediated proteolysis and p53 signaling pathway. Six hub genes (UBA52, RNF114, UBE2H, TRIP12, HNRNPC, and PTBP1) may be key genes with the progression of osteosarcoma. CONCLUSION The results could better understand the mechanism of osteosarcoma, which may facilitate a novel insight into treatment targets.
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Affiliation(s)
- Zhongqiu Li
- Department of Toxicology, College of Public Health, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan Province 450001, China
| | - Peng Zhang
- Department of Bone and Soft Tissue Cancer, The Affiliated Cancer Hospital of Zhengzhou University (Henan Cancer Hospital), Zhengzhou, Henan Province 450008, China
| | - Feifei Feng
- Department of Toxicology, College of Public Health, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan Province 450001, China
| | - Qiao Zhang
- Department of Toxicology, College of Public Health, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan Province 450001, China
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19
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Lee KK, Rajagopalan D, Bhatia SS, Tirado-Magallanes R, Chng WJ, Jha S. The oncogenic E3 ligase TRIP12 suppresses epithelial-mesenchymal transition (EMT) and mesenchymal traits through ZEB1/2. Cell Death Discov 2021; 7:95. [PMID: 33963176 PMCID: PMC8105346 DOI: 10.1038/s41420-021-00479-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/20/2021] [Accepted: 03/24/2021] [Indexed: 01/02/2023] Open
Abstract
Thyroid hormone receptor interactor 12 (TRIP12) is an E3 ligase most notably involved in the proteolytic degradation of the tumor suppressor p14ARF. Through this process, it is proposed that TRIP12 plays an oncogenic role in tumor initiation and growth. However, its role in other cancer processes is unknown. In this study, using publicly available cancer patient datasets, we found TRIP12 to be associated with distant metastasis-free survival in breast cancer, suggesting an inhibitory role in metastasis. Following TRIP12 depletion, an epithelial-mesenchymal transition (EMT) shift occurred with concomitant changes in EMT cell adhesion markers identified through RNA-seq. In line with EMT changes, TRIP12-depleted cells gained mesenchymal traits such as loss of cell polarity, dislodgement from bulk cells at a higher frequency, and increased cellular motility. Furthermore, ectopic TRIP12 expression sensitized cells to anoikis. Mechanistically, TRIP12 suppresses EMT through inhibiting ZEB1/2 gene expression, and ZEB1/2 depletion rescues EMT markers and mesenchymal behavior. Overall, our study delineates TRIP12's role in inhibition of EMT and implies a potential suppressive role in breast cancer metastasis.
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Affiliation(s)
- Kwok Kin Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.
| | - Deepa Rajagopalan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shreshtha Sailesh Bhatia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Roberto Tirado-Magallanes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117596, Singapore.,Department of Haematology-Oncology, National University Cancer Institute of Singapore, National University Health System, Singapore, Singapore
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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20
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Donaldson B, Villagomez DAF, King WA. Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective. Animals (Basel) 2021; 11:1257. [PMID: 33925534 PMCID: PMC8146943 DOI: 10.3390/ani11051257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to produce high-quality karyotypes and reveal large-scale chromosome ectopic exchanges. Further refinements to clinical cytogenetics practices have led to the implementation of molecular cytogenetics techniques such as fluorescent in-situ hybridization (FISH), allowing for rearrangements to be visualized and breakpoints refined using fluorescently labelled painting probes. The next-generation of clinical cytogenetics include the implementation of DNA microarrays, and next-generation sequencing (NGS) technologies such as DNA sequencing to better explore tentative genome architecture changes. The implementation of these cytogenomics techniques allow the genomes of rearrangement carriers to be deciphered at the highest resolution, allowing rearrangements to be detected; breakpoints to be delineated; and, most importantly, potential gene implications of those chromosome rearrangements to be interrogated. Clinical cytogenetics has become an integral tool in the livestock industry, identifying rearrangements and allowing breeders to make informed breeding decisions.
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Affiliation(s)
- Brendan Donaldson
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | | | - W. Allan King
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Karyotekk Inc., Box 363 OVC, University of Guelph, Guelph, ON N1G 2W1, Canada
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21
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Stranneheim H, Lagerstedt-Robinson K, Magnusson M, Kvarnung M, Nilsson D, Lesko N, Engvall M, Anderlid BM, Arnell H, Johansson CB, Barbaro M, Björck E, Bruhn H, Eisfeldt J, Freyer C, Grigelioniene G, Gustavsson P, Hammarsjö A, Hellström-Pigg M, Iwarsson E, Jemt A, Laaksonen M, Enoksson SL, Malmgren H, Naess K, Nordenskjöld M, Oscarson M, Pettersson M, Rasi C, Rosenbaum A, Sahlin E, Sardh E, Stödberg T, Tesi B, Tham E, Thonberg H, Töhönen V, von Döbeln U, Vassiliou D, Vonlanthen S, Wikström AC, Wincent J, Winqvist O, Wredenberg A, Ygberg S, Zetterström RH, Marits P, Soller MJ, Nordgren A, Wirta V, Lindstrand A, Wedell A. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med 2021; 13:40. [PMID: 33726816 PMCID: PMC7968334 DOI: 10.1186/s13073-021-00855-5] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/11/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND We report the findings from 4437 individuals (3219 patients and 1218 relatives) who have been analyzed by whole genome sequencing (WGS) at the Genomic Medicine Center Karolinska-Rare Diseases (GMCK-RD) since mid-2015. GMCK-RD represents a long-term collaborative initiative between Karolinska University Hospital and Science for Life Laboratory to establish advanced, genomics-based diagnostics in the Stockholm healthcare setting. METHODS Our analysis covers detection and interpretation of SNVs, INDELs, uniparental disomy, CNVs, balanced structural variants, and short tandem repeat expansions. Visualization of results for clinical interpretation is carried out in Scout-a custom-developed decision support system. Results from both singleton (84%) and trio/family (16%) analyses are reported. Variant interpretation is done by 15 expert teams at the hospital involving staff from three clinics. For patients with complex phenotypes, data is shared between the teams. RESULTS Overall, 40% of the patients received a molecular diagnosis ranging from 19 to 54% for specific disease groups. There was heterogeneity regarding causative genes (n = 754) with some of the most common ones being COL2A1 (n = 12; skeletal dysplasia), SCN1A (n = 8; epilepsy), and TNFRSF13B (n = 4; inborn errors of immunity). Some causative variants were recurrent, including previously known founder mutations, some novel mutations, and recurrent de novo mutations. Overall, GMCK-RD has resulted in a large number of patients receiving specific molecular diagnoses. Furthermore, negative cases have been included in research studies that have resulted in the discovery of 17 published, novel disease-causing genes. To facilitate the discovery of new disease genes, GMCK-RD has joined international data sharing initiatives, including ClinVar, UDNI, Beacon, and MatchMaker Exchange. CONCLUSIONS Clinical WGS at GMCK-RD has provided molecular diagnoses to over 1200 individuals with a broad range of rare diseases. Consolidation and spread of this clinical-academic partnership will enable large-scale national collaboration.
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Affiliation(s)
- Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Måns Magnusson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Malin Kvarnung
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Nicole Lesko
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Martin Engvall
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Henrik Arnell
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | | | - Michela Barbaro
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Björck
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Helene Bruhn
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Christoph Freyer
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Giedre Grigelioniene
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Hammarsjö
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Maritta Hellström-Pigg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Erik Iwarsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anders Jemt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Laaksonen
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Sara Lind Enoksson
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Helena Malmgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Naess
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Mikael Oscarson
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Chiara Rasi
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Adam Rosenbaum
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Eliane Sardh
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Tommy Stödberg
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Håkan Thonberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Virpi Töhönen
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ulrika von Döbeln
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Daphne Vassiliou
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Sofie Vonlanthen
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Ann-Charlotte Wikström
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Josephine Wincent
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ola Winqvist
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wredenberg
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sofia Ygberg
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Rolf H Zetterström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Per Marits
- Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Johansson Soller
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institutet of Technology, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden.
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
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22
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Singh S, Ng J, Sivaraman J. Exploring the "Other" subfamily of HECT E3-ligases for therapeutic intervention. Pharmacol Ther 2021; 224:107809. [PMID: 33607149 DOI: 10.1016/j.pharmthera.2021.107809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/13/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022]
Abstract
The HECT E3 ligase family regulates key cellular signaling pathways, with its 28 members divided into three subfamilies: NEDD4 subfamily (9 members), HERC subfamily (6 members) and "Other" subfamily (13 members). Here, we focus on the less-explored "Other" subfamily and discuss the recent findings pertaining to their biological roles. The N-terminal regions preceding the conserved HECT domains are significantly diverse in length and sequence composition, and are mostly unstructured, except for short regions that incorporate known substrate-binding domains. In some of the better-characterized "Other" members (e.g., HUWE1, AREL1 and UBE3C), structure analysis shows that the extended region (~ aa 50) adjacent to the HECT domain affects the stability and activity of the protein. The enzymatic activity is also influenced by interactions with different adaptor proteins and inter/intramolecular interactions. Primarily, the "Other" subfamily members assemble atypical ubiquitin linkages, with some cooperating with E3 ligases from the other subfamilies to form branched ubiquitin chains on substrates. Viruses and pathogenic bacteria target and hijack the activities of "Other" subfamily members to evade host immune responses and cause diseases. As such, these HECT E3 ligases have emerged as potential candidates for therapeutic drug development.
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Affiliation(s)
- Sunil Singh
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore
| | - Joel Ng
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore
| | - J Sivaraman
- Department of Biological Sciences, 14 Science Drive 4, National University of Singapore, 117543, Singapore.
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23
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Brunet M, Vargas C, Larrieu D, Torrisani J, Dufresne M. E3 Ubiquitin Ligase TRIP12: Regulation, Structure, and Physiopathological Functions. Int J Mol Sci 2020; 21:ijms21228515. [PMID: 33198194 PMCID: PMC7697007 DOI: 10.3390/ijms21228515] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
The Thyroid hormone Receptor Interacting Protein 12 (TRIP12) protein belongs to the 28-member Homologous to the E6-AP C-Terminus (HECT) E3 ubiquitin ligase family. First described as an interactor of the thyroid hormone receptor, TRIP12’s biological importance was revealed by the embryonic lethality of a murine model bearing an inactivating mutation in the TRIP12 gene. Further studies showed the participation of TRIP12 in the regulation of major biological processes such as cell cycle progression, DNA damage repair, chromatin remodeling, and cell differentiation by an ubiquitination-mediated degradation of key protein substrates. Moreover, alterations of TRIP12 expression have been reported in cancers that can serve as predictive markers of therapeutic response. The TRIP12 gene is also referenced as a causative gene associated to intellectual disorders such as Clark–Baraitser syndrome and is clearly implicated in Autism Spectrum Disorder. The aim of the review is to provide an exhaustive and integrated overview of the different aspects of TRIP12 ranging from its regulation, molecular functions and physio-pathological implications.
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Affiliation(s)
- Manon Brunet
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Claire Vargas
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Dorian Larrieu
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
| | - Jérôme Torrisani
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
| | - Marlène Dufresne
- Institut National de la Santé et de la Recherche Médicale, INSERM Unit 1037, Centre de Recherches en Cancérologie de Toulouse, CEDEX 1, 31 037 Toulouse, France; (M.B.); (C.V.); (D.L.)
- Université Toulouse III-Paul Sabatier, CEDEX 9, 31 062 Toulouse, France
- Correspondence: (J.T.); (M.D.); Tel.: +33-582-741-644 (J.T.); +33-582-741-643 (M.D.)
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24
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De novo 2q36.3q37.1 deletion encompassing TRIP12 and NPPC yields distinct phenotypes. Hum Genome Var 2020; 7:19. [PMID: 32528716 PMCID: PMC7261772 DOI: 10.1038/s41439-020-0107-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/01/2020] [Indexed: 12/03/2022] Open
Abstract
We report a patient with developmental delay, extremely short stature, small hands, dysmorphic facial features, hearing loss, and epilepsy carrying a de novo 2.76-Mb deletion of 2q36.3q37.1, including TRIP12 and NPPC. TRIP12 haploinsufficiency causes developmental delay with isolated dysmorphic facial features, whereas NPPC haploinsufficiency causes short stature and small hands. This is the first report of a unique phenotype, which is secondary to a microdeletion encompassing TRIP12 and NPPC.
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25
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Miller CR, Lee K, Pfau RB, Reshmi SC, Corsmeier DJ, Hashimoto S, Dave-Wala A, Jayaraman V, Koboldt D, Matthews T, Mouhlas D, Stein M, McKinney A, Grossman T, Kelly BJ, White P, Magrini V, Wilson RK, Mardis ER, Cottrell CE. Disease-associated mosaic variation in clinical exome sequencing: a two-year pediatric tertiary care experience. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a005231. [PMID: 32371413 PMCID: PMC7304353 DOI: 10.1101/mcs.a005231] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Exome sequencing (ES) has become an important tool in pediatric genomic medicine, improving identification of disease-associated variation due to assay breadth. Depth is also afforded by ES, enabling detection of lower-frequency mosaic variation compared to Sanger sequencing in the studied tissue, thus enhancing diagnostic yield. Within a pediatric tertiary-care hospital, we report two years of clinical ES data from probands evaluated for genetic disease to assess diagnostic yield, characteristics of causal variants, and prevalence of mosaicism among disease-causing variants. Exome-derived, phenotype-driven variant data from 357 probands was analyzed concurrent with parental ES data, when available. Blood was the source of nucleic acid. Sequence read alignments were manually reviewed for all assessed variants. Sanger sequencing was used for suspected de novo or mosaic variation. Clinical provider notes were reviewed to determine concordance between laboratory-reported data and the ordering provider's interpretation of variant-associated disease causality. Laboratory-derived diagnostic yield and provider-substantiated diagnoses had 91.4% concordance. The cohort returned 117 provider-substantiated diagnoses among 115 probands for a diagnostic yield of 32.2%. De novo variants represented 64.9% of disease-associated variation within trio analyses. Among the 115 probands, five harbored disease-associated somatic mosaic variation. Two additional probands were observed to inherit a disease-associated variant from an unaffected mosaic parent. Among inheritance patterns, de novo variation was the most frequent disease etiology. Somatic mosaicism is increasingly recognized as a significant contributor to genetic disease, particularly with increased sequence depth attainable from ES. This report highlights the potential and importance of detecting mosaicism in ES.
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Affiliation(s)
- Cecelia R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology
| | - Ruthann B Pfau
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Shalini C Reshmi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Donald J Corsmeier
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Sayaka Hashimoto
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Ashita Dave-Wala
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Vijayakumar Jayaraman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Daniel Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Theodora Matthews
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Danielle Mouhlas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Maggie Stein
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Aimee McKinney
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Tom Grossman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA.,Department of Pathology.,Department of Pediatrics, The Ohio State University, Columbus, Ohio 43210, USA
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26
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Donoghue T, Garrity L, Ziolkowski A, McPhillips M, Buckman M, Goel H. Novel de novo TRIP12 mutation reveals variable phenotypic presentation while emphasizing core features of TRIP12 variations. Am J Med Genet A 2020; 182:1801-1806. [PMID: 32424948 DOI: 10.1002/ajmg.a.61618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 04/09/2020] [Accepted: 04/20/2020] [Indexed: 11/10/2022]
Abstract
Intellectual disability (ID) is a complicated and multifactorial condition often with an unclear cause. Advancements in diagnostic techniques have identified genetic causes in a significant proportion. Pathogenic variants in TRIP12, encoding for an E3 ligand in the ubiquitin-protease pathway, have previously been identified as a cause of ID with autistic behavior and dysmorphic features. We report two unrelated patients with de novo mutations in TRIP12 and diagnoses of global developmental delay, autism spectrum disorder and dysmorphic features, as well as a range of other characteristics. Exome sequencing was utilized as part of an extensive genetic workup for both individuals. The genotypic and phenotypic data for both patients has been collated with previously reported data. Epilepsy was noted in about 20% published cases. One of our patents had epilepsy. These cases highlight the variable phenotypic presentations of TRIP12 variations while emphasizing the core features of ID and speech delay, with or without autistic features and epilepsy.
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Affiliation(s)
- Tess Donoghue
- University of Newcastle, Callaghan, New South Wales, Australia
| | - Lauren Garrity
- University of Newcastle, Callaghan, New South Wales, Australia
| | - Andrew Ziolkowski
- Department of Molecular Medicine, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Mary McPhillips
- Department of Molecular Medicine, John Hunter Hospital, New Lambton Heights, New South Wales, Australia
| | - Melissa Buckman
- Tamworth Community Health Centre, Tamworth, New South Wales, Australia
| | - Himanshu Goel
- University of Newcastle, Callaghan, New South Wales, Australia.,Hunter Genetics, Waratah, New South Wales, Australia
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27
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Dong X, Liu B, Yang L, Wang H, Wu B, Liu R, Chen H, Chen X, Yu S, Chen B, Wang S, Xu X, Zhou W, Lu Y. Clinical exome sequencing as the first-tier test for diagnosing developmental disorders covering both CNV and SNV: a Chinese cohort. J Med Genet 2020; 57:558-566. [PMID: 32005694 PMCID: PMC7418612 DOI: 10.1136/jmedgenet-2019-106377] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 01/08/2020] [Accepted: 01/11/2020] [Indexed: 12/12/2022]
Abstract
Background Developmental disorders (DDs) are early onset disorders affecting 5%–10% of children worldwide. Chromosomal microarray analysis detecting CNVs is currently recommended as the first-tier test for DD diagnosis. However, this analysis omits a high percentage of disease-causing single nucleotide variations (SNVs) that warrant further sequencing. Currently, next-generation sequencing can be used in clinical scenarios detecting CNVs, and the use of exome sequencing in the DD cohort ahead of the microarray test has not been evaluated. Methods Clinical exome sequencing (CES) was performed on 1090 unrelated Chinese DD patients who were classified into five phenotype subgroups. CNVs and SNVs were both detected and analysed based on sequencing data. Results An overall diagnostic rate of 41.38% was achieved with the combinational analysis of CNV and SNV. Over 12.02% of patients were diagnosed based on CNV, which was comparable with the published CMA diagnostic rate, while 0.74% were traditionally elusive cases who had dual diagnosis or apparently homozygous mutations that were clarified. The diagnostic rates among subgroups ranged from 21.82% to 50.32%. The top three recurrent cytobands with diagnostic CNVs were 15q11.2-q13.1, 22q11.21 and 7q11.23. The top three genes with diagnostic SNVs were: MECP2, SCN1A and SCN2A. Both the diagnostic rate and spectrums of CNVs and SNVs showed differences among the phenotype subgroups. Conclusion With a higher diagnostic rate, more comprehensive observation of variations and lower cost compared with conventional strategies, simultaneous analysis of CNVs and SNVs based on CES showed potential as a new first-tier choice to diagnose DD.
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Affiliation(s)
- Xinran Dong
- Center for Molecular Medicine of Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Bo Liu
- Center for Molecular Medicine of Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Lin Yang
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China.,Clinical Genetic Center, Children's Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Hongbo Chen
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Xiang Chen
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Sha Yu
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Bin Chen
- Shanghai Key Laboratory of Birth Defects, Pediatrics Research Institute, Children's Hospital of Fudan University, Shanghai, China
| | - Sujuan Wang
- Department of Rehabilitation, Children's Hospital of Fudan University, Shanghai, China
| | - Xiu Xu
- Division of Child Health Care, Children's Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine of Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine of Children's Hospital of Fudan University, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
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28
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Larrieu D, Brunet M, Vargas C, Hanoun N, Ligat L, Dagnon L, Lulka H, Pommier RM, Selves J, Jády BE, Bartholin L, Cordelier P, Dufresne M, Torrisani J. The E3 ubiquitin ligase TRIP12 participates in cell cycle progression and chromosome stability. Sci Rep 2020; 10:789. [PMID: 31964993 PMCID: PMC6972862 DOI: 10.1038/s41598-020-57762-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/03/2020] [Indexed: 12/29/2022] Open
Abstract
Several studies have linked the E3 ubiquitin ligase TRIP12 (Thyroid hormone Receptor Interacting Protein 12) to the cell cycle. However, the regulation and the implication of this protein during the cell cycle are largely unknown. In this study, we show that TRIP12 expression is regulated during the cell cycle, which correlates with its nuclear localization. We identify an euchromatin-binding function of TRIP12 mediated by a N-terminal intrinsically disordered region. We demonstrate the functional implication of TRIP12 in the mitotic entry by controlling the duration of DNA replication that is independent from its catalytic activity. We also show the requirement of TRIP12 in the mitotic progression and chromosome stability. Altogether, our findings show that TRIP12 is as a new chromatin-associated protein with several implications in the cell cycle progression and in the maintenance of genome integrity.
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Affiliation(s)
- D Larrieu
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - M Brunet
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - C Vargas
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - N Hanoun
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - L Ligat
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - L Dagnon
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - H Lulka
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - R M Pommier
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, 69008, France
| | - J Selves
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - B E Jády
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, Centre de Biologie Intégrative, Université Toulouse III-Paul Sabatier, Toulouse, Cedex 9, France
| | - L Bartholin
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon, 69008, France
| | - P Cordelier
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - M Dufresne
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
| | - J Torrisani
- Université de Toulouse, INSERM, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France.
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29
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Louie RJ, Friez MJ, Skinner C, Baraitser M, Clark RD, Schwartz CE, Stevenson RE. Clark-Baraitser syndrome is associated with a nonsense alteration in the autosomal gene TRIP12. Am J Med Genet A 2019; 182:595-596. [PMID: 31814248 DOI: 10.1002/ajmg.a.61443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/22/2019] [Accepted: 11/26/2019] [Indexed: 01/07/2023]
Affiliation(s)
- Raymond J Louie
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Michael J Friez
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Cindy Skinner
- J.C. Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, South Carolina
| | - Michael Baraitser
- Department of Clinical Genetics, Hospital for Sick Children, London, UK
| | - Robin D Clark
- Division of Medical Genetics, Loma Linda University School of Medicine, Loma Linda, California
| | - Charles E Schwartz
- 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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30
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Lindstrand A, Eisfeldt J, Pettersson M, Carvalho CMB, Kvarnung M, Grigelioniene G, Anderlid BM, Bjerin O, Gustavsson P, Hammarsjö A, Georgii-Hemming P, Iwarsson E, Johansson-Soller M, Lagerstedt-Robinson K, Lieden A, Magnusson M, Martin M, Malmgren H, Nordenskjöld M, Norling A, Sahlin E, Stranneheim H, Tham E, Wincent J, Ygberg S, Wedell A, Wirta V, Nordgren A, Lundin J, Nilsson D. From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability. Genome Med 2019; 11:68. [PMID: 31694722 PMCID: PMC6836550 DOI: 10.1186/s13073-019-0675-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/09/2019] [Indexed: 12/30/2022] Open
Abstract
Background Since different types of genetic variants, from single nucleotide variants (SNVs) to large chromosomal rearrangements, underlie intellectual disability, we evaluated the use of whole-genome sequencing (WGS) rather than chromosomal microarray analysis (CMA) as a first-line genetic diagnostic test. Methods We analyzed three cohorts with short-read WGS: (i) a retrospective cohort with validated copy number variants (CNVs) (cohort 1, n = 68), (ii) individuals referred for monogenic multi-gene panels (cohort 2, n = 156), and (iii) 100 prospective, consecutive cases referred to our center for CMA (cohort 3). Bioinformatic tools developed include FindSV, SVDB, Rhocall, Rhoviz, and vcf2cytosure. Results First, we validated our structural variant (SV)-calling pipeline on cohort 1, consisting of three trisomies and 79 deletions and duplications with a median size of 850 kb (min 500 bp, max 155 Mb). All variants were detected. Second, we utilized the same pipeline in cohort 2 and analyzed with monogenic WGS panels, increasing the diagnostic yield to 8%. Next, cohort 3 was analyzed by both CMA and WGS. The WGS data was processed for large (> 10 kb) SVs genome-wide and for exonic SVs and SNVs in a panel of 887 genes linked to intellectual disability as well as genes matched to patient-specific Human Phenotype Ontology (HPO) phenotypes. This yielded a total of 25 pathogenic variants (SNVs or SVs), of which 12 were detected by CMA as well. We also applied short tandem repeat (STR) expansion detection and discovered one pathologic expansion in ATXN7. Finally, a case of Prader-Willi syndrome with uniparental disomy (UPD) was validated in the WGS data. Important positional information was obtained in all cohorts. Remarkably, 7% of the analyzed cases harbored complex structural variants, as exemplified by a ring chromosome and two duplications found to be an insertional translocation and part of a cryptic unbalanced translocation, respectively. Conclusion The overall diagnostic rate of 27% was more than doubled compared to clinical microarray (12%). Using WGS, we detected a wide range of SVs with high accuracy. Since the WGS data also allowed for analysis of SNVs, UPD, and STRs, it represents a powerful comprehensive genetic test in a clinical diagnostic laboratory setting.
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Affiliation(s)
- Anna Lindstrand
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden. .,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Jesper Eisfeldt
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Maria Pettersson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Malin Kvarnung
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Giedre Grigelioniene
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olof Bjerin
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Peter Gustavsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Hammarsjö
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Erik Iwarsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maria Johansson-Soller
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Agne Lieden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Måns Magnusson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Marcel Martin
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Helena Malmgren
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Magnus Nordenskjöld
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ameli Norling
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ellika Sahlin
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Henrik Stranneheim
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Josephine Wincent
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sofia Ygberg
- The Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Ann Nordgren
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johanna Lundin
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Nilsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
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31
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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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32
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Genetic mechanisms of regression in autism spectrum disorder. Neurosci Biobehav Rev 2019; 102:208-220. [DOI: 10.1016/j.neubiorev.2019.04.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 02/12/2019] [Accepted: 04/28/2019] [Indexed: 12/17/2022]
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33
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Kweon SM, Chen Y, Moon E, Kvederaviciutė K, Klimasauskas S, Feldman DE. An Adversarial DNA N 6-Methyladenine-Sensor Network Preserves Polycomb Silencing. Mol Cell 2019; 74:1138-1147.e6. [PMID: 30982744 PMCID: PMC6591016 DOI: 10.1016/j.molcel.2019.03.018] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/12/2018] [Accepted: 03/18/2019] [Indexed: 02/07/2023]
Abstract
Adenine N6 methylation in DNA (6mA) is widespread among bacteria and phage and is detected in mammalian genomes, where its function is largely unexplored. Here we show that 6mA deposition and removal are catalyzed by the Mettl4 methyltransferase and Alkbh4 dioxygenase, respectively, and that 6mA accumulation in genic elements corresponds with transcriptional silencing. Inactivation of murine Mettl4 depletes 6mA and causes sublethality and craniofacial dysmorphism in incross progeny. We identify distinct 6mA sensor domains of prokaryotic origin within the MPND deubiquitinase and ASXL1, a component of the Polycomb repressive deubiquitinase (PR-DUB) complex, both of which act to remove monoubiquitin from histone H2A (H2A-K119Ub), a repressive mark. Deposition of 6mA by Mettl4 triggers the proteolytic destruction of both sensor proteins, preserving genome-wide H2A-K119Ub levels. Expression of the bacterial 6mA methyltransferase Dam, in contrast, fails to destroy either sensor. These findings uncover a native, adversarial 6mA network architecture that preserves Polycomb silencing. 6mA deposition and erasure by mammalian Mettl4 and Alkbh4, respectively Mettl4-deficient mice display craniofacial dysmorphism 6mA triggers proteolysis of its cognate sensor proteins ASXL1 and MPND Adversarial 6mA network architecture preserves Polycomb silencing
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Affiliation(s)
- Soo-Mi Kweon
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Yibu Chen
- Bioinformatics Service, Department of Health Sciences Libraries, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Eugene Moon
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Kotryna Kvederaviciutė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Saulius Klimasauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Douglas E Feldman
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA.
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34
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Sher M, Farooq M, Abdullah U, Ali Z, Faryal S, Zakaria M, Ullah F, Bukhari H, Møller RS, Tommerup N, Baig SM. A novel in-frame mutation in CLN3 leads to Juvenile neuronal ceroid lipofuscinosis in a large Pakistani family. Int J Neurosci 2019; 129:890-895. [PMID: 30892110 DOI: 10.1080/00207454.2019.1586686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Aim: Neuronal ceroid lipofuscinosis (NCLs) are the most common neurodegenerative disorders, with global incidence of 1 in 100,000 live births. NCLs affect central nervous system, primarily cerebellar and cerebral cortices. Juvenile neuronal ceroid lipofuscinosis (JNCL), also known as Batten disease, is the most common form of NCLs. JNCL is primarily caused by pathogenic mutations in CLN3 gene, which encodes a transporter transmembrane protein of uncertain function. The 1.02 kb deletion is the most common mutation in CLN3 that results in frame shift and a premature termination leading to nonfunctional protein. Here, we invetigated a large consanguineous family consisting of four affected individuals with clincal symptoms suggestive of Juvenile neuronal ceroid lipofuscinosis. Materials and methods: We conducted clinial and radilogical investigation of the family and performed NGS based Gene Panel sequencing comprising of five hundred and forty five candidate genes to characterize it at genetic level. Results: We identified a novel homozygous c.181_183delGAC mutation in the CLN3 gene seggregating witht the disorder in the family. The mutation induces in-frame deletion, deleting one amino acid (p.Asp61del) in CLN3 protein. The deleted amino acid aspartic acid plays an important role as general acid in enzymes active centers as well as in maintaining the ionic character of proteins. Conclusion: Our finding adds to genetic variability of Juvenile neuronal ceroid lipofuscinosis associated with CLN3 gene and a predicted CLN3 protein interacting domain site.
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Affiliation(s)
- Muhammad Sher
- a Human Molecular Genetics Laboratory , National Institute for Biotechnology and Genetic Engineering (NIBGE)-PIEAS , Faisalabad , Pakistan
| | - Muhammad Farooq
- b Department of Bioinformatics and Biotechnology , Government College University Faisalabad , Pakistan
| | - Uzma Abdullah
- a Human Molecular Genetics Laboratory , National Institute for Biotechnology and Genetic Engineering (NIBGE)-PIEAS , Faisalabad , Pakistan
| | - Zafar Ali
- a Human Molecular Genetics Laboratory , National Institute for Biotechnology and Genetic Engineering (NIBGE)-PIEAS , Faisalabad , Pakistan
| | - Sanam Faryal
- a Human Molecular Genetics Laboratory , National Institute for Biotechnology and Genetic Engineering (NIBGE)-PIEAS , Faisalabad , Pakistan
| | - Mohammad Zakaria
- a Human Molecular Genetics Laboratory , National Institute for Biotechnology and Genetic Engineering (NIBGE)-PIEAS , Faisalabad , Pakistan.,c Department of Genetics , Hazara University , Mansehra , Pakistan
| | - Farid Ullah
- a Human Molecular Genetics Laboratory , National Institute for Biotechnology and Genetic Engineering (NIBGE)-PIEAS , Faisalabad , Pakistan
| | - Hassan Bukhari
- d Radiology Department , Allied Hospital , Faisalabad , Pakistan
| | - Rikke S Møller
- e Danish Epilepsy Centre, Institute for Regional Health Services , University of Southern Denmark , Odense , Denmark
| | - Niels Tommerup
- f Department of Cellular and Molecular Medicine, Wilhelm Johannsen Centre for Functional Genome Research , University of Copenhagen , Copenhagen , Denmark
| | - Shahid Mahmood Baig
- a Human Molecular Genetics Laboratory , National Institute for Biotechnology and Genetic Engineering (NIBGE)-PIEAS , Faisalabad , Pakistan
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35
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Bustos F, Segarra-Fas A, Chaugule VK, Brandenburg L, Branigan E, Toth R, Macartney T, Knebel A, Hay RT, Walden H, Findlay GM. RNF12 X-Linked Intellectual Disability Mutations Disrupt E3 Ligase Activity and Neural Differentiation. Cell Rep 2018; 23:1599-1611. [PMID: 29742418 PMCID: PMC5976579 DOI: 10.1016/j.celrep.2018.04.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 03/13/2018] [Accepted: 04/03/2018] [Indexed: 11/29/2022] Open
Abstract
X-linked intellectual disability (XLID) is a heterogeneous syndrome affecting mainly males. Human genetics has identified >100 XLID genes, although the molecular and developmental mechanisms underpinning this disorder remain unclear. Here, we employ an embryonic stem cell model to explore developmental functions of a recently identified XLID gene, the RNF12/RLIM E3 ubiquitin ligase. We show that RNF12 catalytic activity is required for proper stem cell maintenance and neural differentiation, and this is disrupted by patient-associated XLID mutation. We further demonstrate that RNF12 XLID mutations specifically impair ubiquitylation of developmentally relevant substrates. XLID mutants disrupt distinct RNF12 functional modules by either inactivating the catalytic RING domain or interfering with a distal regulatory region required for efficient ubiquitin transfer. Our data thereby uncover a key function for RNF12 E3 ubiquitin ligase activity in stem cell and neural development and identify mechanisms by which this is disrupted in intellectual disability.
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Affiliation(s)
- Francisco Bustos
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Anna Segarra-Fas
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Viduth K Chaugule
- Institute of Molecular Cell and Systems Biology, The University of Glasgow, Glasgow G12 8QQ, UK
| | - Lennart Brandenburg
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Emma Branigan
- Centre for Gene Regulation and Expression, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Rachel Toth
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Thomas Macartney
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Axel Knebel
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Ronald T Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Helen Walden
- Institute of Molecular Cell and Systems Biology, The University of Glasgow, Glasgow G12 8QQ, UK
| | - Greg M Findlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK.
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36
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Gambin T, Yuan B, Bi W, Liu P, Rosenfeld JA, Coban-Akdemir Z, Pursley AN, Nagamani SCS, Marom R, Golla S, Dengle L, Petrie HG, Matalon R, Emrick L, Proud MB, Treadwell-Deering D, Chao HT, Koillinen H, Brown C, Urraca N, Mostafavi R, Bernes S, Roeder ER, Nugent KM, Bader PI, Bellus G, Cummings M, Northrup H, Ashfaq M, Westman R, Wildin R, Beck AE, Immken L, Elton L, Varghese S, Buchanan E, Faivre L, Lefebvre M, Schaaf CP, Walkiewicz M, Yang Y, Kang SHL, Lalani SR, Bacino CA, Beaudet AL, Breman AM, Smith JL, Cheung SW, Lupski JR, Patel A, Shaw CA, Stankiewicz P. Identification of novel candidate disease genes from de novo exonic copy number variants. Genome Med 2017; 9:83. [PMID: 28934986 PMCID: PMC5607840 DOI: 10.1186/s13073-017-0472-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Exon-targeted microarrays can detect small (<1000 bp) intragenic copy number variants (CNVs), including those that affect only a single exon. This genome-wide high-sensitivity approach increases the molecular diagnosis for conditions with known disease-associated genes, enables better genotype-phenotype correlations, and facilitates variant allele detection allowing novel disease gene discovery. METHODS We retrospectively analyzed data from 63,127 patients referred for clinical chromosomal microarray analysis (CMA) at Baylor Genetics laboratories, including 46,755 individuals tested using exon-targeted arrays, from 2007 to 2017. Small CNVs harboring a single gene or two to five non-disease-associated genes were identified; the genes involved were evaluated for a potential disease association. RESULTS In this clinical population, among rare CNVs involving any single gene reported in 7200 patients (11%), we identified 145 de novo autosomal CNVs (117 losses and 28 intragenic gains), 257 X-linked deletion CNVs in males, and 1049 inherited autosomal CNVs (878 losses and 171 intragenic gains); 111 known disease genes were potentially disrupted by de novo autosomal or X-linked (in males) single-gene CNVs. Ninety-one genes, either recently proposed as candidate disease genes or not yet associated with diseases, were disrupted by 147 single-gene CNVs, including 37 de novo deletions and ten de novo intragenic duplications on autosomes and 100 X-linked CNVs in males. Clinical features in individuals with de novo or X-linked CNVs encompassing at most five genes (224 bp to 1.6 Mb in size) were compared to those in individuals with larger-sized deletions (up to 5 Mb in size) in the internal CMA database or loss-of-function single nucleotide variants (SNVs) detected by clinical or research whole-exome sequencing (WES). This enabled the identification of recently published genes (BPTF, NONO, PSMD12, TANGO2, and TRIP12), novel candidate disease genes (ARGLU1 and STK3), and further confirmation of disease association for two recently proposed disease genes (MEIS2 and PTCHD1). Notably, exon-targeted CMA detected several pathogenic single-exon CNVs missed by clinical WES analyses. CONCLUSIONS Together, these data document the efficacy of exon-targeted CMA for detection of genic and exonic CNVs, complementing and extending WES in clinical diagnostics, and the potential for discovery of novel disease genes by genome-wide assay.
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Affiliation(s)
- Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Institute of Computer Science, Warsaw University of Technology, Warsaw, 00-665, Poland.,Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Amber N Pursley
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA
| | - Sailaja Golla
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lauren Dengle
- Division of Pediatric Neurology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Reuben Matalon
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Lisa Emrick
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Monica B Proud
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Treadwell-Deering
- Department of Psychiatry and Behavioral Sciences, Child and Adolescent Psychiatry Division, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Pediatric, Section of Child Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Hannele Koillinen
- Department of Clinical Genetics, Helsinki University Hospital, Helsinki, 00029, Finland
| | - Chester Brown
- Genetics Division, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38105, USA.,Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | - Nora Urraca
- Le Bonheur Children's Hospital, Memphis, TN, 38103, USA
| | | | | | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Kimberly M Nugent
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA
| | - Patricia I Bader
- Northeast Indiana Genetic Counseling Center, Wayne, IN, 46804, USA
| | - Gary Bellus
- Section of Clinical Genetics & Metabolism, Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Michael Cummings
- Department of Psychiatry Erie County Medical Center, Buffalo, NY, 14215, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Myla Ashfaq
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | | | - Robert Wildin
- St. Luke's Children's Hospital, Boise, ID, 83702, USA.,The National Human Genome Research Institute, Bethesda, MD, 20892, USA
| | - Anita E Beck
- Seattle Children's Hospital, Seattle, WA, 98105, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | | | - Lindsay Elton
- Child Neurology Consultants of Austin, Austin, TX, 78731, USA
| | - Shaun Varghese
- THINK Neurology for Kids/Children's Memorial Hermann Hospital, The Woodlands, TX, 77380, USA
| | - Edward Buchanan
- Division of Plastic Surgery, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Mathilde Lefebvre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Est, FHU-TRANSLAD, CHU Dijon, Dijon, France
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Magdalena Walkiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sung-Hae L Kang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Arthur L Beaudet
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA.,Baylor Genetics, Houston, TX, 77021, USA
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030-3411, USA. .,Baylor Genetics, Houston, TX, 77021, USA.
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37
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Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res 2017; 6:664. [PMID: 28781756 DOI: 10.12688/f1000research.11168.1] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/05/2017] [Indexed: 01/07/2023] Open
Abstract
Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is still limited. One well known, but not well-addressed problem is the large number of benign variants and reference errors present in the human genome that further complicates analysis. Even though there is a wide range of SV-callers available, the number of callers that allow detection of the entire spectra of SV at a low computational cost is still relatively limited.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden
| | - Francesco Vezzi
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, 171 21 Stockholm, Sweden
| | - Pall Olason
- Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-752 37, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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38
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Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res 2017; 6:664. [PMID: 28781756 PMCID: PMC5521161 DOI: 10.12688/f1000research.11168.2] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/28/2017] [Indexed: 01/25/2023] Open
Abstract
Reliable detection of large structural variation ( > 1000 bp) is important in both rare and common genetic disorders. Whole genome sequencing (WGS) is a technology that may be used to identify a large proportion of the genomic structural variants (SVs) in an individual in a single experiment. Even though SV callers have been extensively used in research to detect mutations, the potential usage of SV callers within routine clinical diagnostics is still limited. One well known, but not well-addressed problem is the large number of benign variants and reference errors present in the human genome that further complicates analysis. Even though there is a wide range of SV-callers available, the number of callers that allow detection of the entire spectra of SV at a low computational cost is still relatively limited.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden
| | - Francesco Vezzi
- Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Biochemistry and Biophysics, Stockholm University, 171 21 Stockholm, Sweden
| | - Pall Olason
- Science for Life Laboratory, Dept of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-752 37, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, 171 21 Solna, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, 171 76 Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden
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39
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Zhang J, Gambin T, Yuan B, Szafranski P, Rosenfeld JA, Balwi MA, Alswaid A, Al-Gazali L, Shamsi AMA, Komara M, Ali BR, Roeder E, McAuley L, Roy DS, Manchester DK, Magoulas P, King LE, Hannig V, Bonneau D, Denommé-Pichon AS, Charif M, Besnard T, Bézieau S, Cogné B, Andrieux J, Zhu W, He W, Vetrini F, Ward PA, Cheung SW, Bi W, Eng CM, Lupski JR, Yang Y, Patel A, Lalani SR, Xia F, Stankiewicz P. Haploinsufficiency of the E3 ubiquitin-protein ligase gene TRIP12 causes intellectual disability with or without autism spectrum disorders, speech delay, and dysmorphic features. Hum Genet 2017; 136:377-386. [PMID: 28251352 PMCID: PMC5543723 DOI: 10.1007/s00439-017-1763-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 02/08/2017] [Indexed: 02/05/2023]
Abstract
Impairment of ubiquitin-proteasome system activity involving ubiquitin ligase genes UBE3A, UBE3B, and HUWE1 and deubiquitinating enzyme genes USP7 and USP9X has been reported in patients with neurodevelopmental delays. To date, only a handful of single-nucleotide variants (SNVs) and copy-number variants (CNVs) involving TRIP12, encoding a member of the HECT domain E3 ubiquitin ligases family on chromosome 2q36.3 have been reported. Using chromosomal microarray analysis and whole-exome sequencing (WES), we have identified, respectively, five deletion CNVs and four inactivating SNVs (two frameshifts, one missense, and one splicing) in TRIP12. Seven of these variants were found to be de novo; parental studies could not be completed in two families. Quantitative PCR analyses of the splicing mutation showed a dramatically decreased level of TRIP12 mRNA in the proband compared to the family controls, indicating a loss-of-function mechanism. The shared clinical features include intellectual disability with or without autistic spectrum disorders, speech delay, and facial dysmorphism. Our findings demonstrate that E3 ubiquitin ligase TRIP12 plays an important role in nervous system development and function. The nine presented pathogenic variants further document that TRIP12 haploinsufficiency causes a childhood-onset neurodevelopmental disorder. Finally, our data enable expansion of the phenotypic spectrum of ubiquitin-proteasome dependent disorders.
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Affiliation(s)
- Jing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Tomasz Gambin
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Institute of Computer Science, Warsaw University of Technology, Warsaw, 02-038, Poland
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, 01-211, Poland
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Mohammed Al Balwi
- Pathology and Laboratory Medicine, King Abdulaziz Medical City, Riyadh, 11246, Saudi Arabia
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Aisha M Al Shamsi
- Department of Pediatrics, Tawam Hospital, Al Ain, United Arab Emirates
| | - Makanko Komara
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, San Antonio, TX, 78230, USA
| | - Laura McAuley
- UT Southwestern Medical Center, Children's Health Children's Medical Center, Dallas, TX, 75235, USA
| | - Daniel S Roy
- Tripler Army Medical Center, Honolulu, 96859, USA
| | | | - Pilar Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Lauren E King
- Vanderbilt Children's Hospital, Nashville, TN, 37232, USA
| | - Vickie Hannig
- Vanderbilt Children's Hospital, Nashville, TN, 37232, USA
| | - Dominique Bonneau
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers Cedex 9, France
- UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Anne-Sophie Denommé-Pichon
- Department of Biochemistry and Genetics, University Hospital, 49933, Angers Cedex 9, France
- UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Majida Charif
- UMR CNRS 6015-INSERM 1083 and PREMMI, University of Angers, 49933, Angers Cedex 9, France
| | - Thomas Besnard
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Stéphane Bézieau
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Benjamin Cogné
- CHU Nantes, Service de Génétique Médicale, 9 quai Moncousu, 44093, Nantes Cedex 1, France
| | - Joris Andrieux
- Institute of Medical Genetics, Jeanne de Flandre Hospital, Lille University Hospital, Lille, 59800, France
| | - Wenmiao Zhu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin He
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Francesco Vetrini
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Patricia A Ward
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Christine M Eng
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
- Baylor Genetics, Houston, TX, 77021, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Baylor Genetics, Houston, TX, 77021, USA.
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA.
- Baylor Genetics, Houston, TX, 77021, USA.
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