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Zhu S, Chen Z, Liu C, Duong J, Tran T, Liang Z, Fang X, Ouyang K. The essential role of MED27 in stabilizing the mediator complex for cardiac development and function. Life Sci 2024; 356:123020. [PMID: 39209248 DOI: 10.1016/j.lfs.2024.123020] [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: 06/26/2024] [Revised: 08/15/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
AIM Transcriptional regulation of gene expression plays a crucial role in orchestrating complex morphogenetic and molecular events during heart development and function. Mediator complex is an essential multi-subunit protein complex that governs gene expression in eukaryotic cells. Although Mediator subunits (MEDs) work integrally in the complex, individual MED component displays specialized functions. MED27, categorized as an Upper Tail subunit, possesses an as-yet-uncharacterized function. In this study, we aimed to investigate the physiological role of MED27 in cardiomyocytes. MATERIALS AND METHODS we generated a Med27 floxed mouse line, which was further used to generate constitutive (cKO) and inducible (icKO) cardiomyocyte-specific Med27 knockout mouse models. Morphological, histological analysis and cardiac physiological studies were performed in Med27 cKO and icKO mutants. Transcriptional profiles were determined by RNA sequencing (RNAseq) analysis. KEY FUNDINGS Ablation of MED27 in developing mouse cardiomyocytes results in embryonic lethality, while its deletion in adult cardiomyocytes leads to heart failure and mortality. Similar to the ablation of another Upper Tail subunit, MED30 in cardiomyocytes, deletion of MED27 leads to decreased protein levels of most MEDs in cardiomyocytes. Interestingly, overexpression of MED30 fails to restore the protein levels of Mediator subunits in MED27-deficient cardiomyocytes, demonstrating that the role of MED27 in maintaining the integrity and stability of the Mediator complex is independent of MED30. SIGNIFICANCE Our results revealed an essential role of MED27 in cardiac development and function by maintaining the stability of the Mediator core.
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Affiliation(s)
- Siting Zhu
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China; Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Ze'e Chen
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China; Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Canzhao Liu
- Department of Medicine, University of California San Diego, La Jolla, California, USA; Department of Cardiovascular Medicine, Translational Medicine Research Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Janelle Duong
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Tiana Tran
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Zhengyu Liang
- Department of Systems Biology, Southern University of Science and Technology, Shenzhen, China
| | - Xi Fang
- Department of Medicine, University of California San Diego, La Jolla, California, USA.
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China.
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2
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Zubrzycki M, Schramm R, Costard-Jäckle A, Morshuis M, Gummert JF, Zubrzycka M. Pathogenesis and Surgical Treatment of Dextro-Transposition of the Great Arteries (D-TGA): Part II. J Clin Med 2024; 13:4823. [PMID: 39200964 PMCID: PMC11355351 DOI: 10.3390/jcm13164823] [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: 06/12/2024] [Revised: 08/04/2024] [Accepted: 08/13/2024] [Indexed: 09/02/2024] Open
Abstract
Dextro-transposition of the great arteries (D-TGA) is the second most common cyanotic heart disease, accounting for 5-7% of all congenital heart defects (CHDs). It is characterized by ventriculoarterial (VA) connection discordance, atrioventricular (AV) concordance, and a parallel relationship with D-TGA. As a result, the pulmonary and systemic circulations are separated [the morphological right ventricle (RV) is connected to the aorta and the morphological left ventricle (LV) is connected to the pulmonary artery]. This anomaly is included in the group of developmental disorders of embryonic heart conotruncal irregularities, and their pathogenesis is multifactorial. The anomaly's development is influenced by genetic, epigenetic, and environmental factors. It can occur either as an isolated anomaly, or in association with other cardiac defects. The typical concomitant cardiac anomalies that may occur in patients with D-TGA include ventriculoseptal defects, patent ductus arteriosus, left ventricular outflow tract obstruction (LVOTO), mitral and tricuspid valve abnormalities, and coronary artery variations. Correction of the defect during infancy is the preferred treatment for D-TGA. Balloon atrial septostomy (BAS) is necessary prior to the operation. The recommended surgical correction methods include arterial switch operation (ASO) and atrial switch operation (AtrSR), as well as the Rastelli and Nikaidoh procedures. The most common postoperative complications include coronary artery stenosis, neoaortic root dilation, neoaortic insufficiency and neopulmonic stenosis, right ventricular (RV) outflow tract obstruction (RVOTO), left ventricular (LV) dysfunction, arrhythmias, and heart failure. Early diagnosis and treatment of D-TGA is paramount to the prognosis of the patient. Improved surgical techniques have made it possible for patients with D-TGA to survive into adulthood.
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Affiliation(s)
- Marek Zubrzycki
- Department of Surgery for Congenital Heart Defects, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany;
| | - Rene Schramm
- Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany; (R.S.); (A.C.-J.); (M.M.); (J.F.G.)
| | - Angelika Costard-Jäckle
- Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany; (R.S.); (A.C.-J.); (M.M.); (J.F.G.)
| | - Michiel Morshuis
- Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany; (R.S.); (A.C.-J.); (M.M.); (J.F.G.)
| | - Jan F. Gummert
- Clinic for Thoracic and Cardiovascular Surgery, Heart and Diabetes Center NRW, University Hospital, Ruhr-University Bochum, Georgstr. 11, 32545 Bad Oeynhausen, Germany; (R.S.); (A.C.-J.); (M.M.); (J.F.G.)
| | - Maria Zubrzycka
- Department of Clinical Physiology, Faculty of Medicine, Medical University of Lodz, Mazowiecka 6/8, 92-215 Lodz, Poland
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3
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Schiano C, Luongo L, Maione S, Napoli C. Mediator complex in neurological disease. Life Sci 2023; 329:121986. [PMID: 37516429 DOI: 10.1016/j.lfs.2023.121986] [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: 02/13/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 07/31/2023]
Abstract
Neurological diseases, including traumatic brain injuries, stroke (haemorrhagic and ischemic), and inherent neurodegenerative diseases cause acquired disability in humans, representing a leading cause of death worldwide. The Mediator complex (MED) is a large, evolutionarily conserved multiprotein that facilities the interaction between transcription factors and RNA Polymerase II in eukaryotes. Some MED subunits have been found altered in the brain, although their specific functions in neurodegenerative diseases are not fully understood. Mutations in MED subunits were associated with a wide range of genetic diseases for MED12, MED13, MED13L, MED20, MED23, MED25, and CDK8 genes. In addition, MED12 and MED23 were deregulated in the Alzheimer's Disease. Interestingly, most of the genomic mutations have been found in the subunits of the kinase module. To date, there is only one evidence on MED1 involvement in post-stroke cognitive deficits. Although the underlying neurodegenerative disorders may be different, we are confident that the signal cascades of the biological-cognitive mechanisms of brain adaptation, which begin after brain deterioration, may also differ. Here, we analysed relevant studies in English published up to June 2023. They were identified through a search of electronic databases including PubMed, Medline, EMBASE and Scopus, including search terms such as "Mediator complex", "neurological disease", "brains". Thematic content analysis was conducted to collect and summarize all studies demonstrating MED alteration to understand the role of this central transcriptional regulatory complex in the brain. Improved and deeper knowledge of the regulatory mechanisms in neurological diseases can increase the ability of physicians to predict onset and progression, thereby improving diagnostic care and providing appropriate treatment decisions.
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Affiliation(s)
- Concetta Schiano
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Italy.
| | - Livio Luongo
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Italy; IRCSS, Neuromed, Pozzilli, Italy
| | - Sabatino Maione
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Italy; IRCSS, Neuromed, Pozzilli, Italy
| | - Claudio Napoli
- Department of Advanced Medical and Surgical Sciences (DAMSS), University of Campania "Luigi Vanvitelli", Italy; Clinical Department of Internal Medicine and Specialistic Units, Division of Clinical Immunology and Immunohematology, Transfusion Medicine, and Transplant Immunology (SIMT), Regional Reference Laboratory of Transplant Immunology (LIT), Azienda Universitaria Policlinico (AOU), Italy
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Timberlake AT, McGee S, Allington G, Kiziltug E, Wolfe EM, Stiegler AL, Boggon TJ, Sanyoura M, Morrow M, Wenger TL, Fernandes EM, Caluseriu O, Persing JA, Jin SC, Lifton RP, Kahle KT, Kruszka P. De novo variants implicate chromatin modification, transcriptional regulation, and retinoic acid signaling in syndromic craniosynostosis. Am J Hum Genet 2023; 110:846-862. [PMID: 37086723 PMCID: PMC10183468 DOI: 10.1016/j.ajhg.2023.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/24/2023] [Indexed: 04/24/2023] Open
Abstract
Craniosynostosis (CS) is the most common congenital cranial anomaly. Several Mendelian forms of syndromic CS are well described, but a genetic etiology remains elusive in a substantial fraction of probands. Analysis of exome sequence data from 526 proband-parent trios with syndromic CS identified a marked excess (observed 98, expected 33, p = 4.83 × 10-20) of damaging de novo variants (DNVs) in genes highly intolerant to loss-of-function variation (probability of LoF intolerance > 0.9). 30 probands harbored damaging DNVs in 21 genes that were not previously implicated in CS but are involved in chromatin modification and remodeling (4.7-fold enrichment, p = 1.1 × 10-11). 17 genes had multiple damaging DNVs, and 13 genes (CDK13, NFIX, ADNP, KMT5B, SON, ARID1B, CASK, CHD7, MED13L, PSMD12, POLR2A, CHD3, and SETBP1) surpassed thresholds for genome-wide significance. A recurrent gain-of-function DNV in the retinoic acid receptor alpha (RARA; c.865G>A [p.Gly289Arg]) was identified in two probands with similar CS phenotypes. CS risk genes overlap with those identified for autism and other neurodevelopmental disorders, are highly expressed in cranial neural crest cells, and converge in networks that regulate chromatin modification, gene transcription, and osteoblast differentiation. Our results identify several CS loci and have major implications for genetic testing and counseling.
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Affiliation(s)
- Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Medical Center, New York, NY, USA
| | | | - Garrett Allington
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Emre Kiziltug
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Erin M Wolfe
- Division of Plastic and Reconstructive Surgery, University of Miami Hospital, Miami, FL, USA
| | - Amy L Stiegler
- Department of Pharmacology, Yale University, New Haven, CT, USA
| | - Titus J Boggon
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | | | - Tara L Wenger
- Division of Genetic Medicine, University of Washington, Seattle, WA, USA
| | | | - Oana Caluseriu
- Department of Medical Genetics, University of Alberta, AB, Canada
| | - John A Persing
- Section of Plastic and Reconstructive Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY, USA.
| | - Kristopher T Kahle
- Department of Neurosurgery, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA.
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5
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Hamada N, Iwamoto I, Nagata KI. MED13L and its disease-associated variants influence the dendritic development of cerebral cortical neurons in the mammalian brain. J Neurochem 2023; 165:334-347. [PMID: 36798993 DOI: 10.1111/jnc.15783] [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: 06/14/2022] [Revised: 11/04/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
The mediator complex comprises multiple subcellular subunits that collectively function as a molecular interface between RNA polymerase II and gene-specific transcription factors. Recently, genetic variants to one subunit of the complex, known as MED13L (mediator complex subunit 13 like), have been implicated in syndromic intellectual disability and distinct facial features, frequently accompanied by congenital heart defects. We investigated the impact of five disease-associated MED13L variants on the subcellular localization and biochemical stability of MED13L protein in vitro and in vivo. In overexpression assays using cortical neurons from embryonic mouse cerebral cortices transduced by in utero electroporation-mediated gene transfer, we found that mouse orthologues of human MED13L-p.P866L and -p.T2162M missense variants accumulated in the nucleus, while the p.S2163L and p.S2177Y variants were diffusely distributed in the cytoplasm. In contrast, we found that the p.Q1922* truncation variant was barely detectable in transduced cells, a phenotype reminiscent of this variant that results in MED13L haploinsufficiency in humans. Next, we analyzed these variants for their effects on neuronal migration, dendritic growth, spine morphology, and axon elongation of cortical neurons in vivo. There, we found that overexpression of the p.P866L variant resulted in reduced number and length of dendrites of cortical layer II/III pyramidal neurons. Furthermore, we show that mMED13L-knockdown abrogated dendritic growth in vivo, and this effect was significantly rescued by co-electroporation of an RNAi-resistant mMED13L, but weakly by the p.T2162M variant, and not at all by the p.S2163L variant. However, overexpression of the p.S2163L variant inhibited mature dendritic spine formation in vivo. Expression of each of the 5 variants did not affect neuronal cell migration and callosal axon elongation in vivo. Taken together, our results demonstrate that MED13L expression is relevant to corticogenesis and influences the dendritic branching characteristics of cortical excitatory neurons. Our study also suggests that disease-associated MED13L variants may directly cause morphological and functional defects in cortical neurons in different ways.
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Affiliation(s)
- Nanako Hamada
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Ikuko Iwamoto
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Koh-Ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan.,Department of Neurochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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6
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Thomas Q, Motta M, Gautier T, Zaki MS, Ciolfi A, Paccaud J, Girodon F, Boespflug-Tanguy O, Besnard T, Kerkhof J, McConkey H, Masson A, Denommé-Pichon AS, Cogné B, Trochu E, Vignard V, El It F, Rodan LH, Alkhateeb MA, Jamra RA, Duplomb L, Tisserant E, Duffourd Y, Bruel AL, Jackson A, Banka S, McEntagart M, Saggar A, Gleeson JG, Sievert D, Bae H, Lee BH, Kwon K, Seo GH, Lee H, Saeed A, Anjum N, Cheema H, Alawbathani S, Khan I, Pinto-Basto J, Teoh J, Wong J, Sahari UBM, Houlden H, Zhelcheska K, Pannetier M, Awad MA, Lesieur-Sebellin M, Barcia G, Amiel J, Delanne J, Philippe C, Faivre L, Odent S, Bertoli-Avella A, Thauvin C, Sadikovic B, Reversade B, Maroofian R, Govin J, Tartaglia M, Vitobello A. Bi-allelic loss-of-function variants in TMEM147 cause moderate to profound intellectual disability with facial dysmorphism and pseudo-Pelger-Huët anomaly. Am J Hum Genet 2022; 109:1909-1922. [PMID: 36044892 PMCID: PMC9606387 DOI: 10.1016/j.ajhg.2022.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/09/2022] [Indexed: 01/25/2023] Open
Abstract
The transmembrane protein TMEM147 has a dual function: first at the nuclear envelope, where it anchors lamin B receptor (LBR) to the inner membrane, and second at the endoplasmic reticulum (ER), where it facilitates the translation of nascent polypeptides within the ribosome-bound TMCO1 translocon complex. Through international data sharing, we identified 23 individuals from 15 unrelated families with bi-allelic TMEM147 loss-of-function variants, including splice-site, nonsense, frameshift, and missense variants. These affected children displayed congruent clinical features including coarse facies, developmental delay, intellectual disability, and behavioral problems. In silico structural analyses predicted disruptive consequences of the identified amino acid substitutions on translocon complex assembly and/or function, and in vitro analyses documented accelerated protein degradation via the autophagy-lysosomal-mediated pathway. Furthermore, TMEM147-deficient cells showed CKAP4 (CLIMP-63) and RTN4 (NOGO) upregulation with a concomitant reorientation of the ER, which was also witnessed in primary fibroblast cell culture. LBR mislocalization and nuclear segmentation was observed in primary fibroblast cells. Abnormal nuclear segmentation and chromatin compaction were also observed in approximately 20% of neutrophils, indicating the presence of a pseudo-Pelger-Huët anomaly. Finally, co-expression analysis revealed significant correlation with neurodevelopmental genes in the brain, further supporting a role of TMEM147 in neurodevelopment. Our findings provide clinical, genetic, and functional evidence that bi-allelic loss-of-function variants in TMEM147 cause syndromic intellectual disability due to ER-translocon and nuclear organization dysfunction.
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Affiliation(s)
- Quentin Thomas
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France.
| | - Marialetizia Motta
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Thierry Gautier
- University Grenoble Alpes, Inserm, CNRS, Institute for Advanced Biosciences, 38000 Grenoble, France
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt; Armed Forces College of Medicine, Cairo, Egypt
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Julien Paccaud
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - François Girodon
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Biology Division, Department of Biological Hematology, Dijon Hospital, 21000 Dijon, France
| | - Odile Boespflug-Tanguy
- Université Paris Cité, UMR 1141 NeuroDiderot, Inserm, 75019 Paris, France; Service de Neuropédiatrie, reference center for leukodystrophies, APHP, Hopital Robert Debré, 75019 Paris, France
| | - Thomas Besnard
- Service de Génétique Médicale, CHU Nantes, Nantes, France; Université de Nantes, CHU Nantes, CNRS, Inserm, l'Institut du Thorax, 44000 Nantes, France
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Aymeric Masson
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Benjamin Cogné
- Service de Génétique Médicale, CHU Nantes, Nantes, France; Université de Nantes, CHU Nantes, CNRS, Inserm, l'Institut du Thorax, 44000 Nantes, France
| | - Eva Trochu
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Virginie Vignard
- Université de Nantes, CHU Nantes, CNRS, Inserm, l'Institut du Thorax, 44000 Nantes, France
| | - Fatima El It
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center, Leipzig, Germany
| | - Laurence Duplomb
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Emilie Tisserant
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Yannis Duffourd
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France
| | - Ange-Line Bruel
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Meriel McEntagart
- Medical Genetics, St George's University Hospitals NHS FT, London SW17 0RE, UK
| | - Anand Saggar
- Medical Genetics, St George's University Hospitals NHS FT, London SW17 0RE, UK; The Portland Hospital, 205-209 Great Portland St, London W1W 5AH, UK
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, La Jolla, CA 92093, USA
| | - David Sievert
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hyunwoo Bae
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Beom Hee Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | | | | | - Hane Lee
- 3billion, Inc, Seoul, South Korea
| | - Anjum Saeed
- Children's Hospital and University of Child Health Lahore, Lahore, Pakistan
| | - Nadeem Anjum
- Children's Hospital and University of Child Health Lahore, Lahore, Pakistan
| | - Huma Cheema
- Children's Hospital and University of Child Health Lahore, Lahore, Pakistan
| | | | | | | | - Joyce Teoh
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Jasmine Wong
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Umar Bin Mohamad Sahari
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore
| | - Henry Houlden
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Kristina Zhelcheska
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Melanie Pannetier
- Service d'Hématologie cellulaire et hémostase bioclinique, CHU Rennes, Rennes, France
| | - Mona A Awad
- Clinical and Chemical Pathology Department, Medical Research and Clinical Studies Institute National Research Centre, Cairo, Egypt
| | - Marion Lesieur-Sebellin
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfant Malades, AP-HP, Paris, France
| | - Giulia Barcia
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfant Malades, AP-HP, Paris, France
| | - Jeanne Amiel
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfant Malades, AP-HP, Paris, France
| | - Julian Delanne
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Centre de Référence maladies rares « Anomalies du Développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Christophe Philippe
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Laurence Faivre
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Centre de Référence maladies rares « Anomalies du Développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Référence Anomalies du Développement CLAD Ouest, Univ Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS Inserm UMR 6290, ERL 1305, Univ Rennes, Rennes, France
| | | | - Christel Thauvin
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France; Centre de référence maladies rares « déficiences intellectuelles de causes rares », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Bruno Reversade
- Laboratory of Human Genetics & Therapeutics, Genome Institute of Singapore, A(∗)STAR, Singapore, Singapore; Medical Genetics Department, School of Medicine, Koç University, Istanbul, Turkey; Smart-Health Initiative, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Reza Maroofian
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jérôme Govin
- University Grenoble Alpes, Inserm, CNRS, Institute for Advanced Biosciences, 38000 Grenoble, France
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Antonio Vitobello
- UMR1231 GAD, Inserm, Université Bourgogne-Franche Comté, Dijon, France; Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France.
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7
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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8
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Bessenyei B, Balogh I, Mokánszki A, Ujfalusi A, Pfundt R, Szakszon K. MED13L-related intellectual disability due to paternal germinal mosaicism. Cold Spring Harb Mol Case Stud 2022; 8:a006124. [PMID: 34654706 PMCID: PMC8744498 DOI: 10.1101/mcs.a006124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/13/2021] [Indexed: 12/03/2022] Open
Abstract
The MED13L-related intellectual disability or MRFACD syndrome (Mental retardation and distinctive facial features with or without cardiac defects; MIM # 616789) is one of the most common forms of syndromic intellectual disability with about a hundred cases reported so far. Affected individuals share overlapping features comprising intellectual disability, hypotonia, motor delay, remarkable speech delay, and a recognizable facial gestalt. De novo disruption of the MED13L gene by deletions, duplications, or sequence variants has been identified as deleterious. Siblings affected by intragenic deletion transmitted from a mosaic parent have been reported once in the literature. We now present the first case of paternal germinal mosaicism for a missense MED13L variant causing MRFACD syndrome in one of the father's children and being the likely cause of intellectual disability and facial dysmorphism in the other. As part of the Mediator complex, the MED proteins have an essential role in regulating transcription. Thirty-two subunits of the Mediator complex genes have been linked to congenital malformations that are now acknowledged as transcriptomopathies. The MRFACD syndrome has been suggested to represent a recognizable phenotype.
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Affiliation(s)
- Beáta Bessenyei
- Division of Clinical Genetics, Department of Laboratory Medicine, University of Debrecen, Debrecen, 4032 Hungary
| | - István Balogh
- Division of Clinical Genetics, Department of Laboratory Medicine, University of Debrecen, Debrecen, 4032 Hungary
| | - Attila Mokánszki
- Institute of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, 4032 Hungary
| | - Anikó Ujfalusi
- Division of Clinical Genetics, Department of Laboratory Medicine, University of Debrecen, Debrecen, 4032 Hungary
| | - Rolph Pfundt
- Genome Diagnostics Nijmegen, Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
| | - Katalin Szakszon
- Institute of Paediatrics, Faculty of Medicine, University of Debrecen, Debrecen, 4032 Hungary
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9
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Carvalho LML, da Costa SS, Campagnari F, Kaufman A, Bertola DR, da Silva IT, Krepischi ACV, Koiffmann CP, Rosenberg C. Two novel pathogenic variants in MED13L: one familial and one isolated case. JOURNAL OF INTELLECTUAL DISABILITY RESEARCH : JIDR 2021; 65:1049-1057. [PMID: 34713510 DOI: 10.1111/jir.12891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 08/12/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Genetic variants involving the MED13L gene can lead to an autosomal dominant syndrome characterised by intellectual disability/developmental delay and facial dysmorphism. METHODS We investigated two cases (one familial and one isolated) of intellectual disability with speech delay and dysmorphic facial features by whole-exome sequencing analyses. Further, we performed a literature review about clinical and molecular aspects of MED13L gene and syndrome. RESULTS Two MED13L variants have been identified [MED13L(NM_015335.5):c.4417C>T and MED13L(NM_015335.5):c.2318delC] and were classified as pathogenic according to the ACMG (American College of Medical Genetics and Genomics) guidelines. One of the variants was present in sibs. CONCLUSIONS The two pathogenic variants identified have not been previously reported. Importantly, this is the first report of a familial case of MED13L nonsense mutation. Although the parents of the affected children were no longer available for analysis, their apparently normal phenotypes were surmised from familial verbal descriptions corresponding to normal mental behaviour and phenotype. In this situation, the familial component of mutation transmission might be caused by gonadal mosaicism of a MED13L mutation in a gonad from either the father or the mother. The case reports and the literature review presented in this manuscript can be useful for genetic counselling.
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Affiliation(s)
- L M L Carvalho
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - S S da Costa
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | | | - A Kaufman
- Department of Psychiatry, Faculty of Medicine, University of São Paulo (USP), São Paulo, SP, Brazil
| | - D R Bertola
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - I T da Silva
- International Centre for Research, A. C. Camargo Cancer Centre, São Paulo, SP, Brazil
| | - A C V Krepischi
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - C P Koiffmann
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
| | - C Rosenberg
- Human Genome and Stem Cell Research Centre, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo (USP), São Paulo, SP, Brazil
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10
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Parenti I, Kaiser FJ. Cornelia de Lange Syndrome as Paradigm of Chromatinopathies. Front Neurosci 2021; 15:774950. [PMID: 34803598 PMCID: PMC8603810 DOI: 10.3389/fnins.2021.774950] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/18/2021] [Indexed: 12/18/2022] Open
Abstract
Chromatinopathies can be defined as a class of neurodevelopmental disorders caused by mutations affecting proteins responsible for chromatin remodeling and transcriptional regulation. The resulting dysregulation of gene expression favors the onset of a series of clinical features such as developmental delay, intellectual disability, facial dysmorphism, and behavioral disturbances. Cornelia de Lange syndrome (CdLS) is a prime example of a chromatinopathy. It is caused by mutations affecting subunits or regulators of the cohesin complex, a multisubunit protein complex involved in various molecular mechanisms such as sister chromatid cohesion, transcriptional regulation and formation of topologically associated domains. However, disease-causing variants in non-cohesin genes with overlapping functions have also been described in association with CdLS. Notably, the majority of these genes had been previously found responsible for distinct neurodevelopmental disorders that also fall within the category of chromatinopathies and are frequently considered as differential diagnosis for CdLS. In this review, we provide a systematic overview of the current literature to summarize all mutations in non-cohesin genes identified in association with CdLS phenotypes and discuss about the interconnection of proteins belonging to the chromatinopathies network.
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Affiliation(s)
- Ilaria Parenti
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany
| | - Frank J Kaiser
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany.,Essener Zentrum für Seltene Erkrankungen (EZSE), Universitätsklinikum Essen, Essen, Germany
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11
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Smol T, Frénois F, Manouvrier-Hanu S, Petit F, Ghoumid J. Performance of meta-predictors for the classification of MED13L missense variations, implication of raw parameters. Eur J Med Genet 2021; 65:104398. [PMID: 34798324 DOI: 10.1016/j.ejmg.2021.104398] [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: 06/23/2021] [Revised: 09/14/2021] [Accepted: 11/13/2021] [Indexed: 11/26/2022]
Abstract
MED13L syndrome is a rare congenital disorder comprising moderate intellectual disability, hypotonia and facial dysmorphism. Whole exome or genome sequencing in patients with non-specific neurodevelopmental disorders leads to identification of an increasing number of MED13L missense variations of unknown signification. The aim of our study was to identify relevant annotation parameters enhancing discrimination between candidate pathogenic or neutral missense variations, and to assess the performance of seven meta-predictor algorithms: BayesDel, CADD, DANN, FATHMM-XF, M-CAP, MISTIC and REVEL for the classification of MED13L missense variants. Significant differences were identified for five parameters: global conservation through verPhyloP and verPhCons scores; physico-chemical difference between amino acids estimated by Grantham scores; conservation of residues between MED13L and MED13 protein; proximity to phosphorylation sites for pathogenic variations. Among the seven selected in-silico tools, BayesDel, REVEL, and MISTIC provided the most interesting performances to discriminate pathogenic from neutral missense variations. Individual gene parameter studies with MED13L have provided expertise on elements of annotation improving meta-predictor choices. The in-silico approach allows us to make valuable hypotheses to predict the involvement of these amino acids in MED13L pathogenic missense variations.
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Affiliation(s)
- Thomas Smol
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Institut de Génétique Médicale, F-59000, Lille, France
| | - Frédéric Frénois
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France
| | - Sylvie Manouvrier-Hanu
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France
| | - Florence Petit
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France
| | - Jamal Ghoumid
- Université de Lille, ULR7364 RADEME, F-59000, Lille, France; CHU Lille, Clinique de Génétique, Guy Fontaine, F-59000, Lille, France.
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12
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Tan C, Zhu S, Chen Z, Liu C, Li YE, Zhu M, Zhang Z, Zhang Z, Zhang L, Gu Y, Liang Z, Boyer TG, Ouyang K, Evans SM, Fang X. Mediator complex proximal Tail subunit MED30 is critical for Mediator core stability and cardiomyocyte transcriptional network. PLoS Genet 2021; 17:e1009785. [PMID: 34506481 PMCID: PMC8432849 DOI: 10.1371/journal.pgen.1009785] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 08/18/2021] [Indexed: 01/28/2023] Open
Abstract
Dysregulation of cardiac transcription programs has been identified in patients and families with heart failure, as well as those with morphological and functional forms of congenital heart defects. Mediator is a multi-subunit complex that plays a central role in transcription initiation by integrating regulatory signals from gene-specific transcriptional activators to RNA polymerase II (Pol II). Recently, Mediator subunit 30 (MED30), a metazoan specific Mediator subunit, has been associated with Langer-Giedion syndrome (LGS) Type II and Cornelia de Lange syndrome-4 (CDLS4), characterized by several abnormalities including congenital heart defects. A point mutation in MED30 has been identified in mouse and is associated with mitochondrial cardiomyopathy. Very recent structural analyses of Mediator revealed that MED30 localizes to the proximal Tail, anchoring Head and Tail modules, thus potentially influencing stability of the Mediator core. However, in vivo cellular and physiological roles of MED30 in maintaining Mediator core integrity remain to be tested. Here, we report that deletion of MED30 in embryonic or adult cardiomyocytes caused rapid development of cardiac defects and lethality. Importantly, cardiomyocyte specific ablation of MED30 destabilized Mediator core subunits, while the kinase module was preserved, demonstrating an essential role of MED30 in stability of the overall Mediator complex. RNAseq analyses of constitutive cardiomyocyte specific Med30 knockout (cKO) embryonic hearts and inducible cardiomyocyte specific Med30 knockout (icKO) adult cardiomyocytes further revealed critical transcription networks in cardiomyocytes controlled by Mediator. Taken together, our results demonstrated that MED30 is essential for Mediator stability and transcriptional networks in both developing and adult cardiomyocytes. Our results affirm the key role of proximal Tail modular subunits in maintaining core Mediator stability in vivo.
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Affiliation(s)
- Changming Tan
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Siting Zhu
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Zee Chen
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Canzhao Liu
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Yang E. Li
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Mason Zhu
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Zhiyuan Zhang
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhiwei Zhang
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Cardiovascular Surgery, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lunfeng Zhang
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Yusu Gu
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Zhengyu Liang
- Department of Medicine, University of California, San Diego, California, United States of America
| | - Thomas G. Boyer
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, School of Chemical Biology and Biotechnology, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Sylvia M. Evans
- Department of Medicine, University of California, San Diego, California, United States of America
- Department of Pharmacology, University of California, San Diego, California, United States of America
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, California, United States of America
| | - Xi Fang
- Department of Medicine, University of California, San Diego, California, United States of America
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13
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Williams B, Friedenberg SG, Keene BW, Tou SP, DeFrancesco TC, Meurs KM. Use of whole genome analysis to identify shared genomic variants across breeds in canine mitral valve disease. Hum Genet 2021; 140:1563-1568. [PMID: 34176051 DOI: 10.1007/s00439-021-02297-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 05/24/2021] [Indexed: 12/24/2022]
Abstract
Familial mitral valve prolapse in human beings has been associated with several genetic variants; however, in most cases, a known variant has not been identified. Dogs also have a naturally occurring form of familial mitral valve disease (MMVD) with similarities to the human disease. A shared genetic background and clinical phenotype of this disease in some dog breeds has indicated that the disease may share a common genetic cause. We evaluated DNA from 50 affected dogs from five different dog breeds in a whole genome sequencing approach to identify shared variants across and within breeds that could be associated with MMVD. No single causative genetic mutation was found from the 50 dogs with MMVD. Ten variants were identified in 37/50 dogs around and within the MED13L gene. These variants were no longer associated with MMVD when evaluated with a larger cohort including both affected and unaffected dogs. No high/moderate impact variants were identified in 10/10 miniature poodles, one was identified in 10/10 Yorkshire Terriers and 10/10 dachshunds, respectively, 14 were identified in 10/10 Miniature schnauzers, and 19 in 10/10 CKCS. Only one of these could be associated with the cardiac valve (Chr12:36801705, COL12A1; CKCS) but when evaluated in an additional 100 affected CKCS the variant was only identified in 84/100 affected dogs, perhaps indicating genetic heterogeneity in this disease. Our findings indicate that development of MMVD in the dog may be related to a combination of genetic and environmental factors that impact specific molecular pathways rather than a single shared genetic variant across or within breeds.
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Affiliation(s)
- Brian Williams
- Department of Veterinary Clinical Sciences, North Carolina State University, Raleigh, NC, 27607, USA
| | - Steven G Friedenberg
- Department of Veterinary Clinical Sciences, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Bruce W Keene
- Department of Veterinary Clinical Sciences, North Carolina State University, Raleigh, NC, 27607, USA
| | - Sandy P Tou
- Department of Veterinary Clinical Sciences, North Carolina State University, Raleigh, NC, 27607, USA
| | - Teresa C DeFrancesco
- Department of Veterinary Clinical Sciences, North Carolina State University, Raleigh, NC, 27607, USA
| | - Kathryn M Meurs
- Department of Veterinary Clinical Sciences, North Carolina State University, Raleigh, NC, 27607, USA.
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14
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Rogers AP, Friend K, Rawlings L, Barnett CP. A de novo missense variant in MED13 in a patient with global developmental delay, marked facial dysmorphism, macroglossia, short stature, and macrocephaly. Am J Med Genet A 2021; 185:2586-2592. [PMID: 33931951 DOI: 10.1002/ajmg.a.62238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 04/09/2021] [Accepted: 04/12/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Alice P Rogers
- Women's and Children's Hospital, Paediatric and Reproductive Genetics Unit, North Adelaide, South Australia, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, Women's and Children's Hospital, North Adelaide, South Australia, Australia
| | - Lesley Rawlings
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | - Christopher P Barnett
- Women's and Children's Hospital, Paediatric and Reproductive Genetics Unit, North Adelaide, South Australia, Australia
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15
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Hamada N, Iwamoto I, Nishikawa M, Nagata KI. Expression Analyses of Mediator Complex Subunit 13-Like: A Responsible Gene for Neurodevelopmental Disorders during Mouse Brain Development. Dev Neurosci 2021; 43:43-52. [PMID: 33794529 DOI: 10.1159/000515188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/11/2021] [Indexed: 11/19/2022] Open
Abstract
MED13L (mediator complex subunit 13-like) is a component of the mediator complex, which functions as a regulator for gene transcription. Since gene abnormalities in MED13L are responsible for neurodevelopmental disorders, MED13L is presumed to play an essential role in brain development. In this study, we prepared a specific antibody against MED13L, anti-MED13L, and analyzed its expression profile in mouse tissues with focusing on the central nervous system. In Western blotting, MED13L exhibited a tissue-dependent expression profile in the adult mouse and was expressed in a developmental stage-dependent manner in brain. In immunofluorescence analyses, MED13L was at least partially colocalized with pre- and post-synaptic markers, synaptophysin, and PSD95, in primary cultured hippocampal neurons. Immunohistochemical analyses revealed that MED13L was relatively highly expressed in ventricular zone surface of cerebral cortex, and was also located both in the cytoplasm and nucleus of neurons in the cortical plate at embryonic day 14. Then, MED13L showed diffuse cytoplasmic distribution throughout the cerebral cortex at the postnatal day (P) 30. In addition, MED13L appeared to be localized in cell type- and developmental stage-specific manners in the hippocampus and cerebellum. These results suggest that MED13L is involved in the development of the central nervous system and synaptic function.
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Affiliation(s)
- Nanako Hamada
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Ikuko Iwamoto
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Masashi Nishikawa
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan
| | - Koh-Ichi Nagata
- Department of Molecular Neurobiology, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Japan.,Department of Neurochemistry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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16
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Zhou W, Cai H, Li J, Xu H, Wang X, Men H, Zheng Y, Cai L. Potential roles of mediator Complex Subunit 13 in Cardiac Diseases. Int J Biol Sci 2021; 17:328-338. [PMID: 33390853 PMCID: PMC7757031 DOI: 10.7150/ijbs.52290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/25/2020] [Indexed: 12/16/2022] Open
Abstract
Mediator complex subunit 13 (MED13, previously known as THRAP1 and TRAP240) is a subunit of the cyclin-dependent kinase 8 (CDK8) kinase module in the eukaryotic mediator complex. MED13 has been known to play critical roles in cell cycle, development, and growth. The purpose of this review is to comprehensively discuss its newly identified potential roles in myocardial energy metabolism and non-metabolic cardiovascular diseases. Evidence indicates that cardiac MED13 mainly participates in the regulation of nuclear receptor signaling, which drives the transcription of genes involved in modulating cardiac and systemic energy homeostasis. MED13 is also associated with several pathological conditions, such as metabolic syndrome and thyroid disease-associated heart failure. Therefore, MED13 constitutes a potential therapeutic target for the regulation of metabolic disorders and other cardiovascular diseases.
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Affiliation(s)
- Wenqian Zhou
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China.,Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA
| | - He Cai
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China
| | - Jia Li
- Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA.,Department of Nephrology, the First Hospital of Jilin University, Changchun 130021, China
| | - He Xu
- Department of Respiratory Medicine, the First Hospital of Jilin University (Eastern Division), Changchun 130031, China
| | - Xiang Wang
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China.,Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA
| | - Hongbo Men
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China.,Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA
| | - Yang Zheng
- The Center of Cardiovascular Diseases, the First Hospital of Jilin University, Changchun 130021, China
| | - Lu Cai
- Pediatric Research Institute, the Department of Pediatrics of University of Louisville, Louisville, KY 40202, USA.,Department of Pharmacology and Toxicology, the University of Louisville, Louisville, KY 40202, USA
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17
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Straub J, Venigalla S, Newman JJ. Mediator's Kinase Module: A Modular Regulator of Cell Fate. Stem Cells Dev 2020; 29:1535-1551. [PMID: 33161841 DOI: 10.1089/scd.2020.0164] [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] [Indexed: 12/28/2022] Open
Abstract
Selective gene expression is crucial in maintaining the self-renewing and multipotent properties of stem cells. Mediator is a large, evolutionarily conserved, multi-subunit protein complex that modulates gene expression by relaying signals from cell type-specific transcription factors to RNA polymerase II. In humans, this complex consists of 30 subunits arranged in four modules. One critical module of the Mediator complex is the kinase module consisting of four subunits: MED12, MED13, CDK8, and CCNC. The kinase module exists in variable association with the 26-subunit Mediator core and affects transcription through phosphorylation of transcription factors and by controlling Mediator structure and function. Many studies have shown the kinase module to be a key player in the maintenance of stem cells that is distinct from a general role in transcription. Genetic studies have revealed that dysregulation of this kinase subunit contributes to the development of many human diseases. In this review, we discuss the importance of the Mediator kinase module by examining how this module functions with the more recently identified transcriptional super-enhancers, how changes in the kinase module and its activity can lead to the development of human disease, and the role of this unique module in directing and maintaining cell state. As we look to use stem cells to understand human development and treat human disease through both cell-based therapies and tissue engineering, we need to remain aware of the on-going research and address critical gaps in knowledge related to the molecular mechanisms that control cell fate.
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Affiliation(s)
- Joseph Straub
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Sree Venigalla
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Jamie J Newman
- School of Biological Sciences, Louisiana Tech University, Ruston, Louisiana, USA
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18
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Sabo A, Murdock D, Dugan S, Meng Q, Gingras MC, Hu J, Muzny D, Gibbs R. Community-based recruitment and exome sequencing indicates high diagnostic yield in adults with intellectual disability. Mol Genet Genomic Med 2020; 8:e1439. [PMID: 32767738 PMCID: PMC7549560 DOI: 10.1002/mgg3.1439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/12/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Establishing a genetic diagnosis for individuals with intellectual disability (ID) benefits patients and their families as it may inform the prognosis, lead to appropriate therapy, and facilitate access to medical and supportive services. Exome sequencing has been successfully applied in a diagnostic setting, but most clinical exome referrals are pediatric patients, with many adults with ID lacking a comprehensive genetic evaluation. METHODS Our unique recruitment strategy involved partnering with service and education providers for individuals with ID. We performed exome sequencing and analysis, and clinical variant interpretation for each recruited family. RESULTS All five families enrolled in the study opted-in for the return of genetic results. In three out of five families exome sequencing analysis identified pathogenic or likely pathogenic variants in KANSL1, TUSC3, and MED13L genes. Families discussed the results and any potential medical follow-up in an appointment with a board certified clinical geneticist. CONCLUSION Our study suggests high yield of exome sequencing as a diagnostic tool in adult patients with ID who have not undergone comprehensive sequencing-based genetic testing. Research studies including an option of return of results through a genetic clinic could help minimize the disparity in exome diagnostic testing between pediatric and adult patients with ID.
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Affiliation(s)
- Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - David Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | | | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
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19
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van Weerd JH, Mohan RA, van Duijvenboden K, Hooijkaas IB, Wakker V, Boukens BJ, Barnett P, Christoffels VM. Trait-associated noncoding variant regions affect TBX3 regulation and cardiac conduction. eLife 2020; 9:56697. [PMID: 32672536 PMCID: PMC7365664 DOI: 10.7554/elife.56697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/28/2020] [Indexed: 11/21/2022] Open
Abstract
Genome-wide association studies have implicated common genomic variants in the gene desert upstream of TBX3 in cardiac conduction velocity. Whether these noncoding variants affect expression of TBX3 or neighboring genes and how they affect cardiac conduction is not understood. Here, we use high-throughput STARR-seq to test the entire 1.3 Mb human and mouse TBX3 locus, including two cardiac conduction-associated variant regions, for regulatory function. We identified multiple accessible and functional regulatory DNA elements that harbor variants affecting their activity. Both variant regions drove gene expression in the cardiac conduction tissue in transgenic reporter mice. Genomic deletion from the mouse genome of one of the regions caused increased cardiac expression of only Tbx3, PR interval shortening and increased QRS duration. Combined, our findings address the mechanistic link between trait-associated variants in the gene desert, TBX3 regulation and cardiac conduction.
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Affiliation(s)
- Jan Hendrik van Weerd
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Rajiv A Mohan
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Karel van Duijvenboden
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Ingeborg B Hooijkaas
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Vincent Wakker
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Bastiaan J Boukens
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Phil Barnett
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Vincent M Christoffels
- Department of Medical Biology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
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20
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Yi Z, Zhang Y, Song Z, Pan H, Yang C, Li F, Xue J, Qu Z. Report of a de novo c.2605C > T (p.Pro869Ser) change in the MED13L gene and review of the literature for MED13L-related intellectual disability. Ital J Pediatr 2020; 46:95. [PMID: 32646507 PMCID: PMC7350599 DOI: 10.1186/s13052-020-00847-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/08/2020] [Indexed: 11/25/2022] Open
Abstract
Background MED13L-related intellectual disability is a new syndrome that is characterized by intellectual disability (ID), motor developmental delay, speech impairment, hypotonia and facial dysmorphism. Both the MED13L haploinsufficiency mutation and missense mutation were reported to be causative. It has also been reported that patients carrying missense mutations have more frequent epilepsy and show a more severe phenotype. Case presentation We report a child with ID, speech impairment, severe motor developmental delay, facial deformity, hypotonia, muscular atrophy, scoliosis, odontoprisis, abnormal electroencephalogram (EEG), and congenital ureteropelvic junction obstruction (UPJO) combined with high ureter attachment. We used whole-exome sequencing (WES) to detect the genetic aberration of the child and found a de novo mutation, c.2605C > T (p.Pro869Ser), in the MED13L gene. Neither of her parents carried the mutation. Additionally, we review the literature and summarize the phenotypes and features of reported missense mutations. After reviewing the literature, approximately 17 missense mutations in 20 patients have been reported thus far. For 18 patients (including our case) whose clinical manifestations were provided, 100% of the patients had ID or developmental delay (DD). A total of 88.9, 83.3 and 66.7% of the patients had speech impairment, delayed milestones and hypotonia, respectively. A total of 83.3% of the patients exhibited craniofacial deformity or other dysmorphic features. Behavioral difficulties and autistic features were observed in 55.6% of the patients. Cardiac anomalies were seen in only 27.8% of the patients. Of these patients, 44.4% had epileptic seizures. Of the 17 mutations, 2 were located in the N-terminal domain, 8 were located in the C-terminal domain, and 1 was located in an α-helical sequence stretch. One of them was located in the MID domain of the MedPIWI module. Conclusions We report a new patient with a reported missense mutation, c.2605C > T (p.Pro869Ser), who exhibited some infrequent manifestations except common phenotypes, which may broaden the known clinical spectrum. Additionally, by reviewing the literature, we also found that patients with missense mutations have a higher incidence of seizures, MRI abnormalities, autistic features and cardiac anomalies. They also have more severe ID and hypotonia. Our case further demonstrates that Pro869Ser is a hotspot mutation of the MED13L gene.
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Affiliation(s)
- Zhi Yi
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Ying Zhang
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Zhenfeng Song
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Hong Pan
- Department of Central Laboratory, Peking University First Hospital, Beijing, China
| | - Chengqing Yang
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Fei Li
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Jiao Xue
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Zhenghai Qu
- Department of Pediatric, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China.
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21
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Abstract
Pathological cardiac remodeling is induced through multiple mechanisms that include neurohumoral and biomechanical stress resulting in transcriptional alterations that ultimately become maladaptive and lead to the development of heart failure (HF). Although cardiac transcriptional remodeling is mediated by the activation of numerous signaling pathways that converge on a limited number of transcription factors (TFs) that promote hypertrophy (pro-hypertrophic TFs), the current therapeutic approach to prevent HF utilizes pharmacological inhibitors that largely target specific receptors that are activated in response to pathological stimuli. Thus, there is limited efficacy with the current pharmacological approaches to inhibit transcriptional remodeling associated with the development of HF. Recent evidence suggests that these pro-hypertrophic TFs co-localize at enhancers to cooperatively activate transcription associated with pathological cardiac remodeling. In disease states, including cancer and HF, evidence suggests that the general transcriptional machinery is disproportionately bound at enhancers. Therefore, pharmacological inhibition of transcriptional machinery that integrates pro-hypertrophic TFs may represent a promising alternative therapeutic approach to limit pathological remodeling associated with the development of HF.
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22
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Chung HL, Mao X, Wang H, Park YJ, Marcogliese PC, Rosenfeld JA, Burrage LC, Liu P, Murdock DR, Yamamoto S, Wangler MF, Chao HT, Long H, Feng L, Bacino CA, Bellen HJ, Xiao B. De Novo Variants in CDK19 Are Associated with a Syndrome Involving Intellectual Disability and Epileptic Encephalopathy. Am J Hum Genet 2020; 106:717-725. [PMID: 32330417 PMCID: PMC7212481 DOI: 10.1016/j.ajhg.2020.04.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 03/30/2020] [Indexed: 10/24/2022] Open
Abstract
We identified three unrelated individuals with de novo missense variants in CDK19, encoding a cyclin-dependent kinase protein family member that predominantly regulates gene transcription. These individuals presented with hypotonia, global developmental delay, epileptic encephalopathy, and dysmorphic features. CDK19 is conserved between vertebrate and invertebrate model organisms, but currently abnormalities in CDK19 are not known to be associated with a human disorder. Loss of Cdk8, the fly homolog of CDK19, causes larval lethality, which is suppressed by expression of human CDK19 reference cDNA. In contrast, the CDK19 p.Tyr32His and p.Thr196Ala variants identified in the affected individuals fail to rescue the loss of Cdk8 and behave as null alleles. Additionally, neuronal RNAi-mediated knockdown of Cdk8 in flies results in semi-lethality. The few eclosing flies exhibit severe seizures and a reduced lifespan. Both phenotypes are fully suppressed by moderate expression of the CDK19 reference cDNA but not by expression of the two variants. Finally, loss of Cdk8 causes an obvious loss of boutons and synapses at larval neuromuscular junctions (NMJs). Together, our findings demonstrate that human CDK19 fully replaces the function of Cdk8 in the fly, the human disease-associated CDK19 variants behave as strong loss-of-function variants, and deleterious CDK19 variants underlie a syndromic neurodevelopmental disorder.
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Affiliation(s)
- Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiao Mao
- National Health Commission Key Laboratory of Birth Defects Research, Prevention, and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, China; Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Hua Wang
- National Health Commission Key Laboratory of Birth Defects Research, Prevention, and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, China; Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Ye-Jin Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 22021, USA
| | - David R Murdock
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX 77030, USA
| | - Hongyu Long
- Neurology Department, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Li Feng
- Neurology Department, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Bo Xiao
- Neurology Department, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
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23
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Zhang J, Li S, Ma S, Liu Y, Wang X, Li Y. Whole‑exome sequencing study identifies two novel rare variations associated with congenital talipes equinovarus. Mol Med Rep 2020; 21:2597-2602. [PMID: 32236576 DOI: 10.3892/mmr.2020.11038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 03/06/2020] [Indexed: 11/05/2022] Open
Abstract
Congenital talipes equinovarus (CTEV) is a common birth defect with an unclear genetic pathogenesis that results from both genetic and environmental factors. The present study aimed to identify novel variants in patients with CTEV using whole‑exome sequencing (WES) and to investigate the genetic factors responsible for the development of CTEV.A cohort of nine neonates/infants with suspected CTEV was recruited. Subsequently, sequential tests, including chromosome karyotyping and WES, were performed for each of the participants. Familial validation was performed using Sanger sequencing and low‑coverage copy‑number variation (CNV) sequencing. A novel CNV containing the mediator complex subunit 13L gene at 12q24.21‑q24.23 was detected by WES and further investigated by CNVseq. Additionally, a novel de novo missense variation, transforming growth factor‑β receptor 2: c.1280T>C, was identified by WES and further investigated by Sanger sequencing. The two identified variations were hypothesized to be causative genetic factors for the development of CTEV in the two cases the variations were identified in. In the present study, two pathogenic variations (one CNV and one single‑base variation) were detected in two Chinese families with CTEV. The results of the present study may aid in investigating the molecular basis of CTEV; however, further investigation is required.
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Affiliation(s)
- Jing Zhang
- Center of Prenatal Diagnosis, Shijiazhuang Obstetrics and Gynecology Hospital, Shijiazhuang, Hebei 050011, P.R. China
| | - Shang Li
- Department of Anesthesiology and Operating Room, Peking University People's Hospital, Beijing 100044, P.R. China
| | - Suling Ma
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| | - Yan Liu
- Department of Pediatric Orthopedics, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Xuan Wang
- Department of Pediatric Orthopedics, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
| | - Yazhou Li
- Department of Pediatric Orthopedics, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei 050051, P.R. China
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24
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Poot M. Mutations in Mediator Complex Genes CDK8, MED12, MED13, and MEDL13 Mediate Overlapping Developmental Syndromes. Mol Syndromol 2019; 10:239-242. [PMID: 32021594 DOI: 10.1159/000502346] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/22/2019] [Indexed: 12/18/2022] Open
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25
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Variants in MED12L, encoding a subunit of the mediator kinase module, are responsible for intellectual disability associated with transcriptional defect. Genet Med 2019; 21:2713-2722. [PMID: 31155615 PMCID: PMC7243155 DOI: 10.1038/s41436-019-0557-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/20/2019] [Indexed: 12/19/2022] Open
Abstract
Purpose Mediator is a multiprotein complex that allows the transfer of
genetic information from DNA binding proteins to the RNA polymerase II
during transcription initiation. MED12L is a subunit of the kinase module,
which is one of the four sub-complexes of the mediator complex. Other
subunits of the kinase module have been already implicated in intellectual
disability, namely MED12, MED13L, MED13 and CDK19. Methods We describe an international cohort of seven affected individuals
harboring variants involving MED12L identified by array
CGH, exome or genome sequencing. Results All affected individuals presented with intellectual disability
and/or developmental delay, including speech impairment. Other features
included autism spectrum disorder, aggressive behavior, corpus callosum
abnormality and mild facial morphological features. Three individuals had a
MED12L deletion or duplication. The other four
individuals harbored single nucleotide variants (one nonsense, one
frameshift and two splicing variants). Functional analysis confirmed a
moderate and significant alteration of RNA synthesis in two individuals. Conclusion Overall data suggest that MED12L haploinsufficiency is responsible
for intellectual disability and transcriptional defect. Our findings confirm
that the integrity of this kinase module is a critical factor for
neurological development.
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26
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Calpena E, Hervieu A, Kaserer T, Swagemakers SM, Goos JA, Popoola O, Ortiz-Ruiz MJ, Barbaro-Dieber T, Bownass L, Brilstra EH, Brimble E, Foulds N, Grebe TA, Harder AV, Lees MM, Monaghan KG, Newbury-Ecob RA, Ong KR, Osio D, Reynoso Santos FJ, Ruzhnikov MR, Telegrafi A, van Binsbergen E, van Dooren MF, van der Spek PJ, Blagg J, Twigg SR, Mathijssen IM, Clarke PA, Wilkie AO, Wilkie AOM. De Novo Missense Substitutions in the Gene Encoding CDK8, a Regulator of the Mediator Complex, Cause a Syndromic Developmental Disorder. Am J Hum Genet 2019; 104:709-720. [PMID: 30905399 PMCID: PMC6451695 DOI: 10.1016/j.ajhg.2019.02.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022] Open
Abstract
The Mediator is an evolutionarily conserved, multi-subunit complex that regulates multiple steps of transcription. Mediator activity is regulated by the reversible association of a four-subunit module comprising CDK8 or CDK19 kinases, together with cyclin C, MED12 or MED12L, and MED13 or MED13L. Mutations in MED12, MED13, and MED13L were previously identified in syndromic developmental disorders with overlapping phenotypes. Here, we report CDK8 mutations (located at 13q12.13) that cause a phenotypically related disorder. Using whole-exome or whole-genome sequencing, and by international collaboration, we identified eight different heterozygous missense CDK8 substitutions, including 10 shown to have arisen de novo, in 12 unrelated subjects; a recurrent mutation, c.185C>T (p.Ser62Leu), was present in five individuals. All predicted substitutions localize to the ATP-binding pocket of the kinase domain. Affected individuals have overlapping phenotypes characterized by hypotonia, mild to moderate intellectual disability, behavioral disorders, and variable facial dysmorphism. Congenital heart disease occurred in six subjects; additional features present in multiple individuals included agenesis of the corpus callosum, ano-rectal malformations, seizures, and hearing or visual impairments. To evaluate the functional impact of the mutations, we measured phosphorylation at STAT1-Ser727, a known CDK8 substrate, in a CDK8 and CDK19 CRISPR double-knockout cell line transfected with wild-type (WT) or mutant CDK8 constructs. These experiments demonstrated a reduction in STAT1 phosphorylation by all mutants, in most cases to a similar extent as in a kinase-dead control. We conclude that missense mutations in CDK8 cause a developmental disorder that has phenotypic similarity to syndromes associated with mutations in other subunits of the Mediator kinase module, indicating probable overlap in pathogenic mechanisms.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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27
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Dannappel MV, Sooraj D, Loh JJ, Firestein R. Molecular and in vivo Functions of the CDK8 and CDK19 Kinase Modules. Front Cell Dev Biol 2019; 6:171. [PMID: 30693281 PMCID: PMC6340071 DOI: 10.3389/fcell.2018.00171] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/06/2018] [Indexed: 12/21/2022] Open
Abstract
CDK8 and its paralog, CDK19, collectively termed ‘Mediator Kinase,’ are cyclin-dependent kinases that have been implicated as key rheostats in cellular homeostasis and developmental programming. CDK8 and CDK19 are incorporated, in a mutually exclusive manner, as part of a 4-protein complex called the Mediator kinase module. This module reversibly associates with the Mediator, a 26 subunit protein complex that regulates RNA Polymerase II mediated gene expression. As part of this complex, the Mediator kinases have been implicated in diverse process such as developmental signaling, metabolic homeostasis and in innate immunity. In recent years, dysregulation of Mediator kinase module proteins, including CDK8/19, has been implicated in the development of different human diseases, and in particular cancer. This has led to intense efforts to understand how CDK8/19 regulate diverse biological outputs and develop Mediator kinase inhibitors that can be exploited therapeutically. Herein, we review both context and function of the Mediator kinases at a molecular, cellular and animal level. In so doing, we illuminate emerging concepts underpinning Mediator kinase biology and highlight certain aspects that remain unsolved.
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Affiliation(s)
- Marius Volker Dannappel
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Dhanya Sooraj
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - Jia Jian Loh
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Faculty of Science, School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Ron Firestein
- Hudson Institute of Medical Research, Clayton, VIC, Australia.,Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
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28
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Gieldon L, Mackenroth L, Kahlert AK, Lemke JR, Porrmann J, Schallner J, von der Hagen M, Markus S, Weidensee S, Novotna B, Soerensen C, Klink B, Wagner J, Tzschach A, Jahn A, Kuhlee F, Hackmann K, Schrock E, Di Donato N, Rump A. Diagnostic value of partial exome sequencing in developmental disorders. PLoS One 2018; 13:e0201041. [PMID: 30091983 PMCID: PMC6084857 DOI: 10.1371/journal.pone.0201041] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 07/06/2018] [Indexed: 12/15/2022] Open
Abstract
Although intellectual disability is one of the major indications for genetic counselling, there are no homogenous diagnostic algorithms for molecular testing. While whole exome sequencing is increasingly applied, we questioned whether analyzing a partial exome, enriched for genes associated with Mendelian disorders, might be a valid alternative approach that yields similar detection rates but requires less sequencing capacities. Within this context 106 patients with different intellectual disability forms were analyzed for mutations in 4.813 genes after pre-exclusion of copy number variations by array-CGH. Subsequent variant interpretation was performed in accordance with the ACMG guidelines. By this, a molecular diagnosis was established in 34% of cases and candidate mutations were identified in additional 24% of patients. Detection rates of causative mutations were above 30%, regardless of further symptoms, except for patients with seizures (23%). We did not detect an advantage from partial exome sequencing for patients with severe intellectual disability (36%) as compared to those with mild intellectual disability (44%). Specific clinical diagnoses pre-existed for 20 patients. Of these, 5 could be confirmed and an additional 6 cases could be solved, but showed mutations in other genes than initially suspected. In conclusion partial exome sequencing solved >30% of intellectual disability cases, which is similar to published rates obtained by whole exome sequencing. The approach therefore proved to be a valid alternative to whole exome sequencing for molecular diagnostics in this cohort. The method proved equally suitable for both syndromic and non-syndromic intellectual disability forms of all severity grades.
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Affiliation(s)
- Laura Gieldon
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
- * E-mail:
| | - Luisa Mackenroth
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Anne-Karin Kahlert
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
- Klinik für angeborene Herzfehler und Kinderkardiologie, Universitätsklinikum Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johannes R. Lemke
- Institut für Humangenetik, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Joseph Porrmann
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Jens Schallner
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Maja von der Hagen
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | | | - Sabine Weidensee
- Mitteldeutscher Praxisverbund Humangenetik, Praxis Erfurt, Erfurt, Germany
| | - Barbara Novotna
- Abteilung Neuropädiatrie, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Charlotte Soerensen
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Barbara Klink
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Johannes Wagner
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Andreas Tzschach
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Arne Jahn
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Franziska Kuhlee
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Karl Hackmann
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Evelin Schrock
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Nataliya Di Donato
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
| | - Andreas Rump
- Institut für Klinische Genetik, Medizinische Fakultät Carl Gustav Carus, Dresden, Technische Universität Dresden, Germany
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29
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Tørring PM, Larsen MJ, Brasch-Andersen C, Krogh LN, Kibæk M, Laulund L, Illum N, Dunkhase-Heinl U, Wiesener A, Popp B, Marangi G, Hjortshøj TD, Ek J, Vogel I, Becher N, Roos L, Zollino M, Fagerberg CR. Is MED13L-related intellectual disability a recognizable syndrome? Eur J Med Genet 2018; 62:129-136. [PMID: 29959045 DOI: 10.1016/j.ejmg.2018.06.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 05/22/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
Abstract
INTRODUCTION MED13L-related intellectual disability is characterized by moderate intellectual disability (ID), speech impairment, and dysmorphic facial features. We present 8 patients with MED13L-related intellectual disability and review the literature for phenotypical and genetic aspects of previously described patients. MATERIALS AND METHODS In the search for genetic aberrations in individuals with ID, two of the patients were identified by chromosomal microarray analysis, and five by exome sequencing. One of the individuals, suspected of MED13L-related intellectual disability, based on clinical features, was identified by Sanger sequencing. RESULTS All 8 individuals had de novo MED13L aberrations, including two intragenic microdeletions, two frameshift, three nonsense variants, and one missense variant. Phenotypically, they all had intellectual disability, speech and motor delay, and features of the mouth (open mouth appearance, macroglossia, and/or macrostomia). Two individuals were diagnosed with autism, and one had autistic features. One had complex congenital heart defect, and one had persistent foramen ovale. The literature was reviewed with respect to clinical and dysmorphic features, and genetic aberrations. CONCLUSIONS Even if most clinical features of MED13L-related intellectual disability are rather non-specific, the syndrome may be suspected in some individuals based on the association of developmental delay, speech impairment, bulbous nasal tip, and macroglossia, macrostomia, or open mouth appearance.
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Affiliation(s)
| | - Martin Jakob Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | | | - Maria Kibæk
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | - Lone Laulund
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | - Niels Illum
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | | | - Antje Wiesener
- Institute of Human Genetics, University of Erlangen-Nürnberg, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Erlangen-Nürnberg, Germany
| | - Giuseppe Marangi
- Institute of Genomic Medicine, Catholic University, Hospital A. Gemelli Foundation, Rome, Italy
| | | | - Jakob Ek
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Ida Vogel
- Department of Clinical Genetics, Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark
| | - Naja Becher
- Department of Clinical Genetics, Center for Fetal Diagnostics, Aarhus University Hospital, Aarhus, Denmark
| | - Laura Roos
- Department of Clinical Genetics, University Hospital of Copenhagen, Copenhagen, Denmark
| | - Marcella Zollino
- Institute of Genomic Medicine, Catholic University, Hospital A. Gemelli Foundation, Rome, Italy
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30
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Thomford NE, Dzobo K, Yao NA, Chimusa E, Evans J, Okai E, Kruszka P, Muenke M, Awandare G, Wonkam A, Dandara C. Genomics and Epigenomics of Congenital Heart Defects: Expert Review and Lessons Learned in Africa. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:301-321. [PMID: 29762087 PMCID: PMC6016577 DOI: 10.1089/omi.2018.0033] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Congenital heart defects (CHD) are structural malformations found at birth with a prevalence of 1%. The clinical trajectory of CHD is highly variable and thus in need of robust diagnostics and therapeutics. Major surgical interventions are often required for most CHDs. In Africa, despite advances in life sciences infrastructure and improving education of medical scholars, the limited clinical data suggest that CHD detection and correction are still not at par with the rest of the world. But the toll and genetics of CHDs in Africa has seldom been systematically investigated. We present an expert review on CHD with lessons learned on Africa. We found variable CHD phenotype prevalence in Africa across countries and populations. There are important gaps and paucity in genomic studies of CHD in African populations. Among the available genomic studies, the key findings in Africa were variants in GATA4 (P193H), MTHFR 677TT, and MTHFR 1298CC that were associated with atrial septal defect, ventricular septal defect (VSD), Tetralogy of Fallot (TOF), and patent ductus arteriosus phenotypes and 22q.11 deletion, which is associated with TOF. There were no data on epigenomic association of CHD in Africa, however, other studies have shown an altered expression of miR-421 and miR-1233-3p to be associated with TOF and hypermethylation of CpG islands in the promoter of SCO2 gene also been associated with TOF and VSD in children with non-syndromic CHD. These findings signal the urgent need to develop and implement genetic and genomic research on CHD to identify the hereditary and genome-environment interactions contributing to CHD. These projected studies would also offer comparisons on CHD pathophysiology between African and other populations worldwide. Genomic research on CHD in Africa should be developed in parallel with next generation technology policy research and responsible innovation frameworks that examine the social and political factors that shape the emergence and societal embedding of new technologies.
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Affiliation(s)
- Nicholas Ekow Thomford
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
- 2 School of Medical Sciences, University of Cape Coast , Cape Coast, Ghana
| | - Kevin Dzobo
- 3 ICGEB, Cape Town Component, University of Cape Town , Cape Town, South Africa
- 4 Division of Medical Biochemistry, IIDMM, Department of IBM, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
| | - Nana Akyaa Yao
- 5 National Cardiothoracic Centre, Korle Bu Teaching Hospital , Accra, Ghana
- 6 University of Ghana Medical School, University of Ghana , Accra, Ghana
| | - Emile Chimusa
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Jonathan Evans
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Emmanuel Okai
- 2 School of Medical Sciences, University of Cape Coast , Cape Coast, Ghana
- 7 Cape Coast Teaching Hospital , Cape Coast, Ghana
| | - Paul Kruszka
- 8 National Human Genome Research Institute, Medical Genetics Branch, National Institutes of Health , Bethesda, Maryland, USA
| | - Maximilian Muenke
- 8 National Human Genome Research Institute, Medical Genetics Branch, National Institutes of Health , Bethesda, Maryland, USA
| | - Gordon Awandare
- 9 Department of Biochemistry, WACCBIP, University of Ghana , Legon, Accra, Ghana
| | - Ambroise Wonkam
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Collet Dandara
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
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31
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Snijders Blok L, Hiatt SM, Bowling KM, Prokop JW, Engel KL, Cochran JN, Bebin EM, Bijlsma EK, Ruivenkamp CAL, Terhal P, Simon MEH, Smith R, Hurst JA, McLaughlin H, Person R, Crunk A, Wangler MF, Streff H, Symonds JD, Zuberi SM, Elliott KS, Sanders VR, Masunga A, Hopkin RJ, Dubbs HA, Ortiz-Gonzalez XR, Pfundt R, Brunner HG, Fisher SE, Kleefstra T, Cooper GM. De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder. Hum Genet 2018; 137:375-388. [PMID: 29740699 PMCID: PMC5973976 DOI: 10.1007/s00439-018-1887-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/21/2018] [Indexed: 01/15/2023]
Abstract
Many genetic causes of developmental delay and/or intellectual disability (DD/ID) are extremely rare, and robust discovery of these requires both large-scale DNA sequencing and data sharing. Here we describe a GeneMatcher collaboration which led to a cohort of 13 affected individuals harboring protein-altering variants, 11 of which are de novo, in MED13; the only inherited variant was transmitted to an affected child from an affected mother. All patients had intellectual disability and/or developmental delays, including speech delays or disorders. Other features that were reported in two or more patients include autism spectrum disorder, attention deficit hyperactivity disorder, optic nerve abnormalities, Duane anomaly, hypotonia, mild congenital heart abnormalities, and dysmorphisms. Six affected individuals had mutations that are predicted to truncate the MED13 protein, six had missense mutations, and one had an in-frame-deletion of one amino acid. Out of the seven non-truncating mutations, six clustered in two specific locations of the MED13 protein: an N-terminal and C-terminal region. The four N-terminal clustering mutations affect two adjacent amino acids that are known to be involved in MED13 ubiquitination and degradation, p.Thr326 and p.Pro327. MED13 is a component of the CDK8-kinase module that can reversibly bind Mediator, a multi-protein complex that is required for Polymerase II transcription initiation. Mutations in several other genes encoding subunits of Mediator have been previously shown to associate with DD/ID, including MED13L, a paralog of MED13. Thus, our findings add MED13 to the group of CDK8-kinase module-associated disease genes.
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Affiliation(s)
- Lot Snijders Blok
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jeremy W Prokop
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Krysta L Engel
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - J Nicholas Cochran
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | | | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Claudia A L Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Paulien Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rosemarie Smith
- Division of Genetics, Department of Pediatrics, Maine Medical Center, Portland, ME, USA
| | - Jane A Hurst
- Great Ormond Street Hospital for Children, London, UK
| | | | | | - Amy Crunk
- GeneDx, 207 Perry Parkway, Gaithersburg, MD, 20877, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haley Streff
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joseph D Symonds
- Paediatric Neurosciences Research Group, University of Glasgow and Royal Hospital for Children, Glasgow, G51 4TF, UK
| | - Sameer M Zuberi
- Paediatric Neurosciences Research Group, University of Glasgow and Royal Hospital for Children, Glasgow, G51 4TF, UK
| | | | - Victoria R Sanders
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Abigail Masunga
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Robert J Hopkin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Rolph Pfundt
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Han G Brunner
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
- Department of Clinical Genetics, GROW School for Oncology and Developmental Biology, Maastricht UMC, Maastricht, The Netherlands
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA.
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32
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Smol T, Petit F, Piton A, Keren B, Sanlaville D, Afenjar A, Baker S, Bedoukian EC, Bhoj EJ, Bonneau D, Boudry-Labis E, Bouquillon S, Boute-Benejean O, Caumes R, Chatron N, Colson C, Coubes C, Coutton C, Devillard F, Dieux-Coeslier A, Doco-Fenzy M, Ewans LJ, Faivre L, Fassi E, Field M, Fournier C, Francannet C, Genevieve D, Giurgea I, Goldenberg A, Green AK, Guerrot AM, Heron D, Isidor B, Keena BA, Krock BL, Kuentz P, Lapi E, Le Meur N, Lesca G, Li D, Marey I, Mignot C, Nava C, Nesbitt A, Nicolas G, Roche-Lestienne C, Roscioli T, Satre V, Santani A, Stefanova M, Steinwall Larsen S, Saugier-Veber P, Picker-Minh S, Thuillier C, Verloes A, Vieville G, Wenzel M, Willems M, Whalen S, Zarate YA, Ziegler A, Manouvrier-Hanu S, Kalscheuer VM, Gerard B, Ghoumid J. MED13L-related intellectual disability: involvement of missense variants and delineation of the phenotype. Neurogenetics 2018; 19:93-103. [PMID: 29511999 DOI: 10.1007/s10048-018-0541-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/17/2018] [Indexed: 12/30/2022]
Abstract
Molecular anomalies in MED13L, leading to haploinsufficiency, have been reported in patients with moderate to severe intellectual disability (ID) and distinct facial features, with or without congenital heart defects. Phenotype of the patients was referred to "MED13L haploinsufficiency syndrome." Missense variants in MED13L were already previously described to cause the MED13L-related syndrome, but only in a limited number of patients. Here we report 36 patients with MED13L molecular anomaly, recruited through an international collaboration between centers of expertise for developmental anomalies. All patients presented with intellectual disability and severe language impairment. Hypotonia, ataxia, and recognizable facial gestalt were frequent findings, but not congenital heart defects. We identified seven de novo missense variations, in addition to protein-truncating variants and intragenic deletions. Missense variants clustered in two mutation hot-spots, i.e., exons 15-17 and 25-31. We found that patients carrying missense mutations had more frequently epilepsy and showed a more severe phenotype. This study ascertains missense variations in MED13L as a cause for MED13L-related intellectual disability and improves the clinical delineation of the condition.
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Affiliation(s)
- T Smol
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France.,University of Lille, EA 7364-RADEME, Lille, France
| | - F Petit
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - A Piton
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - B Keren
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - D Sanlaville
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - A Afenjar
- Service de Génétique, Hôpital d'Enfants Armand-Trousseau, AP-HP, Paris, France
| | - S Baker
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - E C Bedoukian
- Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - E J Bhoj
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - D Bonneau
- Service de Génétique, CHU d'Angers, Angers, France
| | - E Boudry-Labis
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - S Bouquillon
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - O Boute-Benejean
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - R Caumes
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - N Chatron
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - C Colson
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - C Coubes
- Département de Génétique Médicale, CHU Montpellier, Montpellier, France
| | - C Coutton
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - F Devillard
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - A Dieux-Coeslier
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - M Doco-Fenzy
- Service de Génétique, EA3801, SFR-CAP Santé, CHU de Reims, Reims, France
| | - L J Ewans
- St Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - L Faivre
- Centre de Génétique et Centre de Référence Maladies Rares 'Anomalies du Développement, CHU Dijon, Dijon, France.,Equipe GAD, UMR INSERM 1231, Université de Bourgogne, Dijon, France
| | - E Fassi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - M Field
- The Genetics of Learning Disability Service, Waratah, New South Wales, Australia
| | - C Fournier
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - C Francannet
- Service de Génétique Médicale, CHU de Clermont-Ferrand, Clermont-Ferrand, France
| | - D Genevieve
- Département de Génétique Médicale, CHU Montpellier, Montpellier, France
| | - I Giurgea
- Service de Génétique, Hôpital Trousseau, AP-HP, Paris, France
| | - A Goldenberg
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - A K Green
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - A M Guerrot
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - D Heron
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - B Isidor
- Service de Génétique Médicale, Unité de Génétique Clinique, CHU de Nantes, Nantes, France
| | - B A Keena
- Clinical Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - B L Krock
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - P Kuentz
- Equipe GAD, UMR INSERM 1231, Université de Bourgogne, Dijon, France
| | - E Lapi
- Medical Genetics Unit, Anna Meyer Children's University Hospital, Florence, Italy
| | - N Le Meur
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - G Lesca
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - D Li
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - I Marey
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - C Mignot
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - C Nava
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - A Nesbitt
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - G Nicolas
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - C Roche-Lestienne
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - T Roscioli
- St Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales, Australia
| | - V Satre
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - A Santani
- Department of Pathology Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M Stefanova
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - S Steinwall Larsen
- Department of Clinical Genetics, University Hospital Linköping, Linköping, Sweden
| | - P Saugier-Veber
- Service de Génétique et Inserm U1079, Centre Normand de Génomique Médicale et Médecine Personnalisée, CHU de Rouen, Inserm et Université de Rouen, Rouen, France
| | - S Picker-Minh
- Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - C Thuillier
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - A Verloes
- Unité Fonctionnelle de Génétique Clinique, Hôpital Robert Debré, AP-HP, Paris, France
| | - G Vieville
- Laboratoire de Génétique Chromosomique, CHU Grenoble Alpes, Grenoble, France
| | - M Wenzel
- Clinical Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - M Willems
- Département de Génétique Médicale, CHU Montpellier, Montpellier, France
| | - S Whalen
- Département de Génétique, Groupe Hospitalier Pitié-Salpêtrière, AP-HP, Paris, France
| | - Y A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A Ziegler
- Service de Génétique, CHU d'Angers, Angers, France
| | - S Manouvrier-Hanu
- University of Lille, EA 7364-RADEME, Lille, France.,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France
| | - V M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - B Gerard
- Laboratoire de diagnostic génétique, Institut de Génétique Médicale d'Alsace, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jamal Ghoumid
- University of Lille, EA 7364-RADEME, Lille, France. .,Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, avenue Eugène Avinée, Lille, France.
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33
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Jiménez-Romero S, Carrasco-Salas P, Benítez-Burraco A. Language and Cognitive Impairment Associated with a Novel p.Cys63Arg Change in the MED13L Transcriptional Regulator. Mol Syndromol 2018; 9:83-91. [PMID: 29593475 DOI: 10.1159/000485638] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2017] [Indexed: 12/12/2022] Open
Abstract
Mutations in the MED13L gene, which encodes a subunit of a transcriptional regulatory complex, result in a complex phenotype entailing physical and cognitive anomalies. Deep language impairment has been reported in affected individuals, mostly in patients with copy number variations. We report on a child with a nonsynonymous p.Cys63Arg change in MED13L (chr12:116675396A>G, GRCh37) who exhibits profound language impairment in the expressive domain, cognitive delay, behavioral disturbances, and an autism-like phenotype. Because of the brain areas in which MED13L is expressed and because of the functional links between MED13L and the products of selected candidate genes for cognitive disorders involving language deficits, the proband's linguistic phenotype may result from changes in a functional network important for language development and evolution.
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Affiliation(s)
- Salud Jiménez-Romero
- Maimónides Institute of Biomedical Research, Córdoba, Spain.,Department of Psychology, University of Córdoba, Córdoba, Spain
| | | | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, University of Seville, Seville, Spain
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34
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Gordon CT, Chopra M, Oufadem M, Alibeu O, Bras M, Boddaert N, Bole-Feysot C, Nitschké P, Abadie V, Lyonnet S, Amiel J. MED13L
loss-of-function variants in two patients with syndromic Pierre Robin sequence. Am J Med Genet A 2017; 176:181-186. [DOI: 10.1002/ajmg.a.38536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 09/06/2017] [Accepted: 10/15/2017] [Indexed: 02/02/2023]
Affiliation(s)
- Christopher T. Gordon
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
| | - Maya Chopra
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Département de Génétique; Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (AP-HP); Paris France
| | - Myriam Oufadem
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
| | - Olivier Alibeu
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Genomics Platform, INSERM UMR 1163; Institut Imagine; Paris France
| | - Marc Bras
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Bioinformatics Platform, INSERM UMR 1163; Institut Imagine; Paris France
| | - Nathalie Boddaert
- Service de Radiologie Pédiatrique; Hôpital Necker-Enfants Malades, AP-HP; Paris France
- INSERM U1000 and UMR 1163; Institut Imagine; Paris France
| | - Christine Bole-Feysot
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Genomics Platform, INSERM UMR 1163; Institut Imagine; Paris France
| | - Patrick Nitschké
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Bioinformatics Platform, INSERM UMR 1163; Institut Imagine; Paris France
| | - Véronique Abadie
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Service de Pédiatrie Générale; Hôpital Necker-Enfants Malades, AP-HP; Paris France
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Département de Génétique; Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (AP-HP); Paris France
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Congenital Malformations; Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163; Institut Imagine; Paris France
- Paris Descartes-Sorbonne Paris Cité Université; Institut Imagine; Paris France
- Département de Génétique; Hôpital Necker-Enfants Malades; Assistance Publique Hôpitaux de Paris (AP-HP); Paris France
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Meng QJ, He XL, Xiao H, Xia Q, Bi B, Xiang Y. [Clinical phenotype and genetic analysis of MED13L syndrome]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2017; 19:1083-1086. [PMID: 29046205 PMCID: PMC7389282 DOI: 10.7499/j.issn.1008-8830.2017.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/13/2017] [Indexed: 06/07/2023]
Abstract
A boy aged 4 years and 2 months was found to have delayed language and motor development, instability of gait, poor eye contact, stereotyped behavior, and seizure at the age of 3 years. Physical examination showed special facial features, including plagiocephaly, blepharoptosis, wide nasal bridge, down-turned mouth corners at both sides, and low-set ears. There were only two knuckles at the little finger of the left hand. The anteroposterior and lateral films of the spine showed scoliosis; echocardiography showed ventricular septal defect; the Gesell Developmental Scale showed delayed language development and moderate intellectual disability; there were no abnormalities in the karyotype; genome-wide SNP arrays found a duplication in 12q24.21 region with a size of 1.03 Mb in chromosome 12, while this was not seen in his parents. The boy was diagnosed with MED13L syndrome. Point mutation, deletion, and duplication in the MED13L gene can lead to MED13L syndrome. The patients with different genotypes may have different phenotypes. Genome-wide SNP arrays may help with the diagnosis of this disease.
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Affiliation(s)
- Qing-Jie Meng
- Clinical Laboratory, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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Asadollahi R, Zweier M, Gogoll L, Schiffmann R, Sticht H, Steindl K, Rauch A. Genotype-phenotype evaluation of MED13L defects in the light of a novel truncating and a recurrent missense mutation. Eur J Med Genet 2017. [PMID: 28645799 DOI: 10.1016/j.ejmg.2017.06.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A decade after the designation of MED13L as a gene and its link to intellectual disability (ID) and dextro-looped transposition of great arteries in 2003, we previously described a recognizable syndrome due to MED13L haploinsufficiency. Subsequent reports of 22 further patients diagnosed by genome-wide testing further delineated the syndrome with expansion of the phenotypic spectrum and showed reduced penetrance for congenital heart defects. We now report two novel patients identified by whole exome sequencing, one with a de novo MED13L truncating mutation and the other with a de novo missense mutation. The first patient indicates some facial resemblance to Kleefstra syndrome as a novel differential diagnosis, and the second patient shows, for the first time, recurrence of a MED13L missense mutation (p.(Asp860Gly)). Notably, our in silico modelling predicted this missense mutation to decrease the stability of an alpha-helix and thereby affecting the MED13L secondary structure, while the majority of published missense mutations remain variants of uncertain significance. Review of the reported patients with MED13L haploinsufficiency indicates moderate to severe ID and facial anomalies in all patients, as well as severe speech delay and muscular hypotonia in the majority. Further common signs include abnormal MRI findings of myelination defects and abnormal corpus callosum, ataxia and coordination problems, autistic features, seizures/abnormal EEG, or congenital heart defects, present in about 20-50% of the patients. With reference to facial anomalies, the majority of patients were reported to show broad/prominent forehead, low set ears, bitemporal narrowing, upslanting palpebral fissures, depressed/flat nasal bridge, bulbous nose, and abnormal chin, but macroglossia and horizontal eyebrows were also observed in ∼30%. The latter are especially important in the differential diagnosis of 1p36 deletion and Kleefstra syndromes, while the more common facial gestalt shows some resemblance to 22q11.2 deletion syndrome. Despite the fact that MED13L was found to be one of the most common ID genes in the Deciphering Developmental Disorders Study, further detailed patient descriptions are needed to explore the full clinical spectrum, potential genotype-phenotype correlations, as well as the role of missense mutations and potential mutational hotspots along the gene.
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Affiliation(s)
- Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Laura Gogoll
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Raphael Schiffmann
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Heinrich Sticht
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland; Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland; Zurich Center of Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
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37
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Mullegama SV, Jensik P, Li C, Dorrani N, Kantarci S, Blumberg B, Grody WW, Strom SP. Coupling clinical exome sequencing with functional characterization studies to diagnose a patient with familial Mediterranean fever and MED13L haploinsufficiency syndromes. Clin Case Rep 2017; 5:833-840. [PMID: 28588821 PMCID: PMC5458005 DOI: 10.1002/ccr3.904] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/28/2017] [Accepted: 02/11/2017] [Indexed: 02/06/2023] Open
Abstract
Clinicians should consider that clinical exome sequencing provides the unique potential to disentangle complex phenotypes into multiple genetic etiologies. Further, functional studies on variants of uncertain significance are necessary to arrive at an accurate diagnosis for the patient.
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Affiliation(s)
- Sureni V Mullegama
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | - Phillip Jensik
- Department of Physiology Southern Illinois University School of Medicine Carbondale Illinois
| | - Chen Li
- Department of Cellular and Genetic Medicine School of Basic Medical Sciences Fudan University Shanghai China
| | - Naghmeh Dorrani
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Human Genetics David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Pediatrics David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | | | - Sibel Kantarci
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | | | - Wayne W Grody
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Human Genetics David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,Department of Pediatrics David Geffen School of Medicine University of California, Los Angeles Los Angeles California
| | - Samuel P Strom
- UCLA Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California, Los Angeles Los Angeles California.,UCLA Clinical Genomics Center David Geffen School of Medicine University of California, Los Angeles Los Angeles California
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38
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Yamamoto T, Shimojima K, Ondo Y, Shimakawa S, Okamoto N. MED13L
haploinsufficiency syndrome: A de novo frameshift and recurrent intragenic deletions due to parental mosaicism. Am J Med Genet A 2017; 173:1264-1269. [DOI: 10.1002/ajmg.a.38168] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 11/08/2016] [Accepted: 01/13/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Toshiyuki Yamamoto
- Institute of Medical Genetics; Tokyo Women's Medical University; Tokyo Japan
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
| | - Keiko Shimojima
- Institute of Medical Genetics; Tokyo Women's Medical University; Tokyo Japan
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
| | - Yumiko Ondo
- Tokyo Women's Medical University Institute for Integrated Medical Sciences; Tokyo Japan
| | | | - Nobuhiko Okamoto
- Department of Medical Genetics; Osaka Medical Center and Research Institute for Maternal and Child Health; Osaka Japan
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39
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Wang T, Guo H, Xiong B, Stessman HAF, Wu H, Coe BP, Turner TN, Liu Y, Zhao W, Hoekzema K, Vives L, Xia L, Tang M, Ou J, Chen B, Shen Y, Xun G, Long M, Lin J, Kronenberg ZN, Peng Y, Bai T, Li H, Ke X, Hu Z, Zhao J, Zou X, Xia K, Eichler EE. De novo genic mutations among a Chinese autism spectrum disorder cohort. Nat Commun 2016; 7:13316. [PMID: 27824329 PMCID: PMC5105161 DOI: 10.1038/ncomms13316] [Citation(s) in RCA: 240] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 09/22/2016] [Indexed: 12/27/2022] Open
Abstract
Recurrent de novo (DN) and likely gene-disruptive (LGD) mutations contribute significantly to autism spectrum disorders (ASDs) but have been primarily investigated in European cohorts. Here, we sequence 189 risk genes in 1,543 Chinese ASD probands (1,045 from trios). We report an 11-fold increase in the odds of DN LGD mutations compared with expectation under an exome-wide neutral model of mutation. In aggregate, ∼4% of ASD patients carry a DN mutation in one of just 29 autism risk genes. The most prevalent gene for recurrent DN mutations is SCN2A (1.1% of patients) followed by CHD8, DSCAM, MECP2, POGZ, WDFY3 and ASH1L. We identify novel DN LGD recurrences (GIGYF2, MYT1L, CUL3, DOCK8 and ZNF292) and DN mutations in previous ASD candidates (ARHGAP32, NCOR1, PHIP, STXBP1, CDKL5 and SHANK1). Phenotypic follow-up confirms potential subtypes and highlights how large global cohorts might be leveraged to prove the pathogenic significance of individually rare mutations. Recurrent sporadic mutations are important risk factors for autism spectrum disorders (ASDs) but have been primarily investigated in European cohorts. Here, Eichler, Xia and colleagues analyse risk genes in a large Chinese ASD cohort and find novel recurrences of potential pathogenic significance.
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Affiliation(s)
- Tianyun Wang
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Hui Guo
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China.,Mental Health Institute, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Bo Xiong
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Holly A F Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Huidan Wu
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Tychele N Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Yanling Liu
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Wenjing Zhao
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Lu Xia
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Meina Tang
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Jianjun Ou
- Mental Health Institute, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Biyuan Chen
- Children's Development Behavior Center, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Yidong Shen
- Mental Health Institute, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Guanglei Xun
- Mental Health Center of Shandong Province, Jinan, Shandong 250014, China
| | - Min Long
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Janice Lin
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Zev N Kronenberg
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Yu Peng
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Ting Bai
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Honghui Li
- Child Healthcare Department, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi 545000, China
| | - Xiaoyan Ke
- Child Mental Health Research Center, Nanjing Brain Hospital Affiliated of Nanjing Medical University, Nanjing, Jiangsu 210029, China
| | - Zhengmao Hu
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Jingping Zhao
- Mental Health Institute, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Xiaobing Zou
- Children's Development Behavior Center, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Kun Xia
- The State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China.,Collaborative Innovation Center for Genetics and Development, Shanghai 200433, China.,Key Laboratory of Medical Information Research, Central South University, Changsha, Hunan 410013, China
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA
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40
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Regulation of metabolism by the Mediator complex. BIOPHYSICS REPORTS 2016; 2:69-77. [PMID: 28018965 PMCID: PMC5138257 DOI: 10.1007/s41048-016-0031-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 02/15/2016] [Indexed: 01/11/2023] Open
Abstract
The Mediator complex was originally discovered in yeast, but it is conserved in all eukaryotes. Its best-known function is to regulate RNA polymerase II-dependent gene transcription. Although the mechanisms by which the Mediator complex regulates transcription are often complicated by the context-dependent regulation, this transcription cofactor complex plays a pivotal role in numerous biological pathways. Biochemical, molecular, and physiological studies using cancer cell lines or model organisms have established the current paradigm of the Mediator functions. However, the physiological roles of the mammalian Mediator complex remain poorly defined, but have attracted a great interest in recent years. In this short review, we will summarize some of the reported functions of selective Mediator subunits in the regulation of metabolism. These intriguing findings suggest that the Mediator complex may be an important player in nutrient sensing and energy balance in mammals.
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41
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Jia Y, Chang HC, Schipma MJ, Liu J, Shete V, Liu N, Sato T, Thorp EB, Barger PM, Zhu YJ, Viswakarma N, Kanwar YS, Ardehali H, Thimmapaya B, Reddy JK. Cardiomyocyte-Specific Ablation of Med1 Subunit of the Mediator Complex Causes Lethal Dilated Cardiomyopathy in Mice. PLoS One 2016; 11:e0160755. [PMID: 27548259 PMCID: PMC4993490 DOI: 10.1371/journal.pone.0160755] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/25/2016] [Indexed: 11/19/2022] Open
Abstract
Mediator, an evolutionarily conserved multi-protein complex consisting of about 30 subunits, is a key component of the polymerase II mediated gene transcription. Germline deletion of the Mediator subunit 1 (Med1) of the Mediator in mice results in mid-gestational embryonic lethality with developmental impairment of multiple organs including heart. Here we show that cardiomyocyte-specific deletion of Med1 in mice (csMed1-/-) during late gestational and early postnatal development by intercrossing Med1fl/fl mice to α-MyHC-Cre transgenic mice results in lethality within 10 days after weaning due to dilated cardiomyopathy-related ventricular dilation and heart failure. The csMed1-/- mouse heart manifests mitochondrial damage, increased apoptosis and interstitial fibrosis. Global gene expression analysis revealed that loss of Med1 in heart down-regulates more than 200 genes including Acadm, Cacna1s, Atp2a2, Ryr2, Pde1c, Pln, PGC1α, and PGC1β that are critical for calcium signaling, cardiac muscle contraction, arrhythmogenic right ventricular cardiomyopathy, dilated cardiomyopathy and peroxisome proliferator-activated receptor regulated energy metabolism. Many genes essential for oxidative phosphorylation and proper mitochondrial function such as genes coding for the succinate dehydrogenase subunits of the mitochondrial complex II are also down-regulated in csMed1-/- heart contributing to myocardial injury. Data also showed up-regulation of about 180 genes including Tgfb2, Ace, Atf3, Ctgf, Angpt14, Col9a2, Wisp2, Nppa, Nppb, and Actn1 that are linked to cardiac muscle contraction, cardiac hypertrophy, cardiac fibrosis and myocardial injury. Furthermore, we demonstrate that cardiac specific deletion of Med1 in adult mice using tamoxifen-inducible Cre approach (TmcsMed1-/-), results in rapid development of cardiomyopathy and death within 4 weeks. We found that the key findings of the csMed1-/- studies described above are highly reproducible in TmcsMed1-/- mouse heart. Collectively, these observations suggest that Med1 plays a critical role in the maintenance of heart function impacting on multiple metabolic, compensatory and reparative pathways with a likely therapeutic potential in the management of heart failure.
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MESH Headings
- Animals
- Apoptosis
- Cadherins/genetics
- Cadherins/metabolism
- Calcium Channels, L-Type/genetics
- Calcium Channels, L-Type/metabolism
- Calcium Signaling
- Cardiomyopathy, Dilated/genetics
- Cardiomyopathy, Dilated/metabolism
- Cardiomyopathy, Dilated/pathology
- Cyclic Nucleotide Phosphodiesterases, Type 1/genetics
- Cyclic Nucleotide Phosphodiesterases, Type 1/metabolism
- Embryo, Mammalian
- Energy Metabolism
- Female
- Gene Deletion
- Gene Expression Profiling
- Gene Expression Regulation
- Genes, Lethal
- Gestational Age
- Heart Failure/genetics
- Heart Failure/metabolism
- Heart Failure/pathology
- Mediator Complex Subunit 1/deficiency
- Mediator Complex Subunit 1/genetics
- Mice
- Mice, Knockout
- Mitochondria/metabolism
- Mitochondria/pathology
- Myocardial Contraction
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/pathology
- Peroxisome Proliferator-Activated Receptors/genetics
- Peroxisome Proliferator-Activated Receptors/metabolism
- Pregnancy
- Ryanodine Receptor Calcium Release Channel/genetics
- Ryanodine Receptor Calcium Release Channel/metabolism
- Sarcoplasmic Reticulum Calcium-Transporting ATPases/genetics
- Sarcoplasmic Reticulum Calcium-Transporting ATPases/metabolism
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Affiliation(s)
- Yuzhi Jia
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Hsiang-Chun Chang
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Matthew J. Schipma
- Next Generation Sequencing Core Facility, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Jing Liu
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Varsha Shete
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Ning Liu
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Tatsuya Sato
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Edward B. Thorp
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Philip M. Barger
- Center for Cardiovascular Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yi-Jun Zhu
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Navin Viswakarma
- Department of Surgery, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Yashpal S. Kanwar
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Hossein Ardehali
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Bayar Thimmapaya
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- * E-mail: (JKR); (BT)
| | - Janardan K. Reddy
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
- * E-mail: (JKR); (BT)
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42
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Clark AD, Oldenbroek M, Boyer TG. Mediator kinase module and human tumorigenesis. Crit Rev Biochem Mol Biol 2015; 50:393-426. [PMID: 26182352 DOI: 10.3109/10409238.2015.1064854] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mediator is a conserved multi-subunit signal processor through which regulatory informatiosn conveyed by gene-specific transcription factors is transduced to RNA Polymerase II (Pol II). In humans, MED13, MED12, CDK8 and Cyclin C (CycC) comprise a four-subunit "kinase" module that exists in variable association with a 26-subunit Mediator core. Genetic and biochemical studies have established the Mediator kinase module as a major ingress of developmental and oncogenic signaling through Mediator, and much of its function in signal-dependent gene regulation derives from its resident CDK8 kinase activity. For example, CDK8-targeted substrate phosphorylation impacts transcription factor half-life, Pol II activity and chromatin chemistry and functional status. Recent structural and biochemical studies have revealed a precise network of physical and functional subunit interactions required for proper kinase module activity. Accordingly, pathologic change in this activity through altered expression or mutation of constituent kinase module subunits can have profound consequences for altered signaling and tumor formation. Herein, we review the structural organization, biological function and oncogenic potential of the Mediator kinase module. We focus principally on tumor-associated alterations in kinase module subunits for which mechanistic relationships as opposed to strictly correlative associations are established. These considerations point to an emerging picture of the Mediator kinase module as an oncogenic unit, one in which pathogenic activation/deactivation through component change drives tumor formation through perturbation of signal-dependent gene regulation. It follows that therapeutic strategies to combat CDK8-driven tumors will involve targeted modulation of CDK8 activity or pharmacologic manipulation of dysregulated CDK8-dependent signaling pathways.
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Affiliation(s)
- Alison D Clark
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
| | - Marieke Oldenbroek
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
| | - Thomas G Boyer
- a Department of Molecular Medicine , Institute of Biotechnology, University of Texas Health Science Center at San Antonio , San Antonio , TX , USA
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43
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Codina-Solà M, Rodríguez-Santiago B, Homs A, Santoyo J, Rigau M, Aznar-Laín G, Del Campo M, Gener B, Gabau E, Botella MP, Gutiérrez-Arumí A, Antiñolo G, Pérez-Jurado LA, Cuscó I. Integrated analysis of whole-exome sequencing and transcriptome profiling in males with autism spectrum disorders. Mol Autism 2015; 6:21. [PMID: 25969726 PMCID: PMC4427998 DOI: 10.1186/s13229-015-0017-0] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/19/2015] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Autism spectrum disorders (ASD) are a group of neurodevelopmental disorders with high heritability. Recent findings support a highly heterogeneous and complex genetic etiology including rare de novo and inherited mutations or chromosomal rearrangements as well as double or multiple hits. METHODS We performed whole-exome sequencing (WES) and blood cell transcriptome by RNAseq in a subset of male patients with idiopathic ASD (n = 36) in order to identify causative genes, transcriptomic alterations, and susceptibility variants. RESULTS We detected likely monogenic causes in seven cases: five de novo (SCN2A, MED13L, KCNV1, CUL3, and PTEN) and two inherited X-linked variants (MAOA and CDKL5). Transcriptomic analyses allowed the identification of intronic causative mutations missed by the usual filtering of WES and revealed functional consequences of some rare mutations. These included aberrant transcripts (PTEN, POLR3C), deregulated expression in 1.7% of mutated genes (that is, SEMA6B, MECP2, ANK3, CREBBP), allele-specific expression (FUS, MTOR, TAF1C), and non-sense-mediated decay (RIT1, ALG9). The analysis of rare inherited variants showed enrichment in relevant pathways such as the PI3K-Akt signaling and the axon guidance. CONCLUSIONS Integrative analysis of WES and blood RNAseq data has proven to be an efficient strategy to identify likely monogenic forms of ASD (19% in our cohort), as well as additional rare inherited mutations that can contribute to ASD risk in a multifactorial manner. Blood transcriptomic data, besides validating 88% of expressed variants, allowed the identification of missed intronic mutations and revealed functional correlations of genetic variants, including changes in splicing, expression levels, and allelic expression.
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Affiliation(s)
- Marta Codina-Solà
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
| | | | - Aïda Homs
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
| | - Javier Santoyo
- Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), C/Albert Einstein, Cartuja Scientific and Technology Park, INSUR Builiding, Sevilla, 41092 Spain
| | - Maria Rigau
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain
| | - Gemma Aznar-Laín
- Pediatric Neurology, Hospital del Mar, Passeig Marítim 25-29, Barcelona, 08003 Spain
| | - Miguel Del Campo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain ; Servicio de Genética, Hospital Vall d'Hebron, Passeig Vall d'Hebron, 119-129, Barcelona, 08015 Spain
| | - Blanca Gener
- Genetics Service, BioCruces Health Research Institute, Hospital Universitario Cruces, Plaza de Cruces 12, Barakaldo, Bizkaia 48093 Spain
| | - Elisabeth Gabau
- Pediatrics Service, Corporació Sanitària Parc Taulí, Parc Taulí 1, Sabadell, 08208 Spain
| | - María Pilar Botella
- Pediatric Neurology, Hospital de Txagorritxu, C/José de Atxotegui s/n, Victoria-Gasteiz, 01009 Spain
| | - Armand Gutiérrez-Arumí
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
| | - Guillermo Antiñolo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain ; Medical Genome Project, Genomics and Bioinformatics Platform of Andalusia (GBPA), C/Albert Einstein, Cartuja Scientific and Technology Park, INSUR Builiding, Sevilla, 41092 Spain ; Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Avda Manuel Siurot s/n, Sevilla, 41013 Spain
| | - Luis Alberto Pérez-Jurado
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
| | - Ivon Cuscó
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, C/Doctor Aiguader 88, 422, Barcelona, 08003 Spain ; Hospital del Mar Research Institute (IMIM), C/Doctor Aiguader 88, Barcelona, 08003 Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), C/ Monforte de Lemos 3-5, Madrid, 28029 Spain
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Adegbola A, Musante L, Callewaert B, Maciel P, Hu H, Isidor B, Picker-Minh S, Le Caignec C, Delle Chiaie B, Vanakker O, Menten B, Dheedene A, Bockaert N, Roelens F, Decaestecker K, Silva J, Soares G, Lopes F, Najmabadi H, Kahrizi K, Cox GF, Angus SP, Staropoli JF, Fischer U, Suckow V, Bartsch O, Chess A, Ropers HH, Wienker TF, Hübner C, Kaindl AM, Kalscheuer VM. Redefining the MED13L syndrome. Eur J Hum Genet 2015; 23:1308-17. [PMID: 25758992 DOI: 10.1038/ejhg.2015.26] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 12/19/2014] [Accepted: 01/06/2015] [Indexed: 11/09/2022] Open
Abstract
Congenital cardiac and neurodevelopmental deficits have been recently linked to the mediator complex subunit 13-like protein MED13L, a subunit of the CDK8-associated mediator complex that functions in transcriptional regulation through DNA-binding transcription factors and RNA polymerase II. Heterozygous MED13L variants cause transposition of the great arteries and intellectual disability (ID). Here, we report eight patients with predominantly novel MED13L variants who lack such complex congenital heart malformations. Rather, they depict a syndromic form of ID characterized by facial dysmorphism, ID, speech impairment, motor developmental delay with muscular hypotonia and behavioral difficulties. We thereby define a novel syndrome and significantly broaden the clinical spectrum associated with MED13L variants. A prominent feature of the MED13L neurocognitive presentation is profound language impairment, often in combination with articulatory deficits.
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Affiliation(s)
- Abidemi Adegbola
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luciana Musante
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Patricia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bertrand Isidor
- CHU Nantes, Service de Genetique Medicale, Institut de Biologie, Nantes, France.,INSERM, UMR 957, Pathophysiology of Bone Resorption and Therapy of Primary Bone Tumours, Equipe Ligue Contre le Cancer 2012, Université de Nantes, Nantes, France
| | - Sylvie Picker-Minh
- Department of Pediatric Neurology, Charité University Medicine, Berlin, Germany.,Institute of Cell Biology and Neurobiology, Charité University Medicine, Berlin, Germany
| | - Cedric Le Caignec
- CHU Nantes, Service de Genetique Medicale, Institut de Biologie, Nantes, France.,INSERM, UMR 957, Pathophysiology of Bone Resorption and Therapy of Primary Bone Tumours, Equipe Ligue Contre le Cancer 2012, Université de Nantes, Nantes, France
| | | | - Olivier Vanakker
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Nele Bockaert
- Pediatric Neurology, Ghent University Hospital, Ghent, Belgium
| | - Filip Roelens
- Pediatrics Department, Heilig Hart Hospital, Roeselare, Belgium
| | | | - João Silva
- Institute for Molecular and Celular Biology (IBMC), Porto, Portugal
| | - Gabriela Soares
- Center for Medical Genetics Dr Jacinto Magalhães, Porto Hospital Centre, Porto, Portugal
| | - Fátima Lopes
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Hossein Najmabadi
- Genetic Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetic Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Gerald F Cox
- Division of Genetics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Steven P Angus
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - John F Staropoli
- Biogen Idec, 12 Cambridge Center, Building 6, Cambridge, MA, USA
| | - Ute Fischer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Vanessa Suckow
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Oliver Bartsch
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Andrew Chess
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Thomas F Wienker
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Christoph Hübner
- Department of Pediatric Neurology, Charité University Medicine, Berlin, Germany
| | - Angela M Kaindl
- Department of Pediatric Neurology, Charité University Medicine, Berlin, Germany.,Institute of Cell Biology and Neurobiology, Charité University Medicine, Berlin, Germany
| | - Vera M Kalscheuer
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, Germany
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45
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Novel de novo heterozygous loss-of-function variants in MED13L and further delineation of the MED13L haploinsufficiency syndrome. Eur J Hum Genet 2015; 23:1499-504. [PMID: 25712080 DOI: 10.1038/ejhg.2015.19] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 12/09/2014] [Accepted: 12/19/2014] [Indexed: 01/16/2023] Open
Abstract
MED13L haploinsufficiency has recently been described as responsible for syndromic intellectual disability. We planned a search for causative gene variants in seven subjects with intellectual disability and overlapping dysmorphic facial features such as bulbous nasal tip, short mouth and straight eyebrows. We found two de novo frameshift variants in MED13L, consisting in single-nucleotide deletion (c.3765delC) and duplication (c.607dupT). A de novo nonsense variant (c.4420A>T) in MED13L was detected in a further subject in the course of routine whole-exome sequencing. By analyzing the clinical data of our patients along with those recently described in the literature, we confirm that there is a common, recognizable phenotype associated with MED13L haploinsufficiency, which includes intellectual disability and a distinctive facial appearance. Congenital heart diseases are found in some subjects with various degree of severity. Our observation of cleft palate, ataxia, epilepsy and childhood leukemia observed in single cases broadens the known clinical spectrum. Haploinsufficiency for MED13L should be considered in the differential diagnosis of the 1p36 microdeletion syndrome, due to overlapping dysmorphic facial features in some patients. The introduction of massive parallel-sequencing techniques into clinical practice is expected to allow for detection of other causative point variants in MED13L. Analysis of genomic data in connection with deep clinical evaluation of patients could elucidate genetic heterogeneity of the MED13L haploinsufficiency phenotype.
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46
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Coutton C, Dieterich K, Satre V, Vieville G, Amblard F, David M, Cans C, Jouk PS, Devillard F. Array-CGH in children with mild intellectual disability: a population-based study. Eur J Pediatr 2015; 174:75-83. [PMID: 24985125 DOI: 10.1007/s00431-014-2367-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 01/24/2023]
Abstract
UNLABELLED Intellectual disability (ID) is characterized by limitation in intellectual function and adaptive behavior, with onset in childhood. Frequent identifiable causes of ID originate from chromosomal imbalances. During the last years, array-CGH has successfully contributed to improve the diagnostic detection rate of genetic abnormalities in patients with ID. Most array-CGH studies focused on patients with moderate or severe intellectual disability. Studies on genetic etiology in children with mild intellectual disability (ID) are very rare. We performed array-CGH analysis in 66 children with mild intellectual disability assessed in a population-based study and for whom no genetic etiology was identified. We found one or more copy number variations (CNVs) in 20 out of 66 (~30 %) patients with a mild ID. In eight of them (~12 %), the CNVs were certainly responsible for the phenotype and in six they were potentially pathogenic for ID. Altogether, array-CGH helped to determine the etiology of ID in 14 patients (~21 %). CONCLUSION Our results underscore the clinical relevance of array-CGH to investigate the etiology of isolated idiopathic mild ID in patients or associated with even subtle dysmorphic features or congenital malformations.
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Affiliation(s)
- Charles Coutton
- Laboratoire de Génétique Chromosomique, Département de Génétique et Procréation, Hôpital Couple Enfant, CHU Grenoble, 38700, Grenoble, France,
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47
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Villafañe J, Lantin-Hermoso MR, Bhatt AB, Tweddell JS, Geva T, Nathan M, Elliott MJ, Vetter VL, Paridon SM, Kochilas L, Jenkins KJ, Beekman RH, Wernovsky G, Towbin JA. D-transposition of the great arteries: the current era of the arterial switch operation. J Am Coll Cardiol 2014; 64:498-511. [PMID: 25082585 DOI: 10.1016/j.jacc.2014.06.1150] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 01/25/2023]
Abstract
This paper aims to update clinicians on "hot topics" in the management of patients with D-loop transposition of the great arteries (D-TGA) in the current surgical era. The arterial switch operation (ASO) has replaced atrial switch procedures for D-TGA, and 90% of patients now reach adulthood. The Adult Congenital and Pediatric Cardiology Council of the American College of Cardiology assembled a team of experts to summarize current knowledge on genetics, pre-natal diagnosis, surgical timing, balloon atrial septostomy, prostaglandin E1 therapy, intraoperative techniques, imaging, coronary obstruction, arrhythmias, sudden death, neoaortic regurgitation and dilation, neurodevelopmental (ND) issues, and lifelong care of D-TGA patients. In simple D-TGA: 1) familial recurrence risk is low; 2) children diagnosed pre-natally have improved cognitive skills compared with those diagnosed post-natally; 3) echocardiography helps to identify risk factors; 4) routine use of BAS and prostaglandin E1 may not be indicated in all cases; 5) early ASO improves outcomes and reduces costs with a low mortality; 6) single or intramural coronary arteries remain risk factors; 7) post-ASO arrhythmias and cardiac dysfunction should raise suspicion of coronary insufficiency; 8) coronary insufficiency and arrhythmias are rare but are associated with sudden death; 9) early- and late-onset ND abnormalities are common; 10) aortic regurgitation and aortic root dilation are well tolerated; and 11) the aging ASO patient may benefit from "exercise-prescription" rather than restriction. Significant strides have been made in understanding risk factors for cardiac, ND, and other important clinical outcomes after ASO.
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Affiliation(s)
- Juan Villafañe
- Department of Pediatrics (Cardiology), University of Kentucky, Lexington, Kentucky.
| | | | - Ami B Bhatt
- Adult Congenital Heart Disease Program, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - James S Tweddell
- Cardiothoracic Surgery, Children's Hospital of Wisconsin, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Tal Geva
- Department of Cardiology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Meena Nathan
- Department of Cardiac Surgery, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Martin J Elliott
- Department of Pediatric Cardiothoracic Surgery, The Great Ormond Street Hospital for Children, NHS Foundation Trust, London, United Kingdom
| | - Victoria L Vetter
- Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Stephen M Paridon
- Department of Exercise Physiology, Perlman School of Medicine, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania
| | - Lazaros Kochilas
- University of Minnesota Children's Hospital, Minneapolis, Minnesota
| | - Kathy J Jenkins
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Robert H Beekman
- Division of Cardiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Gil Wernovsky
- The Heart Program, Miami Children's Hospital, Florida International University Herbert Wertheim College of Medicine, Miami, Florida
| | - Jeffrey A Towbin
- The Heart Institute, Division of Cardiology, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio
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48
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Hamdan FF, Srour M, Capo-Chichi JM, Daoud H, Nassif C, Patry L, Massicotte C, Ambalavanan A, Spiegelman D, Diallo O, Henrion E, Dionne-Laporte A, Fougerat A, Pshezhetsky AV, Venkateswaran S, Rouleau GA, Michaud JL. De novo mutations in moderate or severe intellectual disability. PLoS Genet 2014; 10:e1004772. [PMID: 25356899 PMCID: PMC4214635 DOI: 10.1371/journal.pgen.1004772] [Citation(s) in RCA: 307] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 09/22/2014] [Indexed: 01/09/2023] Open
Abstract
Genetics is believed to have an important role in intellectual disability (ID). Recent studies have emphasized the involvement of de novo mutations (DNMs) in ID but the extent to which they contribute to its pathogenesis and the identity of the corresponding genes remain largely unknown. Here, we report a screen for DNMs in subjects with moderate or severe ID. We sequenced the exomes of 41 probands and their parents, and confirmed 81 DNMs affecting the coding sequence or consensus splice sites (1.98 DNMs/proband). We observed a significant excess of de novo single nucleotide substitutions and loss-of-function mutations in these cases compared to control subjects, suggesting that at least a subset of these variations are pathogenic. A total of 12 likely pathogenic DNMs were identified in genes previously associated with ID (ARID1B, CHD2, FOXG1, GABRB3, GATAD2B, GRIN2B, MBD5, MED13L, SETBP1, TBR1, TCF4, WDR45), resulting in a diagnostic yield of ∼29%. We also identified 12 possibly pathogenic DNMs in genes (HNRNPU, WAC, RYR2, SET, EGR1, MYH10, EIF2C1, COL4A3BP, CHMP2A, PPP1CB, VPS4A, PPP2R2B) that have not previously been causally linked to ID. Interestingly, no case was explained by inherited mutations. Protein network analysis indicated that the products of many of these known and candidate genes interact with each other or with products of other ID-associated genes further supporting their involvement in ID. We conclude that DNMs represent a major cause of moderate or severe ID.
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Affiliation(s)
| | - Myriam Srour
- CHU Sainte-Justine Research Center, Montreal, Canada
- Division of Pediatric Neurology, Montreal Children's Hospital, Montreal, Canada
| | | | - Hussein Daoud
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | | | - Lysanne Patry
- CHU Sainte-Justine Research Center, Montreal, Canada
| | | | | | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Ousmane Diallo
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Edouard Henrion
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | | | - Anne Fougerat
- CHU Sainte-Justine Research Center, Montreal, Canada
| | | | | | - Guy A. Rouleau
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | - Jacques L. Michaud
- CHU Sainte-Justine Research Center, Montreal, Canada
- Department of Pediatrics and Department of Neurosciences, University of Montreal, Montreal, Canada
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49
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Redin C, Gérard B, Lauer J, Herenger Y, Muller J, Quartier A, Masurel-Paulet A, Willems M, Lesca G, El-Chehadeh S, Le Gras S, Vicaire S, Philipps M, Dumas M, Geoffroy V, Feger C, Haumesser N, Alembik Y, Barth M, Bonneau D, Colin E, Dollfus H, Doray B, Delrue MA, Drouin-Garraud V, Flori E, Fradin M, Francannet C, Goldenberg A, Lumbroso S, Mathieu-Dramard M, Martin-Coignard D, Lacombe D, Morin G, Polge A, Sukno S, Thauvin-Robinet C, Thevenon J, Doco-Fenzy M, Genevieve D, Sarda P, Edery P, Isidor B, Jost B, Olivier-Faivre L, Mandel JL, Piton A. Efficient strategy for the molecular diagnosis of intellectual disability using targeted high-throughput sequencing. J Med Genet 2014; 51:724-36. [PMID: 25167861 PMCID: PMC4215287 DOI: 10.1136/jmedgenet-2014-102554] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background Intellectual disability (ID) is characterised by an extreme genetic heterogeneity. Several hundred genes have been associated to monogenic forms of ID, considerably complicating molecular diagnostics. Trio-exome sequencing was recently proposed as a diagnostic approach, yet remains costly for a general implementation. Methods We report the alternative strategy of targeted high-throughput sequencing of 217 genes in which mutations had been reported in patients with ID or autism as the major clinical concern. We analysed 106 patients with ID of unknown aetiology following array-CGH analysis and other genetic investigations. Ninety per cent of these patients were males, and 75% sporadic cases. Results We identified 26 causative mutations: 16 in X-linked genes (ATRX, CUL4B, DMD, FMR1, HCFC1, IL1RAPL1, IQSEC2, KDM5C, MAOA, MECP2, SLC9A6, SLC16A2, PHF8) and 10 de novo in autosomal-dominant genes (DYRK1A, GRIN1, MED13L, TCF4, RAI1, SHANK3, SLC2A1, SYNGAP1). We also detected four possibly causative mutations (eg, in NLGN3) requiring further investigations. We present detailed reasoning for assigning causality for each mutation, and associated patients’ clinical information. Some genes were hit more than once in our cohort, suggesting they correspond to more frequent ID-associated conditions (KDM5C, MECP2, DYRK1A, TCF4). We highlight some unexpected genotype to phenotype correlations, with causative mutations being identified in genes associated to defined syndromes in patients deviating from the classic phenotype (DMD, TCF4, MECP2). We also bring additional supportive (HCFC1, MED13L) or unsupportive (SHROOM4, SRPX2) evidences for the implication of previous candidate genes or mutations in cognitive disorders. Conclusions With a diagnostic yield of 25% targeted sequencing appears relevant as a first intention test for the diagnosis of ID, but importantly will also contribute to a better understanding regarding the specific contribution of the many genes implicated in ID and autism.
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Affiliation(s)
- Claire Redin
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Bénédicte Gérard
- Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Julia Lauer
- Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yvan Herenger
- Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jean Muller
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Angélique Quartier
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Alice Masurel-Paulet
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Marjolaine Willems
- Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Gaétan Lesca
- Département de Génétique Médicale, Hospices Civils de Lyon, Bron, France
| | - Salima El-Chehadeh
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Stéphanie Le Gras
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Serge Vicaire
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Muriel Philipps
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Michaël Dumas
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Véronique Geoffroy
- Plateforme de Bioinformatique de Strasbourg (BIPS), IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Claire Feger
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Nicolas Haumesser
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
| | - Yves Alembik
- Département de Génétique, CHU de Hautepierre, Strasbourg, France
| | - Magalie Barth
- Départment de Biochimie et de Génétique, CHU d'Angers, Angers, France
| | - Dominique Bonneau
- Départment de Biochimie et de Génétique, CHU d'Angers, Angers, France
| | - Estelle Colin
- Départment de Biochimie et de Génétique, CHU d'Angers, Angers, France
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, INSERM U1112, Faculté de Médecine de Strasbourg, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Bérénice Doray
- Département de Génétique, CHU de Hautepierre, Strasbourg, France
| | - Marie-Ange Delrue
- CHU de Bordeaux, Génétique Médicale, Université de Bordeaux, Laboratoire MRGM, Bordeaux, France
| | | | - Elisabeth Flori
- Département de Génétique, CHU de Hautepierre, Strasbourg, France
| | - Mélanie Fradin
- Service de Génétique Médicale, Centre De Référence Anomalies du Développement, CHU de Rennes, Rennes, France
| | | | | | | | | | | | - Didier Lacombe
- CHU de Bordeaux, Génétique Médicale, Université de Bordeaux, Laboratoire MRGM, Bordeaux, France
| | - Gilles Morin
- Unité de Génétique Clinique, CHU d'Amiens, Amiens, France
| | - Anne Polge
- Laboratoire de Biochimie, CHU de Nîmes, Nîmes, France
| | - Sylvie Sukno
- Service de Neuropédiatrie, Hôpital Saint Vincent de Paul, Groupe Hospitalier de l'Institut Catholique Lillois, Faculté Libre de Médecine, Lille, France
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | | | - David Genevieve
- Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Pierre Sarda
- Département de Génétique Médicale, Centre de Référence Maladies Rares Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Patrick Edery
- Département de Génétique Médicale, Hospices Civils de Lyon, Bron, France
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - Bernard Jost
- Plateforme de Biopuces et Séquençage, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France
| | - Laurence Olivier-Faivre
- Centre de Génétique et Centre de Référence Anomalies du développement et Syndromes malformatifs, Hôpital d'Enfants, CHU de Dijon, Dijon, France
| | - Jean-Louis Mandel
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France Laboratoire de diagnostic génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Amélie Piton
- Département de Médicine translationnelle et Neurogénétique, IGBMC, CNRS UMR 7104/INSERM U964/Université de Strasbourg, Illkirch, France Chaire de Génétique Humaine, Collège de France, Illkirch, France
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Asadollahi R, Oneda B, Joset P, Azzarello-Burri S, Bartholdi D, Steindl K, Vincent M, Cobilanschi J, Sticht H, Baldinger R, Reissmann R, Sudholt I, Thiel CT, Ekici AB, Reis A, Bijlsma EK, Andrieux J, Dieux A, FitzPatrick D, Ritter S, Baumer A, Latal B, Plecko B, Jenni OG, Rauch A. The clinical significance of small copy number variants in neurodevelopmental disorders. J Med Genet 2014; 51:677-88. [PMID: 25106414 PMCID: PMC4173859 DOI: 10.1136/jmedgenet-2014-102588] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Despite abundant evidence for pathogenicity of large copy number variants (CNVs) in neurodevelopmental disorders (NDDs), the individual significance of genome-wide rare CNVs <500 kb has not been well elucidated in a clinical context. METHODS By high-resolution chromosomal microarray analysis, we investigated the clinical significance of all rare non-polymorphic exonic CNVs sizing 1-500 kb in a cohort of 714 patients with undiagnosed NDDs. RESULTS We detected 96 rare CNVs <500 kb affecting coding regions, of which 58 (60.4%) were confirmed. 6 of 14 confirmed de novo, one of two homozygous and four heterozygous inherited CNVs affected the known microdeletion regions 17q21.31, 16p11.2 and 2p21 or OMIM morbid genes (CASK, CREBBP, PAFAH1B1, SATB2; AUTS2, NRXN3, GRM8). Two further de novo CNVs affecting single genes (MED13L, CTNND2) were instrumental in delineating novel recurrent conditions. For the first time, we here report exonic deletions of CTNND2 causing low normal IQ with learning difficulties with or without autism spectrum disorder. Additionally, we discovered a homozygous out-of-frame deletion of ACOT7 associated with features comparable to the published mouse model. In total, 24.1% of the confirmed small CNVs were categorised as pathogenic or likely pathogenic (median size 130 kb), 17.2% as likely benign, 3.4% represented incidental findings and 55.2% remained unclear. CONCLUSIONS These results verify the diagnostic relevance of genome-wide rare CNVs <500 kb, which were found pathogenic in ∼2% (14/714) of cases (1.1% de novo, 0.3% homozygous, 0.6% inherited) and highlight their inherent potential for discovery of new conditions.
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Affiliation(s)
- Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | | | - Deborah Bartholdi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Marie Vincent
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Joana Cobilanschi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Regina Reissmann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Irene Sudholt
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Christian T Thiel
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Arif B Ekici
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Joris Andrieux
- Institut de Génétique Médicale, Hôpital Jeanne de Flandre, CHRU de Lille, Lille, France
| | - Anne Dieux
- Clinique de Génétique Guy Fontaine, Hôpital Jeanne de Flandre, CHRU de Lille, Lille, France
| | - David FitzPatrick
- MRC Human Genetics Unit, MRC Institute for Genetic and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Susanne Ritter
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
| | - Beatrice Latal
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Barbara Plecko
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, Switzerland
| | - Oskar G Jenni
- Child Development Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, Switzerland
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