1
|
Wei AD, Wakenight P, Zwingman TA, Bard AM, Sahai N, Willemsen MH, Schelhaas HJ, Stegmann APA, Verhoeven JS, de Man SA, Wessels MW, Kleefstra T, Shinde DN, Helbig KL, Basinger A, Wagner VF, Rodriguez-Buritica D, Bryant E, Millichap JJ, Millen KJ, Dobyns WB, Ramirez JM, Kalume FK. Human KCNQ5 de novo mutations underlie epilepsy and intellectual disability. J Neurophysiol 2022; 128:40-61. [PMID: 35583973 PMCID: PMC9236882 DOI: 10.1152/jn.00509.2021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We identified six novel de novo human KCNQ5 variants in children with motor/language delay, intellectual disability (ID), and/or epilepsy by whole exome sequencing. These variants, comprising two nonsense and four missense alterations, were functionally characterized by electrophysiology in HEK293/CHO cells, together with four previously reported KCNQ5 missense variants (Lehman A, Thouta S, Mancini GM, Naidu S, van Slegtenhorst M, McWalter K, Person R, Mwenifumbo J, Salvarinova R; CAUSES Study; EPGEN Study; Guella I, McKenzie MB, Datta A, Connolly MB, Kalkhoran SM, Poburko D, Friedman JM, Farrer MJ, Demos M, Desai S, Claydon T. Am J Hum Genet 101: 65-74, 2017). Surprisingly, all eight missense variants resulted in gain of function (GOF) due to hyperpolarized voltage dependence of activation or slowed deactivation kinetics, whereas the two nonsense variants were confirmed to be loss of function (LOF). One severe GOF allele (P369T) was tested and found to extend a dominant GOF effect to heteromeric KCNQ5/3 channels. Clinical presentations were associated with altered KCNQ5 channel gating: milder presentations with LOF or smaller GOF shifts in voltage dependence [change in voltage at half-maximal conduction (ΔV50) = ∼-15 mV] and severe presentations with larger GOF shifts in voltage dependence (ΔV50 = ∼-30 mV). To examine LOF pathogenicity, two Kcnq5 LOF mouse lines were created with CRISPR/Cas9. Both lines exhibited handling- and thermal-induced seizures and abnormal cortical EEGs consistent with epileptiform activity. Our study thus provides evidence for in vivo KCNQ5 LOF pathogenicity and strengthens the contribution of both LOF and GOF mutations to global pediatric neurological impairment, including ID/epilepsy.NEW & NOTEWORTHY Six novel de novo human KCNQ5 variants were identified from children with neurodevelopmental delay, intellectual disability, and/or epilepsy. Expression of these variants along with four previously reported KCNQ5 variants from a similar cohort revealed GOF potassium channels, negatively shifted in V50 of activation and/or delayed deactivation kinetics. GOF is extended to KCNQ5/3 heteromeric channels, making these the predominant channels affected in heterozygous de novo patients. Kcnq5 LOF mice exhibited seizures, consistent with in vivo pathogenicity.
Collapse
Affiliation(s)
- Aguan D Wei
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - Paul Wakenight
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - Theresa A Zwingman
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - Angela M Bard
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - Nikhil Sahai
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington
| | - Marjolein H Willemsen
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Helenius J Schelhaas
- Department of Neurology, Academic Centre for Epileptology Kempenhaeghe, Heeze, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Judith S Verhoeven
- Department of Neurology, Academic Centre for Epileptology Kempenhaeghe, Heeze, The Netherlands
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands.,Department of Human Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Marja W Wessels
- Department of Human Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Katherine L Helbig
- Ambry Genetics, Aliso Viejo, California.,Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alice Basinger
- Medical Genetics, Cook Children's Hospital, Fort Worth, Texas
| | - Victoria F Wagner
- Department of Pediatrics, University of Texas Health Science Center, Houston, Texas
| | | | - Emily Bryant
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - John J Millichap
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois.,Epilepsy Center, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington.,Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Jan-Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington
| | - Franck K Kalume
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington.,Department of Neurological Surgery, University of Washington School of Medicine, Seattle, Washington
| |
Collapse
|
2
|
Towne MC, Rossi M, Wayburn B, Huang JM, Radtke K, Alcaraz W, Farwell Hagman KD, Shinde DN. Diagnostic testing laboratories are valuable partners for disease gene discovery: 5-year experience with GeneMatcher. Hum Mutat 2022; 43:772-781. [PMID: 35143109 PMCID: PMC9313781 DOI: 10.1002/humu.24342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 02/01/2022] [Accepted: 02/07/2022] [Indexed: 12/01/2022]
Abstract
Although the rates of disease gene discovery have steadily increased with the expanding use of genome and exome sequencing by clinical and research laboratories, only ~16% of genes in the genome have confirmed disease associations. Here we describe our clinical laboratory's experience utilizing GeneMatcher, an online portal designed to promote disease gene discovery and data sharing. Since 2016, we submitted 246 candidates from 243 unique genes to GeneMatcher, of which 111 (45%) are now clinically characterized. Submissions meeting our candidate gene‐reporting criteria based on a scoring system using patient and molecular‐weighted evidence were significantly more likely to be characterized as of October 2021 versus genes that did not meet our clinical‐reporting criteria (p = 0.025). We reported relevant findings related to these newly characterized gene–disease associations in 477 probands. In 218 (46%) instances, we issued reclassifications after an initial negative or candidate gene (uncertain) report. We coauthored 104 publications delineating gene–disease relationships, including descriptions of new associations (60%), additional supportive evidence (13%), subsequent descriptive cohorts (23%), and phenotypic expansions (4%). Clinical laboratories are pivotal for disease gene discovery efforts and can screen phenotypes based on genotype matches, contact clinicians of relevant cases, and issue proactive reclassification reports.
Collapse
Affiliation(s)
| | - Mari Rossi
- Ambry Genetics, Enterprise, Aliso Viejo, CA, USA
| | - Bess Wayburn
- Ambry Genetics, Enterprise, Aliso Viejo, CA, USA
| | | | - Kelly Radtke
- Ambry Genetics, Enterprise, Aliso Viejo, CA, USA
| | | | | | | |
Collapse
|
3
|
Radio FC, Pang K, Ciolfi A, Levy MA, Hernández-García A, Pedace L, Pantaleoni F, Liu Z, de Boer E, Jackson A, Bruselles A, McConkey H, Stellacci E, Lo Cicero S, Motta M, Carrozzo R, Dentici ML, McWalter K, Desai M, Monaghan KG, Telegrafi A, Philippe C, Vitobello A, Au M, Grand K, Sanchez-Lara PA, Baez J, Lindstrom K, Kulch P, Sebastian J, Madan-Khetarpal S, Roadhouse C, MacKenzie JJ, Monteleone B, Saunders CJ, Jean Cuevas JK, Cross L, Zhou D, Hartley T, Sawyer SL, Monteiro FP, Secches TV, Kok F, Schultz-Rogers LE, Macke EL, Morava E, Klee EW, Kemppainen J, Iascone M, Selicorni A, Tenconi R, Amor DJ, Pais L, Gallacher L, Turnpenny PD, Stals K, Ellard S, Cabet S, Lesca G, Pascal J, Steindl K, Ravid S, Weiss K, Castle AMR, Carter MT, Kalsner L, de Vries BBA, van Bon BW, Wevers MR, Pfundt R, Stegmann APA, Kerr B, Kingston HM, Chandler KE, Sheehan W, Elias AF, Shinde DN, Towne MC, Robin NH, Goodloe D, Vanderver A, Sherbini O, Bluske K, Hagelstrom RT, Zanus C, Faletra F, Musante L, Kurtz-Nelson EC, Earl RK, Anderlid BM, Morin G, van Slegtenhorst M, Diderich KEM, Brooks AS, Gribnau J, Boers RG, Finestra TR, Carter LB, Rauch A, Gasparini P, Boycott KM, Barakat TS, Graham JM, Faivre L, Banka S, Wang T, Eichler EE, Priolo M, Dallapiccola B, Vissers LELM, Sadikovic B, Scott DA, Holder JL, Tartaglia M. SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females. Am J Hum Genet 2021; 108:502-516. [PMID: 33596411 DOI: 10.1016/j.ajhg.2021.01.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023] Open
Abstract
Deletion 1p36 (del1p36) syndrome is the most common human disorder resulting from a terminal autosomal deletion. This condition is molecularly and clinically heterogeneous. Deletions involving two non-overlapping regions, known as the distal (telomeric) and proximal (centromeric) critical regions, are sufficient to cause the majority of the recurrent clinical features, although with different facial features and dysmorphisms. SPEN encodes a transcriptional repressor commonly deleted in proximal del1p36 syndrome and is located centromeric to the proximal 1p36 critical region. Here, we used clinical data from 34 individuals with truncating variants in SPEN to define a neurodevelopmental disorder presenting with features that overlap considerably with those of proximal del1p36 syndrome. The clinical profile of this disease includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females. SPEN also emerges as a relevant gene for del1p36 syndrome by co-expression analyses. Finally, we show that haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females, providing further evidence of a specific contribution of the protein to the epigenetic control of this chromosome, and a paradigm of an X chromosome-specific episignature that classifies syndromic traits. We conclude that SPEN is required for multiple developmental processes and SPEN haploinsufficiency is a major contributor to a disorder associated with deletions centromeric to the previously established 1p36 critical regions.
Collapse
Affiliation(s)
| | - Kaifang Pang
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea Ciolfi
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michael A Levy
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Andrés Hernández-García
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lucia Pedace
- Oncohaematology Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Francesca Pantaleoni
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Zhandong Liu
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elke de Boer
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Adam Jackson
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Haley McConkey
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Emilia Stellacci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Stefania Lo Cicero
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Marialetizia Motta
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Rosalba Carrozzo
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Maria Lisa Dentici
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | | | | | | | | | - Christophe Philippe
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Antonio Vitobello
- Inserm UMR 1231 GAD (Génétique des Anomalies du Développement), Université de Bourgogne, 21070 Dijon, France; UF Innovation en Diagnostic Génomique des Maladies Rares, CHU, Dijon Bourgogne, 21079 Dijon, France
| | - Margaret Au
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Katheryn Grand
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Pedro A Sanchez-Lara
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Joanne Baez
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | | | - Peggy Kulch
- Phoenix Children's Hospital, Phoenix, AZ 85016, USA
| | - Jessica Sebastian
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Suneeta Madan-Khetarpal
- Division of Medical Genetics, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | | | | | - Berrin Monteleone
- Clinical genetics, NYU Langone Long Island School of Medicine, Mineola, NY 11501, USA
| | - Carol J Saunders
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - July K Jean Cuevas
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Laura Cross
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Dihong Zhou
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO 64108, USA
| | - Taila Hartley
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Sarah L Sawyer
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | | | | | - Fernando Kok
- Mendelics Genomic Analysis, Campo Belo - São Paulo 04013-000, Brazil
| | | | - Erica L Macke
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Eva Morava
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA; Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | | | | | | | - Romano Tenconi
- Dipartimento di Pediatria, Università di Padova, 35137 Padua, Italy
| | - David J Amor
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | - Lynn Pais
- Medical and Populations Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Lyndon Gallacher
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC 3052, Australia
| | | | - Karen Stals
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sian Ellard
- Royal Devon & Exeter NHS Foundation Trust, Exeter EX2 5DW, UK
| | - Sara Cabet
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Gaetan Lesca
- Department of Genetics, Hospices Civils de Lyon, Groupement Hospitalier Est, Claude Bernard Lyon 1 University, 69002 Lyon, France
| | - Joset Pascal
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Sarit Ravid
- Pediatric Neurology Unit, Ruth Children's Hospital, Rambam Health Care Campus, Haifa 3109601, Israel
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Campus, Rappaport Faculty of Medicine, Israel Institute of Technology, Haifa 3109601, Israel
| | - Alison M R Castle
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Melissa T Carter
- Department of Genetics, CHEO, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Louisa Kalsner
- Connecticut Children's Medical Center, University of Connecticut School of Medicine, Farmington, CT 06032, USA
| | - Bert B A de Vries
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Marijke R Wevers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands
| | - Alexander P A Stegmann
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center+, 6229 HX Maastricht, the Netherlands
| | - Bronwyn Kerr
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Helen M Kingston
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Kate E Chandler
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Willow Sheehan
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | - Abdallah F Elias
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT 59601, USA
| | | | | | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Dana Goodloe
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Omar Sherbini
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Krista Bluske
- Illumina Clinical Services Laboratory, San Diego, CA 92122, USA
| | | | - Caterina Zanus
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Flavio Faletra
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | - Luciana Musante
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy
| | | | - Rachel K Earl
- Department of Psychiatry & Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Gilles Morin
- CA de Génétique Clinique & Oncogénétique, CHU Amiens-Picardie, 80054 Amiens, France
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Karin E M Diderich
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Teresa Robert Finestra
- Department of Developmental Biology, Oncode Institute, Erasmus MC, University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - Lauren B Carter
- Department of Pediatrics, Division of Medical Genetics, Levine Children's Hospital Atrium Health, Charlotte, NC 28203, USA
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Zurich, Switzerland
| | - Paolo Gasparini
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," 34137 Trieste, Italy; Department of Medicine, Surgery & Health Science, University of Trieste, 34143 Trieste, Italy
| | - Kym M Boycott
- Children's Hospital of Eastern Ontario, Ottawa, ON K1H 8L1, Canada
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, 3015 GD Rotterdam, the Netherlands
| | - John M Graham
- Division of Medical Genetics, Department of Pediatrics, Cedars Sinai Medical Center, David Geffen School of Medicine at UCLA, Los Angeles, CA 90048, USA
| | - Laurence Faivre
- Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD et Institut GIMI, 77908 Dijon, France; UMR 1231 GAD, Inserm - Université Bourgogne-Franche Comté, 77908 Dijon, France
| | - Siddharth Banka
- Division of Evolution & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, M13 9 WL Manchester, UK; Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, M13 9WL Manchester, UK
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Manuela Priolo
- UOSD Genetica Medica del Grande Ospedale Metropolitano "Bianchi Melacrino Morelli" di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, 6525 GA Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University, 6525 GA Nijmegen, the Netherlands
| | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jimmy Lloyd Holder
- Division of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Marco Tartaglia
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy.
| |
Collapse
|
4
|
Glinton KE, Hurst ACE, Bowling KM, Cristian I, Haynes D, Adstamongkonkul D, Schnappauf O, Beck DB, Brewer C, Parikh AS, Shinde DN, Donaldson A, Brautbar A, Koene S, van Haeringen A, Piton A, Capri Y, Furlan M, Gardella E, Møller RS, van de Beek I, Zuurbier L, Lakeman P, Bayat A, Martinez J, Signer R, Torring PM, Engelund MB, Gripp KW, Amlie-Wolf L, Henderson LB, Midro AT, Tarasów E, Stasiewicz-Jarocka B, Moskal-Jasinska D, Vos P, Boschann F, Stoltenburg C, Puk O, Mero IL, Lossius K, Mignot C, Keren B, Acosta Guio JC, Briceño I, Gomez A, Yang Y, Stankiewicz P. Phenotypic expansion of the BPTF-related neurodevelopmental disorder with dysmorphic facies and distal limb anomalies. Am J Med Genet A 2021; 185:1366-1378. [PMID: 33522091 PMCID: PMC8048530 DOI: 10.1002/ajmg.a.62102] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/14/2022]
Abstract
Neurodevelopmental disorder with dysmorphic facies and distal limb anomalies (NEDDFL), defined primarily by developmental delay/intellectual disability, speech delay, postnatal microcephaly, and dysmorphic features, is a syndrome resulting from heterozygous variants in the dosage‐sensitive bromodomain PHD finger chromatin remodeler transcription factor BPTF gene. To date, only 11 individuals with NEDDFL due to de novo BPTF variants have been described. To expand the NEDDFL phenotypic spectrum, we describe the clinical features in 25 novel individuals with 20 distinct, clinically relevant variants in BPTF, including four individuals with inherited changes in BPTF. In addition to the previously described features, individuals in this cohort exhibited mild brain abnormalities, seizures, scoliosis, and a variety of ophthalmologic complications. These results further support the broad and multi‐faceted complications due to haploinsufficiency of BPTF.
Collapse
Affiliation(s)
- Kevin E Glinton
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Ingrid Cristian
- Division of Genetics, Arnold Palmer Hospital for Children - Orlando Health, Orlando, Florida, USA
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children - Orlando Health, Orlando, Florida, USA
| | - Dusit Adstamongkonkul
- CoxHealth, CoxHealth Pediatric Specialties, Springfield, Missouri, USA.,University of Missouri School of Medicine, Springfield Clinical Campus, Springfield, Missouri, USA
| | - Oskar Schnappauf
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Carole Brewer
- Peninsula Clinical Genetics Service, Royal Devon and Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Aditi Shah Parikh
- Center for Human Genetics, University Hospitals Cleveland Medical Center and Case Western Reserve University, Cleveland, Ohio, USA
| | - Deepali N Shinde
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Alan Donaldson
- Clinical Genetics, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Ariel Brautbar
- Medical Genetics Department, Cook Children's Hospital, Fort Worth, Texas, USA
| | - Saskia Koene
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Amélie Piton
- Unité de Génétique Moléculaire Strasbourg University Hospital, 1 place de l'Hôpital, Strasbourg Cedex, France
| | - Yline Capri
- Service de Génétique Clinique, CHU Robert Debré, Paris Cedex, France
| | | | - Elena Gardella
- Danish Epilepsy Centre, Dianalund, Denmark.,University of Southern Denmark, Odense, Denmark
| | | | - Irma van de Beek
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam, the Netherlands
| | - Linda Zuurbier
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam, the Netherlands
| | - Phillis Lakeman
- Amsterdam UMC, University of Amsterdam, Department of Clinical Genetics, Amsterdam, the Netherlands
| | - Allan Bayat
- Danish Epilepsy Centre, Dianalund, Denmark.,University of Southern Denmark, Odense, Denmark.,Department of Pediatrics, University Hospital of Hvidovre, Copenhagen, Denmark
| | - Julian Martinez
- Departments of Human Genetics, Pediatrics and Psychiatry, David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | - Rebecca Signer
- Departments of Human Genetics, Pediatrics and Psychiatry, David Geffen School of Medicine at UCLA, California, Los Angeles, USA
| | - Pernille M Torring
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | | | - Karen W Gripp
- Division of Medical Genetics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | - Louise Amlie-Wolf
- Division of Medical Genetics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware, USA
| | | | - Alina T Midro
- Department of Clinical Genetics, Medical University, Białystok, 15-089, Białystok, Poland
| | | | | | - Diana Moskal-Jasinska
- Department of Clinical Phonoaudiology and Speech Therapy, Medical University, Białystok, Białystok, Poland
| | - Paul Vos
- Department of Pediatrics, Haga Teaching Hospital, Juliana Children's Hospital, The Hague, The Netherlands
| | - Felix Boschann
- Institut für Medizinische Genetik und Humangenetik, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Corinna Stoltenburg
- Department of Neuropaediatrics, Charité - Berlin University of Medicine, Berlin, Germany
| | - Oliver Puk
- Praxis für Humangenetik Tuebingen, Department of Genetic Diagnostics, Tuebingen, Germany
| | - Inger-Lise Mero
- Department of Medical Genetics, Oslo University Hospital, Norway
| | - Kristine Lossius
- Department of Pediatric and Adolescent Medicine, Akershus University Hospital, Norway
| | - Cyril Mignot
- APHP-Sorbonne Université, Département de Génétique, Hôpital Trousseau et Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Boris Keren
- Department of Genetics, APHP, Pitié-Salpêtrière University Hospital, Paris, France
| | - Johanna C Acosta Guio
- Especialista en Genética Médica, Instituto de Ortopedia Infantil Roosevelt, Bogotá, Cundinamarca, Colombia
| | - Ignacio Briceño
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Alberto Gomez
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, DC, Colombia
| | - Yaping Yang
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA.,AiLife Diagnostics, Country Place Pkwy Suite 100, Pearland, Texas, USA
| | - Pawel Stankiewicz
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| |
Collapse
|
5
|
Mochel F, Rastetter A, Ceulemans B, Platzer K, Yang S, Shinde DN, Helbig KL, Lopergolo D, Mari F, Renieri A, Benetti E, Canitano R, Waisfisz Q, Plomp AS, Huisman SA, Wilson GN, Cathey SS, Louie RJ, Gaudio DD, Waggoner D, Kacker S, Nugent KM, Roeder ER, Bruel AL, Thevenon J, Ehmke N, Horn D, Holtgrewe M, Kaiser FJ, Kamphausen SB, Abou Jamra R, Weckhuysen S, Dalle C, Depienne C. Variants in the SK2 channel gene (KCNN2) lead to dominant neurodevelopmental movement disorders. Brain 2020; 143:3564-3573. [PMID: 33242881 DOI: 10.1093/brain/awaa346] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/17/2020] [Accepted: 09/08/2020] [Indexed: 11/14/2022] Open
Abstract
KCNN2 encodes the small conductance calcium-activated potassium channel 2 (SK2). Rodent models with spontaneous Kcnn2 mutations show abnormal gait and locomotor activity, tremor and memory deficits, but human disorders related to KCNN2 variants are largely unknown. Using exome sequencing, we identified a de novo KCNN2 frameshift deletion in a patient with learning disabilities, cerebellar ataxia and white matter abnormalities on brain MRI. This discovery prompted us to collect data from nine additional patients with de novo KCNN2 variants (one nonsense, one splice site, six missense variants and one in-frame deletion) and one family with a missense variant inherited from the affected mother. We investigated the functional impact of six selected variants on SK2 channel function using the patch-clamp technique. All variants tested but one, which was reclassified to uncertain significance, led to a loss-of-function of SK2 channels. Patients with KCNN2 variants had motor and language developmental delay, intellectual disability often associated with early-onset movement disorders comprising cerebellar ataxia and/or extrapyramidal symptoms. Altogether, our findings provide evidence that heterozygous variants, likely causing a haploinsufficiency of the KCNN2 gene, lead to novel autosomal dominant neurodevelopmental movement disorders mirroring phenotypes previously described in rodents.
Collapse
Affiliation(s)
- Fanny Mochel
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France.,AP-HP, Hôpital Pitié-Salpêtrière, Département de Génétique and Centre de Référence Neurométabolique Adulte, F-75013, Paris, France
| | - Agnès Rastetter
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France
| | - Berten Ceulemans
- Division of Paediatric Neurology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Deepali N Shinde
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Diego Lopergolo
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Francesca Mari
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Alessandra Renieri
- Medical Genetics, University of Siena, Siena, Italy.,Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - Elisa Benetti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Roberto Canitano
- Division of Child and Adolescent Neuropsychiatry, University Hospital of Siena, Siena, Italy
| | - Quinten Waisfisz
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sylvia A Huisman
- Department of Pediatrics, Amsterdam UMC, Amsterdam, The Netherlands.,Prinsenstichting, Purmerend, The Netherlands
| | - Golder N Wilson
- Department of Pediatrics, Texas Tech University Health Science Center, Lubbock, Texas, USA
| | - Sara S Cathey
- Greenwood Genetic Center, Greenwood, South Carolina, 29646, USA
| | - Raymond J Louie
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Daniela Del Gaudio
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Darrel Waggoner
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Shawn Kacker
- Department of Pediatrics, Section of Child Neurology, University of Chicago, Chicago, IL, 60637, USA
| | - Kimberly M Nugent
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Elizabeth R Roeder
- Department of Pediatrics, Baylor College of Medicine, San Antonio, TX, 78207, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ange-Line Bruel
- UMR1231 GAD, Inserm - Université Bourgogne-Franche Comté, Dijon, France.,Centre de référence maladies rares 'déficiences intellectuelles de causes rares', Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Julien Thevenon
- Service de Génétique, Génomique, et Procréation, Centre Hospitalier Universitaire Grenoble Alpes, 38700 La Tronche, France.,INSERM 1209, CNRS UMR 5309, Institute for Advanced Biosciences, Université Grenoble Alpes, 38706 Grenoble, France
| | - Nadja Ehmke
- Institute for Human Genetics and Medical Genetics, Charité - Universitaetsmedizin Berlin, Berlin, Germany
| | - Denise Horn
- Institute for Human Genetics and Medical Genetics, Charité - Universitaetsmedizin Berlin, Berlin, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics - CUBI, Berlin Institute of Health (BIH), Berlin, Germany
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany
| | | | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Sarah Weckhuysen
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium.,Translational Neurosciences, Faculty of Medicine and Health Science, University of Antwerp, Antwerp, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Carine Dalle
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France
| | - Christel Depienne
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, F-75013 Paris, France.,Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Hufelandstraße 55, 45147 Essen, Germany
| |
Collapse
|
6
|
Drivas TG, Li D, Nair D, Alaimo JT, Alders M, Altmüller J, Barakat TS, Bebin EM, Bertsch NL, Blackburn PR, Blesson A, Bouman AM, Brockmann K, Brunelle P, Burmeister M, Cooper GM, Denecke J, Dieux-Coëslier A, Dubbs H, Ferrer A, Gal D, Bartik LE, Gunderson LB, Hasadsri L, Jain M, Karimov C, Keena B, Klee EW, Kloth K, Lace B, Macchiaiolo M, Marcadier JL, Milunsky JM, Napier MP, Ortiz-Gonzalez XR, Pichurin PN, Pinner J, Powis Z, Prasad C, Radio FC, Rasmussen KJ, Renaud DL, Rush ET, Saunders C, Selcen D, Seman AR, Shinde DN, Smith ED, Smol T, Snijders Blok L, Stoler JM, Tang S, Tartaglia M, Thompson ML, van de Kamp JM, Wang J, Weise D, Weiss K, Woitschach R, Wollnik B, Yan H, Zackai EH, Zampino G, Campeau P, Bhoj E. A second cohort of CHD3 patients expands the molecular mechanisms known to cause Snijders Blok-Campeau syndrome. Eur J Hum Genet 2020; 28:1422-1431. [PMID: 32483341 PMCID: PMC7608102 DOI: 10.1038/s41431-020-0654-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 02/27/2020] [Accepted: 04/28/2020] [Indexed: 01/18/2023] Open
Abstract
There has been one previous report of a cohort of patients with variants in Chromodomain Helicase DNA-binding 3 (CHD3), now recognized as Snijders Blok-Campeau syndrome. However, with only three previously-reported patients with variants outside the ATPase/helicase domain, it was unclear if variants outside of this domain caused a clinically similar phenotype. We have analyzed 24 new patients with CHD3 variants, including nine outside the ATPase/helicase domain. All patients were detected with unbiased molecular genetic methods. There is not a significant difference in the clinical or facial features of patients with variants in or outside this domain. These additional patients further expand the clinical and molecular data associated with CHD3 variants. Importantly we conclude that there is not a significant difference in the phenotypic features of patients with various molecular disruptions, including whole gene deletions and duplications, and missense variants outside the ATPase/helicase domain. This data will aid both clinical geneticists and molecular geneticists in the diagnosis of this emerging syndrome.
Collapse
Affiliation(s)
- Theodore G. Drivas
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Dong Li
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Divya Nair
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Joseph T. Alaimo
- grid.266756.60000 0001 2179 926XUniversity of Missouri-Kansas City, School of Medicine, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO USA
| | - Mariëlle Alders
- grid.7177.60000000084992262Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Janine Altmüller
- grid.6190.e0000 0000 8580 3777Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Tahsin Stefan Barakat
- grid.5645.2000000040459992XDepartment of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - E. Martina Bebin
- grid.265892.20000000106344187University of Alabama at Birmingham, Birmingham, AL USA
| | - Nicole L. Bertsch
- grid.66875.3a0000 0004 0459 167XDepartment of Clinical Genomics, Mayo Clinic, Rochester, MN 55905 USA
| | - Patrick R. Blackburn
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - Alyssa Blesson
- grid.240023.70000 0004 0427 667XDepartment of Bone and Osteogenesis Imperfecta, Kennedy Krieger Institute, Baltimore, MD 21205 USA
| | - Arjan M. Bouman
- grid.5645.2000000040459992XDepartment of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Knut Brockmann
- grid.411984.10000 0001 0482 5331Pediatrics and Pediatric Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Perrine Brunelle
- grid.503422.20000 0001 2242 6780Univ. Lille, EA 7364—RADEME—Maladies RAres du DEveloppement embryonnaire et du MEtabolisme, F-59000 Lille, France ,grid.410463.40000 0004 0471 8845CHU Lille, Institut de Génétique Médicale, F-59000 Lille, France
| | - Margit Burmeister
- grid.214458.e0000000086837370Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI USA ,grid.214458.e0000000086837370Departments of Computational Medicine & Bioinformatics, Psychiatry and Human Genetics, University of Michigan, Ann Arbor, MI USA
| | - Gregory M. Cooper
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jonas Denecke
- grid.13648.380000 0001 2180 3484Department of Pediatrics, University Medical Center Hamburg, Eppendorf, Germany
| | - Anne Dieux-Coëslier
- grid.503422.20000 0001 2242 6780Univ. Lille, EA 7364—RADEME—Maladies RAres du DEveloppement embryonnaire et du MEtabolisme, F-59000 Lille, France ,grid.410463.40000 0004 0471 8845CHU Lille, Institut de Génétique Médicale, F-59000 Lille, France
| | - Holly Dubbs
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Alejandro Ferrer
- grid.66875.3a0000 0004 0459 167XCenter for Individualized Medicine, Mayo Clinic, Rochester, MN USA
| | - Danna Gal
- grid.6451.60000000121102151The Ruth and Bruce Rappaport Faculty of Medicine, Technion—Israel Institute of Technology, Haifa, 3525433 Israel
| | - Lauren E. Bartik
- grid.266756.60000 0001 2179 926XUniversity of Missouri-Kansas City, School of Medicine, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Division of Clinical Genetics, Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO USA
| | - Lauren B. Gunderson
- grid.66875.3a0000 0004 0459 167XDepartment of Clinical Genomics, Mayo Clinic, Rochester, MN 55905 USA
| | - Linda Hasadsri
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - Mahim Jain
- grid.240023.70000 0004 0427 667XDepartment of Bone and Osteogenesis Imperfecta, Kennedy Krieger Institute, Baltimore, MD 21205 USA
| | - Catherine Karimov
- Department of Medical Genetics, , Children’s Hospital Los Angeles, Keck School of Medicine of University of Southern California, Los Angeles, CA 90027 USA
| | - Beth Keena
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Eric W. Klee
- grid.66875.3a0000 0004 0459 167XCenter for Individualized Medicine, Mayo Clinic, Rochester, MN USA
| | - Katja Kloth
- grid.13648.380000 0001 2180 3484Institute of Human Genetics, University Medical Center Hamburg, Eppendorf, Germany
| | - Baiba Lace
- grid.411081.d0000 0000 9471 1794Clinical Geneticist Medical Genetics Department, CHUQ-CHUL, Quebec, Canada
| | - Marina Macchiaiolo
- grid.414125.70000 0001 0727 6809Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Julien L. Marcadier
- grid.454131.6Division of Medical Genetics, Alberta Children’s Hospital, Calgary, AB Canada
| | | | - Melanie P. Napier
- grid.39381.300000 0004 1936 8884Department of Pediatrics London Health Sciences Centre and Western University, London, ON Canada
| | - Xilma R. Ortiz-Gonzalez
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, Division of Neurology, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Department of Neurology, Pereleman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Pavel N. Pichurin
- grid.66875.3a0000 0004 0459 167XDepartment of Clinical Genomics, Mayo Clinic, Rochester, MN 55905 USA
| | - Jason Pinner
- grid.414009.80000 0001 1282 788XCentre for Clinical Genetics, Sydney Children’s Hospital, Sydney, Australia
| | - Zoe Powis
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA USA
| | - Chitra Prasad
- grid.39381.300000 0004 1936 8884Department of Pediatrics London Health Sciences Centre and Western University, London, ON Canada
| | - Francesca Clementina Radio
- grid.414125.70000 0001 0727 6809Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Kristen J. Rasmussen
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA
| | - Deborah L. Renaud
- grid.66875.3a0000 0004 0459 167XDepartment of Clinical Genomics, Mayo Clinic, Rochester, MN 55905 USA
| | - Eric T. Rush
- grid.266756.60000 0001 2179 926XUniversity of Missouri-Kansas City, School of Medicine, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Division of Clinical Genetics, Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO USA ,grid.412016.00000 0001 2177 6375Division of Endocrinology, Metabolism, Osteoporosis, and Genetics, Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS USA
| | - Carol Saunders
- grid.266756.60000 0001 2179 926XUniversity of Missouri-Kansas City, School of Medicine, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, MO USA ,grid.239559.10000 0004 0415 5050Division of Clinical Genetics, Department of Pediatrics, Children’s Mercy Hospital, Kansas City, MO USA
| | - Duygu Selcen
- grid.66875.3a0000 0004 0459 167XDepartment of Neurology, Mayo Clinic, Rochester, MN 55905 USA
| | - Ann R. Seman
- grid.2515.30000 0004 0378 8438Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA USA
| | | | - Erica D. Smith
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA USA
| | - Thomas Smol
- grid.503422.20000 0001 2242 6780Univ. Lille, EA 7364—RADEME—Maladies RAres du DEveloppement embryonnaire et du MEtabolisme, F-59000 Lille, France ,grid.410463.40000 0004 0471 8845CHU Lille, Institut de Génétique Médicale, F-59000 Lille, France
| | - Lot Snijders Blok
- grid.10417.330000 0004 0444 9382Human Genetics Department, Radboud University Medical Center, Nijmegen, the Netherlands ,grid.419550.c0000 0004 0501 3839Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Joan M. Stoler
- grid.2515.30000 0004 0378 8438Division of Genetics and Genomics, Department of Medicine, Boston Children’s Hospital, Boston, MA USA
| | - Sha Tang
- grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA USA
| | - Marco Tartaglia
- grid.414125.70000 0001 0727 6809Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy
| | - Michelle L. Thompson
- grid.417691.c0000 0004 0408 3720HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Jiddeke M. van de Kamp
- grid.12380.380000 0004 1754 9227Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jingmin Wang
- grid.411472.50000 0004 1764 1621Department of Pediatrics, Peking University First Hospital, Beijing, China ,grid.11135.370000 0001 2256 9319Key Laboratory for Neuroscience, Ministry of Education/National Health and Family Planning Commission, Peking University, Beijing, China
| | - Dagmar Weise
- grid.411984.10000 0001 0482 5331Pediatrics and Pediatric Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Karin Weiss
- grid.413731.30000 0000 9950 8111The Genetics Institute, Rambam Health Care Campus, 3109601 Haifa, Israel
| | - Rixa Woitschach
- grid.13648.380000 0001 2180 3484Institute of Human Genetics, University Medical Center Hamburg, Eppendorf, Germany
| | - Bernd Wollnik
- grid.411984.10000 0001 0482 5331Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany ,grid.7450.60000 0001 2364 4210Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37073 Göttingen, Germany
| | - Huifang Yan
- grid.214458.e0000000086837370Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI USA ,grid.411472.50000 0004 1764 1621Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Elaine H. Zackai
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Giuseppe Zampino
- grid.414603.4Center for Rare Disease and Congenital Defects, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Philippe Campeau
- grid.14848.310000 0001 2292 3357Department of Pediatrics, Medical Genetics Division, University of Montreal, Montreal, Canada
| | - Elizabeth Bhoj
- grid.239552.a0000 0001 0680 8770Children’s Hospital of Philadelphia, Philadelphia, PA USA
| |
Collapse
|
7
|
Powis Z, Farwell Hagman KD, Blanco K, Au M, Graham JM, Singh K, Gallant N, Randolph LM, Towne M, Hunter J, Shinde DN, Palmaer E, Schoenfeld B, Tang S. When moments matter: Finding answers with rapid exome sequencing. Mol Genet Genomic Med 2019; 8:e1027. [PMID: 31872981 PMCID: PMC7005623 DOI: 10.1002/mgg3.1027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/03/2019] [Accepted: 09/18/2019] [Indexed: 01/17/2023] Open
Abstract
Background When time is of the essence in critical care cases, a fast molecular diagnosis is often necessary to help health care providers quickly determine best next steps for treatments, prognosis, and counseling of their patients. In this paper, we present the diagnostic rates and improved quality of life for patients undergoing clinical rapid exome sequencing. Methods The clinical histories and results of 41 patients undergoing rapid exome sequencing were retrospectively reviewed. Results Clinical rapid exome sequencing identified a definitive diagnosis in 13/41 (31.7%) and other relevant findings in 17 of the patients (41.5%). The average time to verbal report was 7 days; to written report was 11 days. Conclusions Our observations demonstrate the utility and effectiveness of rapid family‐based diagnostic exome sequencing in improving patients care.
Collapse
Affiliation(s)
- Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Margaret Au
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - John M Graham
- Department of Pediatrics, Cedars Sinai Medical Center, Los Angeles, CA, USA
| | - Kathryn Singh
- Memorial Care Health System Genetics Clinic, Long Beach, CA, USA
| | - Natalie Gallant
- Memorial Care Health System Genetics Clinic, Long Beach, CA, USA
| | - Linda M Randolph
- Division of Medical Genetics, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | | | - Sha Tang
- Ambry Genetics, Aliso Viejo, CA, USA
| |
Collapse
|
8
|
Snijders Blok L, Kleefstra T, Venselaar H, Maas S, Kroes HY, Lachmeijer AMA, van Gassen KLI, Firth HV, Tomkins S, Bodek S, Õunap K, Wojcik MH, Cunniff C, Bergstrom K, Powis Z, Tang S, Shinde DN, Au C, Iglesias AD, Izumi K, Leonard J, Abou Tayoun A, Baker SW, Tartaglia M, Niceta M, Dentici ML, Okamoto N, Miyake N, Matsumoto N, Vitobello A, Faivre L, Philippe C, Gilissen C, Wiel L, Pfundt R, Deriziotis P, Brunner HG, Fisher SE. De Novo Variants Disturbing the Transactivation Capacity of POU3F3 Cause a Characteristic Neurodevelopmental Disorder. Am J Hum Genet 2019; 105:403-412. [PMID: 31303265 PMCID: PMC6698880 DOI: 10.1016/j.ajhg.2019.06.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/07/2019] [Indexed: 01/22/2023] Open
Abstract
POU3F3, also referred to as Brain-1, is a well-known transcription factor involved in the development of the central nervous system, but it has not previously been associated with a neurodevelopmental disorder. Here, we report the identification of 19 individuals with heterozygous POU3F3 disruptions, most of which are de novo variants. All individuals had developmental delays and/or intellectual disability and impairments in speech and language skills. Thirteen individuals had characteristic low-set, prominent, and/or cupped ears. Brain abnormalities were observed in seven of eleven MRI reports. POU3F3 is an intronless gene, insensitive to nonsense-mediated decay, and 13 individuals carried protein-truncating variants. All truncating variants that we tested in cellular models led to aberrant subcellular localization of the encoded protein. Luciferase assays demonstrated negative effects of these alleles on transcriptional activation of a reporter with a FOXP2-derived binding motif. In addition to the loss-of-function variants, five individuals had missense variants that clustered at specific positions within the functional domains, and one small in-frame deletion was identified. Two missense variants showed reduced transactivation capacity in our assays, whereas one variant displayed gain-of-function effects, suggesting a distinct pathophysiological mechanism. In bioluminescence resonance energy transfer (BRET) interaction assays, all the truncated POU3F3 versions that we tested had significantly impaired dimerization capacities, whereas all missense variants showed unaffected dimerization with wild-type POU3F3. Taken together, our identification and functional cell-based analyses of pathogenic variants in POU3F3, coupled with a clinical characterization, implicate disruptions of this gene in a characteristic neurodevelopmental disorder.
Collapse
Affiliation(s)
- Lot Snijders Blok
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands; Language and Genetics Department, Max Planck Institute for Psycholinguistics, PO Box 310, 6500AH Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, PO Box 9104, 6500HE Nijmegen, the Netherlands.
| | - Tjitske Kleefstra
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, PO Box 9104, 6500HE Nijmegen, the Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands
| | - Saskia Maas
- Amsterdam University Medical Center, University of Amsterdam, Department of Clinical Genetics, Meibergdreef 9, 1105AZ Amsterdam, the Netherlands
| | - Hester Y Kroes
- Department of Genetics, University Medical Center Utrecht, PO Box 85090, 3508AB Utrecht, the Netherlands
| | - Augusta M A Lachmeijer
- Department of Genetics, University Medical Center Utrecht, PO Box 85090, 3508AB Utrecht, the Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, PO Box 85090, 3508AB Utrecht, the Netherlands
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Susan Tomkins
- Clinical Genetics Service, University Hospitals Bristol National Health Service Foundation Trust, Bristol BS2 8HW, UK
| | - Simon Bodek
- Clinical Genetics Service, University Hospitals Bristol National Health Service Foundation Trust, Bristol BS2 8HW, UK
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu 51014, Estonia; Institute of Clinical Medicine, University of Tartu, Tartu 51014, Estonia
| | - Monica H Wojcik
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Newborn Medicine, Division of Genetics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher Cunniff
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Katherine Bergstrom
- Division of Medical Genetics, Department of Pediatrics, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zoë Powis
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sha Tang
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | | | - Catherine Au
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY 10032, USA
| | - Alejandro D Iglesias
- Division of Clinical Genetics, Department of Pediatrics, New York Presbyterian Hospital, Columbia University, New York, NY 10032, USA
| | - Kosuke Izumi
- Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jacqueline Leonard
- Division of Human Genetics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ahmad Abou Tayoun
- Division of Genomic Diagnostics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Samuel W Baker
- Division of Genomic Diagnostics, the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00146 Rome, Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00146 Rome, Italy
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Bambino Gesù Children Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00146 Rome, Italy
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Antonio Vitobello
- UF Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire Dijon Bourgogne, 21000 Dijon, France; INSERM UMR1231 Génétique des Anomalies du Développement, F-21000 Dijon, France
| | - Laurence Faivre
- INSERM UMR1231 Génétique des Anomalies du Développement, F-21000 Dijon, France; Centre de Référence Maladies Rares « Anomalies du Développement et Syndrome Malformatifs » de l'Est, Centre de Génétique, Hôpital d'Enfants, Fédération Hospitalo-Universitaire Médecine TRANSLationnelle et Anomalies du Développement, Centre Hospitalier Universitaire Dijon Bourgogne, 21000 Dijon, France
| | - Christophe Philippe
- UF Innovation en Diagnostic Génomique des Maladies Rares, Centre Hospitalier Universitaire Dijon Bourgogne, 21000 Dijon, France; INSERM UMR1231 Génétique des Anomalies du Développement, F-21000 Dijon, France
| | - Christian Gilissen
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands
| | - Laurens Wiel
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands
| | - Rolph Pfundt
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands
| | - Pelagia Deriziotis
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, PO Box 310, 6500AH Nijmegen, the Netherlands
| | - Han G Brunner
- Human Genetics Department, Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, PO Box 9104, 6500HE Nijmegen, the Netherlands; Department of Clinical Genetics and GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, 6202AZ Maastricht, the Netherlands
| | - Simon E Fisher
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, PO Box 310, 6500AH Nijmegen, the Netherlands; Donders Institute for Brain, Cognition, and Behaviour, PO Box 9104, 6500HE Nijmegen, the Netherlands.
| |
Collapse
|
9
|
Helbig I, Lopez-Hernandez T, Shor O, Galer P, Ganesan S, Pendziwiat M, Rademacher A, Ellis CA, Hümpfer N, Schwarz N, Seiffert S, Peeden J, Shen J, Štěrbová K, Hammer TB, Møller RS, Shinde DN, Tang S, Smith L, Poduri A, Krause R, Benninger F, Helbig KL, Haucke V, Weber YG. A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy. Am J Hum Genet 2019; 104:1060-1072. [PMID: 31104773 PMCID: PMC6556875 DOI: 10.1016/j.ajhg.2019.04.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/29/2019] [Indexed: 11/17/2022] Open
Abstract
The developmental and epileptic encephalopathies (DEEs) are heterogeneous disorders with a strong genetic contribution, but the underlying genetic etiology remains unknown in a significant proportion of individuals. To explore whether statistical support for genetic etiologies can be generated on the basis of phenotypic features, we analyzed whole-exome sequencing data and phenotypic similarities by using Human Phenotype Ontology (HPO) in 314 individuals with DEEs. We identified a de novo c.508C>T (p.Arg170Trp) variant in AP2M1 in two individuals with a phenotypic similarity that was higher than expected by chance (p = 0.003) and a phenotype related to epilepsy with myoclonic-atonic seizures. We subsequently found the same de novo variant in two individuals with neurodevelopmental disorders and generalized epilepsy in a cohort of 2,310 individuals who underwent diagnostic whole-exome sequencing. AP2M1 encodes the μ-subunit of the adaptor protein complex 2 (AP-2), which is involved in clathrin-mediated endocytosis (CME) and synaptic vesicle recycling. Modeling of protein dynamics indicated that the p.Arg170Trp variant impairs the conformational activation and thermodynamic entropy of the AP-2 complex. Functional complementation of both the μ-subunit carrying the p.Arg170Trp variant in human cells and astrocytes derived from AP-2μ conditional knockout mice revealed a significant impairment of CME of transferrin. In contrast, stability, expression levels, membrane recruitment, and localization were not impaired, suggesting a functional alteration of the AP-2 complex as the underlying disease mechanism. We establish a recurrent pathogenic variant in AP2M1 as a cause of DEEs with distinct phenotypic features, and we implicate dysfunction of the early steps of endocytosis as a disease mechanism in epilepsy.
Collapse
Affiliation(s)
- Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | | | - Oded Shor
- Department of Neurology, Rabin Medical Center, Petach Tikva 4941492, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Peter Galer
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiva Ganesan
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manuela Pendziwiat
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Annika Rademacher
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Colin A Ellis
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nadja Hümpfer
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany
| | - Niklas Schwarz
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Simone Seiffert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Joseph Peeden
- East Tennessee Children's Hospital, University of Tennessee Department of Medicine, Knoxville, TN 37916, USA
| | - Joseph Shen
- Division of Genetics, Department of Pediatrics, University of California San Francisco, Fresno, CA 93701, USA
| | - Katalin Štěrbová
- Department of Child Neurology, Charles University 2nd Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | | | - Rikke S Møller
- Danish Epilepsy Centre Filadelfia, 4293 Dianalund, Denmark; Institute for Regional Health Services, University of Southern Denmark, 5230 Odense, Denmark
| | - Deepali N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Lacey Smith
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Felix Benninger
- Department of Neurology, Rabin Medical Center, Petach Tikva 4941492, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany
| | - Yvonne G Weber
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany; Department of Neurosurgery, University of Tübingen, 72076 Tübingen, Germany
| |
Collapse
|
10
|
Smith ED, Blanco K, Sajan SA, Hunter JM, Shinde DN, Wayburn B, Rossi M, Huang J, Stevens CA, Muss C, Alcaraz W, Hagman KDF, Tang S, Radtke K. A retrospective review of multiple findings in diagnostic exome sequencing: half are distinct and half are overlapping diagnoses. Genet Med 2019; 21:2199-2207. [PMID: 30894705 PMCID: PMC6774997 DOI: 10.1038/s41436-019-0477-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/25/2019] [Indexed: 12/31/2022] Open
Abstract
PURPOSE We evaluated clinical and genetic features enriched in patients with multiple Mendelian conditions to determine which patients are more likely to have multiple potentially relevant genetic findings (MPRF). METHODS Results of the first 7698 patients who underwent exome sequencing at Ambry Genetics were reviewed. Clinical and genetic features were examined and degree of phenotypic overlap between the genetic diagnoses was evaluated. RESULTS Among patients referred for exome sequencing, 2% had MPRF. MPRF were more common in patients from consanguineous families and patients with greater clinical complexity. The difference in average number of organ systems affected is small: 4.3 (multiple findings) vs. 3.9 (single finding) and may not be distinguished in clinic. CONCLUSION Patients with multiple genetic diagnoses had a slightly higher number of organ systems affected than patients with single genetic diagnoses, largely because the comorbid conditions affected overlapping organ systems. Exome testing may be beneficial for all cases with multiple organ systems affected. The identification of multiple relevant genetic findings in 2% of exome patients highlights the utility of a comprehensive molecular workup and updated interpretation of existing genomic data; a single definitive molecular diagnosis from analysis of a limited number of genes may not be the end of a diagnostic odyssey.
Collapse
Affiliation(s)
- Erica D Smith
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Samin A Sajan
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Bess Wayburn
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Mari Rossi
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | | | - Candace Muss
- Children's Hospital at Erlanger, Chattanooga, TN, USA
| | - Wendy Alcaraz
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Sha Tang
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Kelly Radtke
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA.
| |
Collapse
|
11
|
Kim JH, Park EY, Chitayat D, Stachura DL, Schaper J, Lindstrom K, Jewett T, Wieczorek D, Draaisma JM, Sinnema M, Hoeberigs C, Hempel M, Bachman KK, Seeley AH, Stone JK, Kong HK, Vukadin L, Richard A, Shinde DN, McWalter K, Si YC, Douglas G, Lim ST, Vissers LELM, Lemaire M, Ahn EYE. SON haploinsufficiency causes impaired pre-mRNA splicing of CAKUT genes and heterogeneous renal phenotypes. Kidney Int 2019; 95:1494-1504. [PMID: 31005274 DOI: 10.1016/j.kint.2019.01.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 12/10/2018] [Accepted: 01/04/2019] [Indexed: 10/27/2022]
Abstract
Although genetic testing is increasingly used in clinical nephrology, a large number of patients with congenital abnormalities of the kidney and urinary tract (CAKUT) remain undiagnosed with current gene panels. Therefore, careful curation of novel genetic findings is key to improving diagnostic yields. We recently described a novel intellectual disability syndrome caused by de novo heterozygous loss-of-function mutations in the gene encoding the splicing factor SON. Here, we show that many of these patients, including two previously unreported, exhibit a wide array of kidney abnormalities. Detailed phenotyping of 14 patients with SON haploinsufficiency identified kidney anomalies in 8 patients, including horseshoe kidney, unilateral renal hypoplasia, and renal cysts. Recurrent urinary tract infections, electrolyte disturbances, and hypertension were also observed in some patients. SON knockdown in kidney cell lines leads to abnormal pre-mRNA splicing, resulting in decreased expression of several established CAKUT genes. Furthermore, these molecular events were observed in patient-derived cells with SON haploinsufficiency. Taken together, our data suggest that the wide spectrum of phenotypes in patients with a pathogenic SON mutation is a consequence of impaired pre-mRNA splicing of several CAKUT genes. We propose that genetic testing panels designed to diagnose children with a kidney phenotype should include the SON gene.
Collapse
Affiliation(s)
- Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Eun Young Park
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada; The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - David L Stachura
- Department of Biological Sciences, California State University Chico, Chico, California, USA
| | - Jörg Schaper
- Institute of Diagnostic and Interventional Radiology, University of Düsseldorf, Düsseldorf, Germany
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, Arizona, USA
| | - Tamison Jewett
- Department of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Dagmar Wieczorek
- Institute of Human Genetics, University Clinic Düsseldorf, Heinrich-Heine-University, Düsseldorf, Germany; Institute of Human Genetics, University Clinic Essen, University Duisburg-Essen, Essen, Germany
| | - Jos M Draaisma
- Department of Pediatrics, Radboudumc Amalia Children's Hospital, Nijmegen, The Netherlands
| | - Margje Sinnema
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, Maastricht, The Netherlands
| | - Christianne Hoeberigs
- Department of Radiology and Nuclear Medicine, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Hyun Kyung Kong
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Lana Vukadin
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | - Alexander Richard
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA
| | | | | | | | | | - Ssang-Taek Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mathieu Lemaire
- Division of Nephrology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, SickKids Research Institute, University of Toronto, Toronto, Ontario, Canada.
| | - Eun-Young Erin Ahn
- Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA; Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.
| |
Collapse
|
12
|
Siekierska A, Stamberger H, Deconinck T, Oprescu SN, Partoens M, Zhang Y, Sourbron J, Adriaenssens E, Mullen P, Wiencek P, Hardies K, Lee JS, Giong HK, Distelmaier F, Elpeleg O, Helbig KL, Hersh J, Isikay S, Jordan E, Karaca E, Kecskes A, Lupski JR, Kovacs-Nagy R, May P, Narayanan V, Pendziwiat M, Ramsey K, Rangasamy S, Shinde DN, Spiegel R, Timmerman V, von Spiczak S, Helbig I, Weckhuysen S, Francklyn C, Antonellis A, de Witte P, De Jonghe P. Biallelic VARS variants cause developmental encephalopathy with microcephaly that is recapitulated in vars knockout zebrafish. Nat Commun 2019; 10:708. [PMID: 30755616 PMCID: PMC6372652 DOI: 10.1038/s41467-018-07953-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 10/03/2018] [Indexed: 11/09/2022] Open
Abstract
Aminoacyl tRNA synthetases (ARSs) link specific amino acids with their cognate transfer RNAs in a critical early step of protein translation. Mutations in ARSs have emerged as a cause of recessive, often complex neurological disease traits. Here we report an allelic series consisting of seven novel and two previously reported biallelic variants in valyl-tRNA synthetase (VARS) in ten patients with a developmental encephalopathy with microcephaly, often associated with early-onset epilepsy. In silico, in vitro, and yeast complementation assays demonstrate that the underlying pathomechanism of these mutations is most likely a loss of protein function. Zebrafish modeling accurately recapitulated some of the key neurological disease traits. These results provide both genetic and biological insights into neurodevelopmental disease and pave the way for further in-depth research on ARS related recessive disorders and precision therapies. tRNAs are linked with their cognate amino acid by aminoacyl tRNA synthetases (ARS). Here, the authors report a developmental encephalopathy associated with biallelic VARS variants (valyl-tRNA synthetase) that lead to loss of function, as determined by several in vitro assays and a vars knockout zebrafish model.
Collapse
Affiliation(s)
- Aleksandra Siekierska
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Hannah Stamberger
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium.,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium.,Department of Neurology, Antwerp University Hospital, Antwerp, 2650, Belgium
| | - Tine Deconinck
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium.,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium
| | - Stephanie N Oprescu
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Michèle Partoens
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Yifan Zhang
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Jo Sourbron
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Elias Adriaenssens
- Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium.,Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Patrick Mullen
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Patrick Wiencek
- Department of Biochemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Katia Hardies
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium.,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium
| | - Jeong-Soo Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,KRIBB School, University of Science and Technology, Daejeon, 34141, Republic of Korea.,Dementia DTC R&D Convergence Program, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Hoi-Khoanh Giong
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea.,KRIBB School, University of Science and Technology, Daejeon, 34141, Republic of Korea.,Dementia DTC R&D Convergence Program, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
| | - Orly Elpeleg
- Monique and Jacques Roboh Department of Genetic Research, Hadassah-Hebrew University Medical Center, Jerusalem, 01120, Israel
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Joseph Hersh
- Department of Pediatrics, Medicine, University of Louisville School of Medicine, 571S Floyd Street, Louisville, Kentucky, 40202, USA
| | - Sedat Isikay
- Department of Physiotherapy and Rehabilitation, Hasan Kalyoncu University, School of Health Sciences, Gaziantep, 27410, Turkey
| | - Elizabeth Jordan
- The Ohio State University Division of Human Genetics, Department of Internal Medicine, 460 W 12th Ave, Columbus, Ohio, 43210, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Genetics, University of Alabama, Birmingham, AL, 35233, USA
| | - Angela Kecskes
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.,Department of Pharmacology and Pharmacotherapy, University of Pecs, Pecs, 7622, Hungary
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.,Texas Children's Hospital, Houston, TX, 77030, USA
| | - Reka Kovacs-Nagy
- Institute of Human Genetics, Technische Universität München, München, 81675, Germany
| | - Patrick May
- Luxembourg Center for Systems Biomedicine, University Luxembourg, Esch-sur-Alzette, 4365, Luxembourg
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Manuela Pendziwiat
- Department of Neuropediatrics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24105, Germany
| | - Keri Ramsey
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Sampathkumar Rangasamy
- Center for Rare Childhood Disorders, The Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Deepali N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, 92656, USA
| | - Ronen Spiegel
- Pediatric Department B' Emek Medical Center, Afula, 1834111, Israel.,Rappaport School of Medicine, Technion, Haifa, 3200003, Israel
| | - Vincent Timmerman
- Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium.,Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, 2610, Belgium
| | - Sarah von Spiczak
- Department of Neuropediatrics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24105, Germany.,Northern German Epilepsy Center for Children and Adolescents, Schwentinental-Raisdorf, 24223, Germany
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Neuropediatrics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24105, Germany
| | | | | | - Sarah Weckhuysen
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium.,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium.,Department of Neurology, Antwerp University Hospital, Antwerp, 2650, Belgium
| | | | - Anthony Antonellis
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Peter de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium.
| | - Peter De Jonghe
- Neurogenetics Group, Center for Molecular Neurology, VIB, University of Antwerp, Antwerp, 2610, Belgium. .,Institute Born Bunge, University of Antwerp, Antwerp, 2610, Belgium. .,Department of Neurology, Antwerp University Hospital, Antwerp, 2650, Belgium.
| |
Collapse
|
13
|
Platzer K, Sticht H, Edwards SL, Allen W, Angione KM, Bonati MT, Brasington C, Cho MT, Demmer LA, Falik-Zaccai T, Gamble CN, Hellenbroich Y, Iascone M, Kok F, Mahida S, Mandel H, Marquardt T, McWalter K, Panis B, Pepler A, Pinz H, Ramos L, Shinde DN, Smith-Hicks C, Stegmann APA, Stöbe P, Stumpel CTRM, Wilson C, Lemke JR, Di Donato N, Miller KG, Jamra R. De Novo Variants in MAPK8IP3 Cause Intellectual Disability with Variable Brain Anomalies. Am J Hum Genet 2019; 104:203-212. [PMID: 30612693 DOI: 10.1016/j.ajhg.2018.12.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/11/2018] [Indexed: 01/28/2023] Open
Abstract
Using exome sequencing, we have identified de novo variants in MAPK8IP3 in 13 unrelated individuals presenting with an overlapping phenotype of mild to severe intellectual disability. The de novo variants comprise six missense variants, three of which are recurrent, and three truncating variants. Brain anomalies such as perisylvian polymicrogyria, cerebral or cerebellar atrophy, and hypoplasia of the corpus callosum were consistent among individuals harboring recurrent de novo missense variants. MAPK8IP3 has been shown to be involved in the retrograde axonal-transport machinery, but many of its specific functions are yet to be elucidated. Using the CRISPR-Cas9 system to target six conserved amino acid positions in Caenorhabditis elegans, we found that two of the six investigated human alterations led to a significantly elevated density of axonal lysosomes, and five variants were associated with adverse locomotion. Reverse-engineering normalized the observed adverse effects back to wild-type levels. Combining genetic, phenotypic, and functional findings, as well as the significant enrichment of de novo variants in MAPK8IP3 within our total cohort of 27,232 individuals who underwent exome sequencing, we implicate de novo variants in MAPK8IP3 as a cause of a neurodevelopmental disorder with intellectual disability and variable brain anomalies.
Collapse
Affiliation(s)
- Konrad Platzer
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig 04103, Germany.
| | - Heinrich Sticht
- Institute of Biochemistry, Emil-Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stacey L Edwards
- Genetic Models of Disease Laboratory, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - William Allen
- Department of Genetics, Fullerton Genetics Center, Asheville, NC 28803, USA
| | - Kaitlin M Angione
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Maria T Bonati
- Clinic of Medical Genetics, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy
| | - Campbell Brasington
- Department of Pediatrics, Clinical Genetics, Levine Children's Hospital at Carolina Healthcare System, Charlotte, NC 28203, USA
| | | | - Laurie A Demmer
- Department of Pediatrics, Clinical Genetics, Levine Children's Hospital at Carolina Healthcare System, Charlotte, NC 28203, USA
| | - Tzipora Falik-Zaccai
- Institute of Human Genetics, Galilee Medical Center, Nahariya 22100, Israel; The Azrieli School of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Candace N Gamble
- Department of Pediatrics, University of Texas Health Medical School, Houston, TX 77030, USA
| | - Yorck Hellenbroich
- Institute of Human Genetics, University of Lübeck, Lübeck 23562, Germany
| | - Maria Iascone
- Laboratorio di Genetica Medica, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo 24127, Italy
| | - Fernando Kok
- Mendelics Genomic Analysis, São Paulo 04013-000, Brazil
| | - Sonal Mahida
- Department of Neurology, Kennedy Krieger Institute, the Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hanna Mandel
- Institute of Human Genetics, Galilee Medical Center, Nahariya 22100, Israel
| | - Thorsten Marquardt
- Department of Pediatrics, University Hospital Münster, Münster 48149, Germany
| | | | - Bianca Panis
- Department of Pediatrics, Zuyderland Medical Center, Heerlen and Sittard 6419, the Netherlands
| | - Alexander Pepler
- CeGaT GmbH and Praxis für Humangenetik Tübingen, Tübingen 72076, Germany
| | - Hailey Pinz
- Division of Medical Genetics, Department of Pediatrics, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Luiza Ramos
- Mendelics Genomic Analysis, São Paulo 04013-000, Brazil
| | - Deepali N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Constance Smith-Hicks
- Department of Neurology, Kennedy Krieger Institute, the Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexander P A Stegmann
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht 6229, the Netherlands
| | - Petra Stöbe
- CeGaT GmbH and Praxis für Humangenetik Tübingen, Tübingen 72076, Germany
| | - Constance T R M Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht 6229, the Netherlands
| | - Carolyn Wilson
- Department of Genetics, Fullerton Genetics Center, Asheville, NC 28803, USA
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig 04103, Germany
| | - Nataliya Di Donato
- Institute for Clinical Genetics, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden 01307, Germany
| | - Kenneth G Miller
- Genetic Models of Disease Laboratory, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Rami Jamra
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig 04103, Germany
| |
Collapse
|
14
|
Sajan SA, Ganesh J, Shinde DN, Powis Z, Scarano MI, Stone J, Winter S, Tang S. Biallelic disruption of PKDCC is associated with a skeletal disorder characterised by rhizomelic shortening of extremities and dysmorphic features. J Med Genet 2018; 56:850-854. [PMID: 30478137 DOI: 10.1136/jmedgenet-2018-105639] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 10/17/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND During mouse embryonic development the protein kinase domain containing, cytoplasmic (Pkdcc) gene, also known as Vlk, is expressed in several tissues including the ventral midbrain, with particularly strong expression in branchial arches and limb buds. Homozygous Pkdcc knockout mice have dysmorphic features and shortened long bones as the most obvious morphological abnormalities. The human PKDCC gene has currently not been associated with any disorders. OBJECTIVE To use clinical diagnostic exome sequencing (DES) for providing genetic diagnoses to two apparently unrelated patients with similar skeletal abnormalities comprising rhizomelic shortening of limbs and dysmorphic features. METHODS Patient-parents trio DES was carried out and the identified candidate variants were confirmed by Sanger sequencing. RESULTS Each patient had a homozygous gene disrupting variant in PKDCC considered to explain the skeletal phenotypes shared by both. The first patient was homozygous for the nonsense variant p.(Tyr217*) (NM_1 38 370 c.651C>A) expected to result in nonsense-mediated decay of the mutant transcripts, whereas the second patient was homozygous for the splice donor variant c.639+1G>T predicted to abolish the donor splice site by three in silico splice prediction algorithms. CONCLUSIONS Biallelic gene disrupting variants in PKDCC in humans, just like in mice, cause dysmorphic features and rhizomelic shortening of limbs.
Collapse
Affiliation(s)
- Samin A Sajan
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Jaya Ganesh
- Division of Genetics, Cooper University Hospital, Camden, New Jersey, USA
| | - Deepali N Shinde
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Zöe Powis
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Maria I Scarano
- Division of Genetics, Cooper University Hospital, Camden, New Jersey, USA
| | - Jennifer Stone
- Division of Genetics, Cooper University Hospital, Camden, New Jersey, USA
| | - Susan Winter
- Valley Children's Hospital, Madera, California, USA
| | - Sha Tang
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| |
Collapse
|
15
|
Scheuerle AE, Sweed NT, Timmons CF, Smith ED, Alcaraz WA, Shinde DN. An additional case of Hennekam lymphangiectasia-lymphedema syndrome caused by loss-of-function mutation in ADAMTS3. Am J Med Genet A 2018; 176:2858-2861. [DOI: 10.1002/ajmg.a.40633] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/13/2018] [Accepted: 08/17/2018] [Indexed: 01/08/2023]
Affiliation(s)
- Angela E. Scheuerle
- Department of Pediatrics; University of Texas Southwestern Medical Center; Dallas Texas, USA
- Department of Pathology; University of Texas Southwestern Medical Center; Dallas Texas, USA
- Department of Pediatrics; Parkland Health and Hospital System; Dallas Texas, USA
| | - Nathan T. Sweed
- Department of Pathology; University of Texas Southwestern Medical Center; Dallas Texas, USA
- Department of Pathology; Parkland Health and Hospital System; Dallas Texas, USA
| | - Charles F. Timmons
- Department of Pathology; University of Texas Southwestern Medical Center; Dallas Texas, USA
- Department of Pathology; Parkland Health and Hospital System; Dallas Texas, USA
| | | | | | | |
Collapse
|
16
|
Peng Y, Shinde DN, Valencia CA, Mo JS, Rosenfeld J, Truitt Cho M, Chamberlin A, Li Z, Liu J, Gui B, Brockhage R, Basinger A, Alvarez-Leon B, Heydemann P, Magoulas PL, Lewis AM, Scaglia F, Gril S, Chong SC, Bower M, Monaghan KG, Willaert R, Plona MR, Dineen R, Milan F, Hoganson G, Powis Z, Helbig KL, Keller-Ramey J, Harris B, Anderson LC, Green T, Sukoff Rizzo SJ, Kaylor J, Chen J, Guan MX, Sellars E, Sparagana SP, Gibson JB, Reinholdt LG, Tang S, Huang T. Biallelic mutations in the ferredoxin reductase gene cause novel mitochondriopathy with optic atrophy. Hum Mol Genet 2018; 26:4937-4950. [PMID: 29040572 PMCID: PMC5886230 DOI: 10.1093/hmg/ddx377] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Accepted: 10/02/2017] [Indexed: 11/13/2022] Open
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous cofactors essential to various cellular processes, including mitochondrial respiration, DNA repair, and iron homeostasis. A steadily increasing number of disorders are being associated with disrupted biogenesis of Fe-S clusters. Here, we conducted whole-exome sequencing of patients with optic atrophy and other neurological signs of mitochondriopathy and identified 17 individuals from 13 unrelated families with recessive mutations in FDXR, encoding the mitochondrial membrane-associated flavoprotein ferrodoxin reductase required for electron transport from NADPH to cytochrome P450. In vitro enzymatic assays in patient fibroblast cells showed deficient ferredoxin NADP reductase activity and mitochondrial dysfunction evidenced by low oxygen consumption rates (OCRs), complex activities, ATP production and increased reactive oxygen species (ROS). Such defects were rescued by overexpression of wild-type FDXR. Moreover, we found that mice carrying a spontaneous mutation allelic to the most common mutation found in patients displayed progressive gait abnormalities and vision loss, in addition to biochemical defects consistent with the major clinical features of the disease. Taken together, these data provide the first demonstration that germline, hypomorphic mutations in FDXR cause a novel mitochondriopathy and optic atrophy in humans.
Collapse
Affiliation(s)
- Yanyan Peng
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | | | - C Alexander Valencia
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Jun-Song Mo
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Jill Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Adam Chamberlin
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Zhuo Li
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Jie Liu
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Baoheng Gui
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Rachel Brockhage
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Alice Basinger
- Department of Metabolic Genetics, Cook Children's Physician Network, Fort Worth, TX 76104, USA
| | - Brenda Alvarez-Leon
- Department of Metabolic Genetics, Cook Children's Physician Network, Fort Worth, TX 76104, USA
| | - Peter Heydemann
- Section of Pediatric Neurology, Rush University Medical Center, Chicago, IL 60612, USA
| | - Pilar L Magoulas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrea M Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Solange Gril
- Neuropediatric Department, Raul Carrea Institute for Neurological Research -FLENI, Montañeses 2325 (C1428AQK), Argentina
| | - Shuk Ching Chong
- Center of Inborn Errors of Metabolism, Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew Bower
- Fairview Molecular Diagnostics Laboratory Neurology Clinic, University of Minnesota Medical Center, Minneapolis, MN 55454, USA
| | | | | | - Maria-Renee Plona
- Pediatric Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Rich Dineen
- Pediatric Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | | | - George Hoganson
- Pediatric Genetics, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Zoe Powis
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | | | | | | | | | | | | | - Julie Kaylor
- Arkansas Children's Hospital, Little Rock, AR 72202, USA
| | - Jiani Chen
- University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Min-Xin Guan
- Institute of Genetics, Zhejiang University, Hangzhou, China
| | | | - Steven P Sparagana
- Pediatric Neurology, Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA
| | | | | | - Sha Tang
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| |
Collapse
|
17
|
Vögtle FN, Brändl B, Larson A, Pendziwiat M, Friederich MW, White SM, Basinger A, Kücükköse C, Muhle H, Jähn JA, Keminer O, Helbig KL, Delto CF, Myketin L, Mossmann D, Burger N, Miyake N, Burnett A, van Baalen A, Lovell MA, Matsumoto N, Walsh M, Yu HC, Shinde DN, Stephani U, Van Hove JLK, Müller FJ, Helbig I. Mutations in PMPCB Encoding the Catalytic Subunit of the Mitochondrial Presequence Protease Cause Neurodegeneration in Early Childhood. Am J Hum Genet 2018; 102:557-573. [PMID: 29576218 PMCID: PMC5985287 DOI: 10.1016/j.ajhg.2018.02.014] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 02/19/2018] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial disorders causing neurodegeneration in childhood are genetically heterogeneous, and the underlying genetic etiology remains unknown in many affected individuals. We identified biallelic variants in PMPCB in individuals of four families including one family with two affected siblings with neurodegeneration and cerebellar atrophy. PMPCB encodes the catalytic subunit of the essential mitochondrial processing protease (MPP), which is required for maturation of the majority of mitochondrial precursor proteins. Mitochondria isolated from two fibroblast cell lines and induced pluripotent stem cells derived from one affected individual and differentiated neuroepithelial stem cells showed reduced PMPCB levels and accumulation of the processing intermediate of frataxin, a sensitive substrate for MPP dysfunction. Introduction of the identified PMPCB variants into the homologous S. cerevisiae Mas1 protein resulted in a severe growth and MPP processing defect leading to the accumulation of mitochondrial precursor proteins and early impairment of the biogenesis of iron-sulfur clusters, which are indispensable for a broad range of crucial cellular functions. Analysis of biopsy materials of an affected individual revealed changes and decreased activity in iron-sulfur cluster-containing respiratory chain complexes and dysfunction of mitochondrial and cytosolic Fe-S cluster-dependent enzymes. We conclude that biallelic mutations in PMPCB cause defects in MPP proteolytic activity leading to dysregulation of iron-sulfur cluster biogenesis and triggering a complex neurological phenotype of neurodegeneration in early childhood.
Collapse
Affiliation(s)
- F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany.
| | - Björn Brändl
- Department of Psychiatry and Psychotherapy, University Hospital Schleswig Holstein, Kiel 24105, Germany
| | - Austin Larson
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Manuela Pendziwiat
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Marisa W Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Susan M White
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alice Basinger
- Cook Children's Physician Network, Department of Genetics, Fort Worth, TX 76102, USA
| | - Cansu Kücükköse
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany; Faculty of Biology, University of Freiburg, Freiburg 79104, Germany
| | - Hiltrud Muhle
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Johanna A Jähn
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Oliver Keminer
- Fraunhofer-Institut für Molekularbiologie und Angewandte Ökologie IME, ScreeningPort, Hamburg 22525, Germany
| | - Katherine L Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carolyn F Delto
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Würzburg 97080, Germany
| | - Lisa Myketin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Dirk Mossmann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Nils Burger
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Audrey Burnett
- Cook Children's Physician Network, Department of Genetics, Fort Worth, TX 76102, USA
| | - Andreas van Baalen
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Mark A Lovell
- Department of Pathology, University of Colorado, Aurora, CO 80045, USA
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama 236-0004, Japan
| | - Maie Walsh
- Adult Genetic Medicine, Royal Melbourne Hospital, Melbourne, VIC 3052, Australia
| | - Hung-Chun Yu
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Deepali N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Ulrich Stephani
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO 80045, USA
| | - Franz-Josef Müller
- Department of Psychiatry and Psychotherapy, University Hospital Schleswig Holstein, Kiel 24105, Germany; Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - Ingo Helbig
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, Kiel 24105, Germany; Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| |
Collapse
|
18
|
Peng Y, Shinde DN, Alexander Valencia C, Mo JS, Rosenfeld J, Cho MT, Chamberlin A, Li Z, Liu J, Gui B. Biallelic mutations in the ferredoxin reductase gene cause novel mitochondriopathy with optic atrophy. Hum Mol Genet 2018; 27:2224. [PMID: 29554255 PMCID: PMC5985726 DOI: 10.1093/hmg/ddy072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
19
|
Martin S, Chamberlin A, Shinde DN, Hempel M, Strom TM, Schreiber A, Johannsen J, Ousager LB, Larsen MJ, Hansen LK, Fatemi A, Cohen JS, Lemke J, Sørensen KP, Helbig KL, Lessel D, Abou Jamra R. De Novo Variants in GRIA4 Lead to Intellectual Disability with or without Seizures and Gait Abnormalities. Am J Hum Genet 2017; 101:1013-1020. [PMID: 29220673 DOI: 10.1016/j.ajhg.2017.11.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 11/13/2017] [Indexed: 01/21/2023] Open
Abstract
Using trio whole-exome sequencing, we have identified de novo heterozygous pathogenic variants in GRIA4 in five unrelated individuals with intellectual disability and other symptoms. GRIA4 encodes an AMPA receptor subunit known as GluR4, which is found on excitatory glutamatergic synapses and is important for learning and memory. Four of the variants are located in the highly conserved SYTANLAAF motif in the transmembrane protein M3, and the fifth is in an extra-cellular domain. Molecular modeling of the altered protein showed that three of the variants in the SYTANLAAF motif orient toward the center of the pore region and most likely lead to disturbance of the gating mechanism. The fourth variant in the SYTANLAAF motif most likely results in reduced permeability. The variant in the extracellular domain potentially interferes with the binding between the monomers. On the basis of clinical information and genetic results, and the fact that other subunits of the AMPA receptor have already been associated with neurodevelopmental disorders, we suggest that pathogenic de novo variants in GRIA4 lead to intellectual disability with or without seizures, gait abnormalities, problems of social behavior, and other variable features.
Collapse
|
20
|
Myers CT, Stong N, Mountier EI, Helbig KL, Freytag S, Sullivan JE, Ben Zeev B, Nissenkorn A, Tzadok M, Heimer G, Shinde DN, Rezazadeh A, Regan BM, Oliver KL, Ernst ME, Lippa NC, Mulhern MS, Ren Z, Poduri A, Andrade DM, Bird LM, Bahlo M, Berkovic SF, Lowenstein DH, Scheffer IE, Sadleir LG, Goldstein DB, Mefford HC, Heinzen EL. De Novo Mutations in PPP3CA Cause Severe Neurodevelopmental Disease with Seizures. Am J Hum Genet 2017; 101:516-524. [PMID: 28942967 DOI: 10.1016/j.ajhg.2017.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/10/2017] [Indexed: 12/30/2022] Open
Abstract
Exome sequencing has readily enabled the discovery of the genetic mutations responsible for a wide range of diseases. This success has been particularly remarkable in the severe epilepsies and other neurodevelopmental diseases for which rare, often de novo, mutations play a significant role in disease risk. Despite significant progress, the high genetic heterogeneity of these disorders often requires large sample sizes to identify a critical mass of individuals with disease-causing mutations in a single gene. By pooling genetic findings across multiple studies, we have identified six individuals with severe developmental delay (6/6), refractory seizures (5/6), and similar dysmorphic features (3/6), each harboring a de novo mutation in PPP3CA. PPP3CA encodes the alpha isoform of a subunit of calcineurin. Calcineurin encodes a calcium- and calmodulin-dependent serine/threonine protein phosphatase that plays a role in a wide range of biological processes, including being a key regulator of synaptic vesicle recycling at nerve terminals. Five individuals with de novo PPP3CA mutations were identified among 4,760 trio probands with neurodevelopmental diseases; this is highly unlikely to occur by chance (p = 1.2 × 10-8) given the size and mutability of the gene. Additionally, a sixth individual with a de novo mutation in PPP3CA was connected to this study through GeneMatcher. Based on these findings, we securely implicate PPP3CA in early-onset refractory epilepsy and further support the emerging role for synaptic dysregulation in epilepsy.
Collapse
Affiliation(s)
- Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Emily I Mountier
- Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand
| | | | - Saskia Freytag
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Joseph E Sullivan
- Department of Neurology & Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bruria Ben Zeev
- Sheba Medical Center, Ramat Gan, Israel, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Andreea Nissenkorn
- Sheba Medical Center, Ramat Gan, Israel, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Michal Tzadok
- Sheba Medical Center, Ramat Gan, Israel, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gali Heimer
- Sheba Medical Center, Ramat Gan, Israel, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | | | - Arezoo Rezazadeh
- Division of Neurology, Epilepsy Genetics Research Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Brigid M Regan
- Division of Neurology, Epilepsy Genetics Research Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Karen L Oliver
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Michelle E Ernst
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Natalie C Lippa
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Maureen S Mulhern
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Zhong Ren
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital and Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Danielle M Andrade
- Division of Neurology, Epilepsy Genetics Research Program, Toronto Western Hospital, Krembil Neuroscience Centre, University of Toronto, Toronto, ON M5T 2S8, Canada
| | - Lynne M Bird
- Department of Pediatrics, University of California, San Diego, San Diego, CA 92037, USA; Rady Children's Hospital, San Diego, CA 92037, USA
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia
| | - Daniel H Lowenstein
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC 3084, Australia; Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia; Department of Paediatrics, Royal Children's Hospital, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington 6242, New Zealand
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA.
| | - Erin L Heinzen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA.
| |
Collapse
|
21
|
Theisen BE, Rumyantseva A, Cohen JS, Alcaraz WA, Shinde DN, Tang S, Srivastava S, Pevsner J, Trifunovic A, Fatemi A. Deficiency of WARS2, encoding mitochondrial tryptophanyl tRNA synthetase, causes severe infantile onset leukoencephalopathy. Am J Med Genet A 2017; 173:2505-2510. [PMID: 28650581 DOI: 10.1002/ajmg.a.38339] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/06/2017] [Indexed: 11/11/2022]
Abstract
Pathogenic variants in the mitochondrial aminoacyl tRNA synthetases lead to deficiencies in mitochondrial protein synthesis and are associated with a broad range of clinical presentations usually with early onset and inherited in an autosomal recessive manner. Of the 19 mitochondrial aminoacyl tRNA synthetases, WARS2, encoding mitochondrial tryptophanyl tRNA synthetase, was as of late the only one that had not been associated with disease in humans. A case of a family with pathogenic variants in WARS2 that caused mainly intellectual disability, speech impairment, aggressiveness, and athetosis was recently reported. Here we substantially extend and consolidate the symptomatology of WARS2 by presenting a patient with severe infantile-onset leukoencephalopathy, profound intellectual disability, spastic quadriplegia, epilepsy, microcephaly, short stature, failure to thrive, cerebral atrophy, and periventricular white matter abnormalities. He was found by whole-exome sequencing to have compound heterozygous variants in WARS2, c.938A>T (p.K313M) and c.298_300delCTT (p.L100del). De novo synthesis of proteins inside mitochondria was reduced in the patient's fibroblasts, leading to significantly lower steady-state levels of respiratory chain subunits compared to control and resulting in lower oxygen consumption rates.
Collapse
Affiliation(s)
- Benjamin E Theisen
- Hugo W. Moser Research Institute at Kennedy Krieger, Kennedy Krieger Institute, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Anastasia Rumyantseva
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine and Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, Cologne, North-Rhine Westfalia, Germany
| | - Julie S Cohen
- Hugo W. Moser Research Institute at Kennedy Krieger, Kennedy Krieger Institute, Baltimore, Maryland
| | | | | | - Sha Tang
- AmbryGenetics, Aliso Viejo, California
| | - Siddarth Srivastava
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jonathan Pevsner
- Hugo W. Moser Research Institute at Kennedy Krieger, Kennedy Krieger Institute, Baltimore, Maryland
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Aleksandra Trifunovic
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine and Institute for Mitochondrial Diseases and Aging, Medical Faculty, University of Cologne, Cologne, North-Rhine Westfalia, Germany
| | - Ali Fatemi
- Hugo W. Moser Research Institute at Kennedy Krieger, Kennedy Krieger Institute, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
22
|
von Spiczak S, Helbig KL, Shinde DN, Huether R, Pendziwiat M, Lourenço C, Nunes ME, Sarco DP, Kaplan RA, Dlugos DJ, Kirsch H, Slavotinek A, Cilio MR, Cervenka MC, Cohen JS, McClellan R, Fatemi A, Yuen A, Sagawa Y, Littlejohn R, McLean SD, Hernandez-Hernandez L, Maher B, Møller RS, Palmer E, Lawson JA, Campbell CA, Joshi CN, Kolbe DL, Hollingsworth G, Neubauer BA, Muhle H, Stephani U, Scheffer IE, Pena SDJ, Sisodiya SM, Helbig I. DNM1 encephalopathy: A new disease of vesicle fission. Neurology 2017; 89:385-394. [PMID: 28667181 PMCID: PMC5574673 DOI: 10.1212/wnl.0000000000004152] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 04/26/2017] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To evaluate the phenotypic spectrum caused by mutations in dynamin 1 (DNM1), encoding the presynaptic protein DNM1, and to investigate possible genotype-phenotype correlations and predicted functional consequences based on structural modeling. METHODS We reviewed phenotypic data of 21 patients (7 previously published) with DNM1 mutations. We compared mutation data to known functional data and undertook biomolecular modeling to assess the effect of the mutations on protein function. RESULTS We identified 19 patients with de novo mutations in DNM1 and a sibling pair who had an inherited mutation from a mosaic parent. Seven patients (33.3%) carried the recurrent p.Arg237Trp mutation. A common phenotype emerged that included severe to profound intellectual disability and muscular hypotonia in all patients and an epilepsy characterized by infantile spasms in 16 of 21 patients, frequently evolving into Lennox-Gastaut syndrome. Two patients had profound global developmental delay without seizures. In addition, we describe a single patient with normal development before the onset of a catastrophic epilepsy, consistent with febrile infection-related epilepsy syndrome at 4 years. All mutations cluster within the GTPase or middle domains, and structural modeling and existing functional data suggest a dominant-negative effect on DMN1 function. CONCLUSIONS The phenotypic spectrum of DNM1-related encephalopathy is relatively homogeneous, in contrast to many other genetic epilepsies. Up to one-third of patients carry the recurrent p.Arg237Trp variant, which is now one of the most common recurrent variants in epileptic encephalopathies identified to date. Given the predicted dominant-negative mechanism of this mutation, this variant presents a prime target for therapeutic intervention.
Collapse
Affiliation(s)
| | | | | | - Robert Huether
- Author affiliations are provided at the end of the article
| | | | | | - Mark E Nunes
- Author affiliations are provided at the end of the article
| | - Dean P Sarco
- Author affiliations are provided at the end of the article
| | | | | | - Heidi Kirsch
- Author affiliations are provided at the end of the article
| | | | - Maria R Cilio
- Author affiliations are provided at the end of the article
| | | | - Julie S Cohen
- Author affiliations are provided at the end of the article
| | | | - Ali Fatemi
- Author affiliations are provided at the end of the article
| | - Amy Yuen
- Author affiliations are provided at the end of the article
| | - Yoshimi Sagawa
- Author affiliations are provided at the end of the article
| | | | - Scott D McLean
- Author affiliations are provided at the end of the article
| | | | - Bridget Maher
- Author affiliations are provided at the end of the article
| | - Rikke S Møller
- Author affiliations are provided at the end of the article
| | | | - John A Lawson
- Author affiliations are provided at the end of the article
| | | | | | - Diana L Kolbe
- Author affiliations are provided at the end of the article
| | | | | | - Hiltrud Muhle
- Author affiliations are provided at the end of the article
| | | | | | | | | | - Ingo Helbig
- Author affiliations are provided at the end of the article.
| | | | | |
Collapse
|
23
|
Smith ED, Radtke K, Rossi M, Shinde DN, Darabi S, El-Khechen D, Powis Z, Helbig K, Waller K, Grange DK, Tang S, Farwell Hagman KD. Classification of Genes: Standardized Clinical Validity Assessment of Gene-Disease Associations Aids Diagnostic Exome Analysis and Reclassifications. Hum Mutat 2017; 38:600-608. [PMID: 28106320 PMCID: PMC5655771 DOI: 10.1002/humu.23183] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 01/16/2017] [Indexed: 12/12/2022]
Abstract
Ascertaining a diagnosis through exome sequencing can provide potential benefits to patients, insurance companies, and the healthcare system. Yet, as diagnostic sequencing is increasingly employed, vast amounts of human genetic data are produced that need careful curation. We discuss methods for accurately assessing the clinical validity of gene-disease relationships to interpret new research findings in a clinical context and increase the diagnostic rate. The specifics of a gene-disease scoring system adapted for use in a clinical laboratory are described. In turn, clinical validity scoring of gene-disease relationships can inform exome reporting for the identification of new or the upgrade of previous, clinically relevant gene findings. Our retrospective analysis of all reclassification reports from the first 4 years of diagnostic exome sequencing showed that 78% were due to new gene-disease discoveries published in the literature. Among all exome positive/likely positive findings in characterized genes, 32% were in genetic etiologies that were discovered after 2010. Our data underscore the importance and benefits of active and up-to-date curation of a gene-disease database combined with critical clinical validity scoring and proactive reanalysis in the clinical genomics era.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA, 92656
| | | | | | - Dorothy K Grange
- Department of Pediatrics, Washington University School of Medicine, St. Louis Children's Hospital, St. Louis, MO, 63110
| | - Sha Tang
- Ambry Genetics, Aliso Viejo, CA, 92656
| | | |
Collapse
|
24
|
Cohen JS, Srivastava S, Farwell Hagman KD, Shinde DN, Huether R, Darcy D, Wallerstein R, Houge G, Berland S, Monaghan KG, Poretti A, Wilson AL, Chung WK, Fatemi A. Further evidence that de novo missense and truncating variants in ZBTB18 cause intellectual disability with variable features. Clin Genet 2016; 91:697-707. [PMID: 27598823 DOI: 10.1111/cge.12861] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/12/2016] [Accepted: 09/01/2016] [Indexed: 01/21/2023]
Abstract
Identification of rare genetic variants in patients with intellectual disability (ID) has been greatly accelerated by advances in next generation sequencing technologies. However, due to small numbers of patients, the complete phenotypic spectrum associated with pathogenic variants in single genes is still emerging. Among these genes is ZBTB18 (ZNF238), which is deleted in patients with 1q43q44 microdeletions who typically present with ID, microcephaly, corpus callosum (CC) abnormalities, and seizures. Here we provide additional evidence for haploinsufficiency or dysfunction of the ZBTB18 gene as the cause of ID in five unrelated patients with variable syndromic features who underwent whole exome sequencing revealing separate de novo pathogenic or likely pathogenic variants in ZBTB18 (two missense alterations and three truncating alterations). The neuroimaging findings in our cohort (CC hypoplasia seen in 4/4 of our patients who underwent MRI) lend further support for ZBTB18 as a critical gene for CC abnormalities. A similar phenotype of microcephaly, CC agenesis, and cerebellar vermis hypoplasia has been reported in mice with central nervous system-specific knockout of Zbtb18. Our five patients, in addition to the previously described cases of de novo ZBTB18 variants, add to knowledge about the phenotypic spectrum associated with ZBTB18 haploinsufficiency/dysfunction.
Collapse
Affiliation(s)
- J S Cohen
- Division of Neurogenetics, Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA
| | - S Srivastava
- Division of Neurogenetics, Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA.,Department of Neurology, The Johns Hopkins Hospital, Baltimore, MD, USA.,Department of Pediatrics, The Johns Hopkins Hospital, Baltimore, MD, USA
| | | | - D N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - R Huether
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA, USA
| | - D Darcy
- Silicon Valley Genetics Center, Santa Clara Valley Medical Center, San Jose, CA, USA
| | - R Wallerstein
- Hawaii Community Genetics, Kapiolani Medical Center for Women and Children, Honolulu, HI, USA
| | - G Houge
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Medical Genetics, St. Olav Hospital, Trondheim, Norway
| | - S Berland
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Medical Genetics, St. Olav Hospital, Trondheim, Norway
| | | | - A Poretti
- Section of Pediatric Neuroradiology, Division of Pediatric Radiology, Russell H. Morgan Department of Radiology and Radiological Science, The Johns Hopkins Hospital, Baltimore, MD, USA
| | - A L Wilson
- Department of Clinical Genetics, New York Presbyterian Hospital, New York, NY, USA
| | - W K Chung
- Department of Pediatrics, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA
| | - A Fatemi
- Division of Neurogenetics, Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD, USA.,Department of Neurology, The Johns Hopkins Hospital, Baltimore, MD, USA.,Department of Pediatrics, The Johns Hopkins Hospital, Baltimore, MD, USA
| |
Collapse
|
25
|
Helbig KL, Hedrich UBS, Shinde DN, Krey I, Teichmann AC, Hentschel J, Schubert J, Chamberlin AC, Huether R, Lu HM, Alcaraz WA, Tang S, Jungbluth C, Dugan SL, Vainionpää L, Karle KN, Synofzik M, Schöls L, Schüle R, Lehesjoki AE, Helbig I, Lerche H, Lemke JR. A recurrent mutation in KCNA2 as a novel cause of hereditary spastic paraplegia and ataxia. Ann Neurol 2016; 80. [PMID: 27543892 PMCID: PMC5129488 DOI: 10.1002/ana.24762] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 08/02/2016] [Accepted: 08/14/2016] [Indexed: 01/30/2023]
Abstract
The hereditary spastic paraplegias (HSPs) are heterogeneous neurodegenerative disorders with over 50 known causative genes. We identified a recurrent mutation in KCNA2 (c.881G>A, p.R294H), encoding the voltage-gated K(+) -channel, KV 1.2, in two unrelated families with HSP, intellectual disability (ID), and ataxia. Follow-up analysis of > 2,000 patients with various neurological phenotypes identified a de novo p.R294H mutation in a proband with ataxia and ID. Two-electrode voltage-clamp recordings of Xenopus laevis oocytes expressing mutant KV 1.2 channels showed loss of function with a dominant-negative effect. Our findings highlight the phenotypic spectrum of a recurrent KCNA2 mutation, implicating ion channel dysfunction as a novel HSP disease mechanism. Ann Neurol 2016.
Collapse
Affiliation(s)
| | - Ulrike B S Hedrich
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | | | - Julia Hentschel
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Julian Schubert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | | | - Robert Huether
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA
| | - Hsiao-Mei Lu
- Department of Bioinformatics, Ambry Genetics, Aliso Viejo, CA
| | - Wendy A Alcaraz
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA
| | - Chelsy Jungbluth
- Department of Medical Genetics, Children's Hospitals and Clinics of Minnesota, Minneapolis, MN
| | - Sarah L Dugan
- Department of Medical Genetics, Children's Hospitals and Clinics of Minnesota, Minneapolis, MN.,Division of Medical Genetics, University of Utah, Salt Lake City, UT
| | - Leena Vainionpää
- Department of Pediatrics and Adolescence, Oulu University Hospital, PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Kathrin N Karle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.,Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany
| | - Matthis Synofzik
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Ludger Schöls
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Rebecca Schüle
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Helsinki, Finland; Research Programs Unit, Molecular Neurology and Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Ingo Helbig
- Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts-University, Kiel, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany.
| |
Collapse
|
26
|
Farwell Hagman KD, Shinde DN, Mroske C, Smith E, Radtke K, Shahmirzadi L, El-Khechen D, Powis Z, Chao EC, Alcaraz WA, Helbig KL, Sajan SA, Rossi M, Lu HM, Huether R, Li S, Wu S, Nuñes ME, Tang S. Candidate-gene criteria for clinical reporting: diagnostic exome sequencing identifies altered candidate genes among 8% of patients with undiagnosed diseases. Genet Med 2016; 19:224-235. [PMID: 27513193 PMCID: PMC5303763 DOI: 10.1038/gim.2016.95] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/25/2016] [Indexed: 02/07/2023] Open
Abstract
Purpose: Diagnostic exome sequencing (DES) is now a commonly ordered test for individuals with undiagnosed genetic disorders. In addition to providing a diagnosis for characterized diseases, exome sequencing has the capacity to uncover novel candidate genes for disease. Methods: Family-based DES included analysis of both characterized and novel genetic etiologies. To evaluate candidate genes for disease in the clinical setting, we developed a systematic, rule-based classification schema. Results: Testing identified a candidate gene among 7.7% (72/934) of patients referred for DES; 37 (4.0%) and 35 (3.7%) of the genes received evidence scores of “candidate” and “suspected candidate,” respectively. A total of 71 independent candidate genes were reported among the 72 patients, and 38% (27/71) were subsequently corroborated in the peer-reviewed literature. This rate of corroboration increased to 51.9% (27/52) among patients whose gene was reported at least 12 months previously. Conclusions: Herein, we provide transparent, comprehensive, and standardized scoring criteria for the clinical reporting of candidate genes. These results demonstrate that DES is an integral tool for genetic diagnosis, especially for elucidating the molecular basis for both characterized and novel candidate genetic etiologies. Gene discoveries also advance the understanding of normal human biology and more common diseases. Genet Med19 2, 224–235.
Collapse
Affiliation(s)
| | - Deepali N Shinde
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Cameron Mroske
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Erica Smith
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Kelly Radtke
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Layla Shahmirzadi
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Dima El-Khechen
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Zöe Powis
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Elizabeth C Chao
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA.,Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, Irvine, California, USA
| | - Wendy A Alcaraz
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Katherine L Helbig
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Samin A Sajan
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Mari Rossi
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Hsiao-Mei Lu
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Robert Huether
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Shuwei Li
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Sitao Wu
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| | - Mark E Nuñes
- Department of Genetics, Kaiser Permanente, San Diego, California, USA
| | - Sha Tang
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California, USA
| |
Collapse
|
27
|
Mroske C, Rasmussen K, Shinde DN, Huether R, Powis Z, Lu HM, Baxter RM, McPherson E, Tang S. Germline activating MTOR mutation arising through gonadal mosaicism in two brothers with megalencephaly and neurodevelopmental abnormalities. BMC Med Genet 2015; 16:102. [PMID: 26542245 PMCID: PMC4635597 DOI: 10.1186/s12881-015-0240-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/03/2015] [Indexed: 01/06/2023]
Abstract
Background In humans, Mammalian Target of Rapamycin (MTOR) encodes a 300 kDa serine/ threonine protein kinase that is ubiquitously expressed, particularly at high levels in brain. MTOR functions as an integrator of multiple cellular processes, and in so doing either directly or indirectly regulates the phosphorylation of at least 800 proteins. While somatic MTOR mutations have been recognized in tumors for many years, and more recently in hemimegalencephaly, germline MTOR mutations have rarely been described. Case presentation We report the successful application of family-trio Diagnostic Exome Sequencing (DES) to identify the underlying molecular etiology in two brothers with multiple neurological and developmental lesions, and for whom previous testing was non-diagnostic. The affected brothers, who were 6 and 23 years of age at the time of DES, presented symptoms including but not limited to mild Autism Spectrum Disorder (ASD), megalencephaly, gross motor skill delay, cryptorchidism and bilateral iris coloboma. Importantly, we determined that each affected brother harbored the MTOR missense alteration p.E1799K (c.5395G>A). This exact variant has been previously identified in multiple independent human somatic cancer samples and has been shown to result in increased MTOR activation. Further, recent independent reports describe two unrelated families in whom p.E1799K co-segregated with megalencephaly and intellectual disability (ID); in both cases, p.E1799K was shown to have originated due to germline mosaicism. In the case of the family reported herein, the absence of p.E1799K in genomic DNA extracted from the blood of either parent suggests that this alteration most likely arose due to gonadal mosaicism. Further, the p.E1799K variant exerts its effect by a gain-of-function (GOF), autosomal dominant mechanism. Conclusion Herein, we describe the use of DES to uncover an activating MTOR missense alteration of gonadal mosaic origin that is likely to be the causative mutation in two brothers who present multiple neurological and developmental abnormalities. Our report brings the total number of families who harbor MTOR p.E1799K in association with megalencephaly and ID to three. In each case, evidence suggests that p.E1799K arose in the affected individuals due to gonadal mosaicism. Thus, MTOR p.E1799K can now be classified as a pathogenic GOF mutation that causes megalencephaly and cognitive impairment in humans. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0240-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cameron Mroske
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | | | | | - Robert Huether
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | - Zoe Powis
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | - Hsiao-Mei Lu
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | - Ruth M Baxter
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| | | | - Sha Tang
- Ambry Genetics Corporation, Aliso Viejo, CA, 92656, USA.
| |
Collapse
|
28
|
Roskos K, Hickerson AI, Lu HW, Ferguson TM, Shinde DN, Klaue Y, Niemz A. Simple system for isothermal DNA amplification coupled to lateral flow detection. PLoS One 2013; 8:e69355. [PMID: 23922706 PMCID: PMC3724848 DOI: 10.1371/journal.pone.0069355] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 06/09/2013] [Indexed: 02/04/2023] Open
Abstract
Infectious disease diagnosis in point-of-care settings can be greatly improved through integrated, automated nucleic acid testing devices. We have developed an early prototype for a low-cost system which executes isothermal DNA amplification coupled to nucleic acid lateral flow (NALF) detection in a mesofluidic cartridge attached to a portable instrument. Fluid handling inside the cartridge is facilitated through one-way passive valves, flexible pouches, and electrolysis-driven pumps, which promotes a compact and inexpensive instrument design. The closed-system disposable prevents workspace amplicon contamination. The cartridge design is based on standard scalable manufacturing techniques such as injection molding. Nucleic acid amplification occurs in a two-layer pouch that enables efficient heat transfer. We have demonstrated as proof of principle the amplification and detection of Mycobacterium tuberculosis (M.tb) genomic DNA in the cartridge, using either Loop Mediated Amplification (LAMP) or the Exponential Amplification Reaction (EXPAR), both coupled to NALF detection. We envision that a refined version of this cartridge, including upstream sample preparation coupled to amplification and detection, will enable fully-automated sample-in to answer-out infectious disease diagnosis in primary care settings of low-resource countries with high disease burden.
Collapse
Affiliation(s)
- Kristina Roskos
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Anna I. Hickerson
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Hsiang-Wei Lu
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Tanya M. Ferguson
- Claremont BioSolutions, Upland, California, United States of America
| | - Deepali N. Shinde
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Yvonne Klaue
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
| | - Angelika Niemz
- Keck Graduate Institute of Applied Life Sciences, Claremont, California, United States of America
- * E-mail:
| |
Collapse
|
29
|
Shinde DN, Elmer DP, Calabrese P, Boulanger J, Arnheim N, Tiemann-Boege I. New evidence for positive selection helps explain the paternal age effect observed in achondroplasia. Hum Mol Genet 2013; 22:4117-26. [PMID: 23740942 PMCID: PMC3781639 DOI: 10.1093/hmg/ddt260] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
There are certain de novo germline mutations associated with genetic disorders whose mutation rates per generation are orders of magnitude higher than the genome average. Moreover, these mutations occur exclusively in the male germ line and older men have a higher probability of having an affected child than younger ones, known as the paternal age effect (PAE). The classic example of a genetic disorder exhibiting a PAE is achondroplasia, caused predominantly by a single-nucleotide substitution (c.1138G>A) in FGFR3. To elucidate what mechanisms might be driving the high frequency of this mutation in the male germline, we examined the spatial distribution of the c.1138G>A substitution in a testis from an 80-year-old unaffected man. Using a technology based on bead-emulsion amplification, we were able to measure mutation frequencies in 192 individual pieces of the dissected testis with a false-positive rate lower than 2.7 × 10−6. We observed that most mutations are clustered in a few pieces with 95% of all mutations occurring in 27% of the total testis. Using computational simulations, we rejected the model proposing an elevated mutation rate per cell division at this nucleotide site. Instead, we determined that the observed mutation distribution fits a germline selection model, where mutant spermatogonial stem cells have a proliferative advantage over unmutated cells. Combined with data on several other PAE mutations, our results support the idea that the PAE, associated with a number of Mendelian disorders, may be explained primarily by a selective mechanism.
Collapse
Affiliation(s)
- Deepali N Shinde
- The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
| | | | | | | | | | | |
Collapse
|
30
|
Qian J, Ferguson TM, Shinde DN, Ramírez-Borrero AJ, Hintze A, Adami C, Niemz A. Sequence dependence of isothermal DNA amplification via EXPAR. Nucleic Acids Res 2012; 40:e87. [PMID: 22416064 PMCID: PMC3367216 DOI: 10.1093/nar/gks230] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Isothermal nucleic acid amplification is becoming increasingly important for molecular diagnostics. Therefore, new computational tools are needed to facilitate assay design. In the isothermal EXPonential Amplification Reaction (EXPAR), template sequences with similar thermodynamic characteristics perform very differently. To understand what causes this variability, we characterized the performance of 384 template sequences, and used this data to develop two computational methods to predict EXPAR template performance based on sequence: a position weight matrix approach with support vector machine classifier, and RELIEF attribute evaluation with Naïve Bayes classification. The methods identified well and poorly performing EXPAR templates with 67–70% sensitivity and 77–80% specificity. We combined these methods into a computational tool that can accelerate new assay design by ruling out likely poor performers. Furthermore, our data suggest that variability in template performance is linked to specific sequence motifs. Cytidine, a pyrimidine base, is over-represented in certain positions of well-performing templates. Guanosine and adenosine, both purine bases, are over-represented in similar regions of poorly performing templates, frequently as GA or AG dimers. Since polymerases have a higher affinity for purine oligonucleotides, polymerase binding to GA-rich regions of a single-stranded DNA template may promote non-specific amplification in EXPAR and other nucleic acid amplification reactions.
Collapse
Affiliation(s)
- Jifeng Qian
- Keck Graduate Institute, Claremont, 535 Watson Drive, Claremont, CA 91711, USA
| | | | | | | | | | | | | |
Collapse
|
31
|
Tiemann-Boege I, Curtis C, Shinde DN, Goodman DB, Tavaré S, Arnheim N. Product length, dye choice, and detection chemistry in the bead-emulsion amplification of millions of single DNA molecules in parallel. Anal Chem 2009; 81:5770-6. [PMID: 19601653 DOI: 10.1021/ac900633y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The amplification of millions of single molecules in parallel can be performed on microscopic magnetic beads that are contained in aqueous compartments of an oil-buffer emulsion. These bead-emulsion amplification (BEA) reactions result in beads that are covered by almost-identical copies derived from a single template. The post-amplification analysis is performed using different fluorophore-labeled probes. We have identified BEA reaction conditions that efficiently produce longer amplicons of up to 450 base pairs. These conditions include the use of a Titanium Taq amplification system. Second, we explored alternate fluorophores coupled to probes for post-PCR DNA analysis. We demonstrate that four different Alexa fluorophores can be used simultaneously with extremely low crosstalk. Finally, we developed an allele-specific extension chemistry that is based on Alexa dyes to query individual nucleotides of the amplified material that is both highly efficient and specific.
Collapse
|
32
|
Kelkar SD, Ray PG, Shinde DN. An epidemic of rotavirus diarrhoea in Jawhar Taluk, Thane district, Maharashtra, India, December 2000-January 2001. Epidemiol Infect 2004; 132:337-41. [PMID: 15061509 PMCID: PMC2870110 DOI: 10.1017/s0950268803001912] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
An epidemic of diarrhoea in Jawhar, a tribal area of Thane district, Maharashtra, India was investigated. Within a period of approximately 2 months 490 cases of acute diarrhoea were reported among children under 5 years of age, with a case fatality rate of 0.40%. Twenty-seven out of 39 (69.23%) rectal swabs/faecal specimens obtained from hospitalized paediatric patients up to 2 years of age from Jawhar were positive by ELISA for rotavirus. Of these, seven were in the age group of < or = 6 months. Seven ELISA-positive faecal specimens were positive for serotype G3 by RT PCR. Out of 15 serum samples collected from these patients, 12 showed the presence of rotavirus-specific IgM. Rotavirus appears to be the aetiological agent of this widespread outbreak in Jawhar, Thane district, Maharashtra state, India.
Collapse
Affiliation(s)
- S D Kelkar
- Rotavirus Department, National Institute of Virology, 20-A, Dr Ambedkar Road, Pune-411 001, India
| | | | | |
Collapse
|
33
|
Ingle ST, Shinde DN, Namdas SB. Effects of rogar and endosulfan on the metabolism of fresh water sponge (Spongilla lacustris). J Environ Biol 2003; 24:63-67. [PMID: 12974413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Spongilla lacustris were exposed to sub lethal concentrations of pesticides, rogar and endosulfan for one month period. Metabolites like carbohydrates, protein and enzymes like those that peroxidase and carbonic anhydrase were estimated in the experimental and control animals. The results show, depletion of carbohydrates while protein elevated as the days progressed. Similarly an enzyme activity found to be decreased in exposed Spongilla lacustris.
Collapse
Affiliation(s)
- S T Ingle
- School of Environmental Sciences, North Maharashtra University, Jalgaon-425 001, India
| | | | | |
Collapse
|