1
|
Stafford-Smith B, Sullivan JA, McAlister M, Walley N, Shashi V, McConkie-Rosell A. The book is just being written: The enduring journey of parents of children with emerging- ultrarare disorders. J Genet Couns 2024. [PMID: 38562053 DOI: 10.1002/jgc4.1894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/07/2023] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
Ultra rare disorders are being diagnosed at an unprecedented rate, due to genomic sequencing. These diagnoses are often a new gene association, for which little is known, and few share the diagnosis. For these diagnoses, we use the term emerging-ultrarare disorder (E-URD), defined as <100 diagnosed individuals. We contacted 20 parents of children diagnosed with an E-URD through the Duke University Research Sequencing Clinic. Seventeen completed semi-structured interviews exploring parental perspectives (7/17 had children in publications describing the phenotype; 4/17 had children in the first publication establishing a new disorder). Data were analyzed using a directed content approach informed by an empowerment framework. Parents reported a range of responses, including benefits of a diagnosis and challenges of facing the unknown, some described feeling lost and confused, while others expressed empowerment. Empowerment characteristics were hope for the future, positive emotions, engagement, and confidence/self-efficacy to connect with similar others, partner with healthcare providers, and seek new knowledge. We identified a subset of parents who proactively engaged researchers, supported research and publications, and created patient advocacy and support organizations to connect with and bolster similarly diagnosed families. Other parents reported challenges of low social support, low tolerance for uncertainty, limited knowledge about their child's disorder, as well as difficulty partnering with HCPs and connecting to an E-URD community. An overarching classification was developed to describe parental actions taken after an E-URD diagnosis: adjusting, managing, and pioneering. These classifications may help genetic counselors identify and facilitate positive steps with parents of a child with an E-URD.
Collapse
Affiliation(s)
- Bethany Stafford-Smith
- Centre for Medical Education, Cardiff University, Cardiff, UK
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, North Carolina, USA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, North Carolina, USA
| | | | - Nicole Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, North Carolina, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, North Carolina, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, North Carolina, USA
| |
Collapse
|
2
|
Xu Y, Song R, Perszyk RE, Chen W, Kim S, Park KL, Allen JP, Nocilla KA, Zhang J, XiangWei W, Tankovic A, McDaniels ED, Sheikh R, Mizu RK, Karamchandani MM, Hu C, Kusumoto H, Pecha J, Cappuccio G, Gaitanis J, Sullivan J, Shashi V, Petrovski S, Jauss RT, Lee HK, Bozarth X, Lynch DR, Helbig I, Pierson TM, Boerkoel CF, Myers SJ, Lemke JR, Benke TA, Yuan H, Traynelis SF. De novo GRIN variants in M3 helix associated with neurological disorders control channel gating of NMDA receptor. Cell Mol Life Sci 2024; 81:153. [PMID: 38538865 PMCID: PMC10973091 DOI: 10.1007/s00018-023-05069-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 05/18/2024]
Abstract
N-methyl-D-aspartate receptors (NMDARs) are members of the glutamate receptor family and participate in excitatory postsynaptic transmission throughout the central nervous system. Genetic variants in GRIN genes encoding NMDAR subunits are associated with a spectrum of neurological disorders. The M3 transmembrane helices of the NMDAR couple directly to the agonist-binding domains and form a helical bundle crossing in the closed receptors that occludes the pore. The M3 functions as a transduction element whose conformational change couples ligand binding to opening of an ion conducting pore. In this study, we report the functional consequences of 48 de novo missense variants in GRIN1, GRIN2A, and GRIN2B that alter residues in the M3 transmembrane helix. These de novo variants were identified in children with neurological and neuropsychiatric disorders including epilepsy, developmental delay, intellectual disability, hypotonia and attention deficit hyperactivity disorder. All 48 variants in M3 for which comprehensive testing was completed produce a gain-of-function (28/48) compared to loss-of-function (9/48); 11 variants had an indeterminant phenotype. This supports the idea that a key structural feature of the M3 gate exists to stabilize the closed state so that agonist binding can drive channel opening. Given that most M3 variants enhance channel gating, we assessed the potency of FDA-approved NMDAR channel blockers on these variant receptors. These data provide new insight into the structure-function relationship of the NMDAR gate, and suggest that variants within the M3 transmembrane helix produce a gain-of-function.
Collapse
Affiliation(s)
- Yuchen Xu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Neurology, The First Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, China
| | - Rui Song
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Neurology, Qilu Hospital of Shandong University, Jinan, Shandong, 250012, China
| | - Riley E Perszyk
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Wenjuan Chen
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Psychiatry, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Sukhan Kim
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Kristen L Park
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - James P Allen
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Kelsey A Nocilla
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jing Zhang
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Wenshu XiangWei
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
| | - Anel Tankovic
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ellington D McDaniels
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Rehan Sheikh
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ruth K Mizu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Manish M Karamchandani
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Chun Hu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Hirofumi Kusumoto
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Joseph Pecha
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Gerarda Cappuccio
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Via Pansini 5, 80131, Naples, Italy
- Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - John Gaitanis
- Hasbro Children's Hospital, The Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Jennifer Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC, USA
| | - Slave Petrovski
- Ce Department of Medicine, University of Melbourne, Austin Health, Melbourne, VIC, Australia
- Centre for Genomics Research, Discovery Sciences, AstraZeneca, BioPharmaceuticals R&D, Cambridge, UK
| | - Robin-Tobias Jauss
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Hyun Kyung Lee
- Provincial Medical Genetics Program, Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, B.C, V6H 3N1, Canada
| | - Xiuhua Bozarth
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Division of Pediatric Neurology, Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, WA, USA
| | - David R Lynch
- Departments of Pediatrics and Neurology, Perelman School of Medicine, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Ingo Helbig
- Division of Child Neurology, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Tyler Mark Pierson
- Department of Pediatrics and Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for the Undiagnosed Patient, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Cornelius F Boerkoel
- Provincial Medical Genetics Program, Department of Medical Genetics, University of British Columbia, Children's and Women's Health Centre of BC, Vancouver, B.C, V6H 3N1, Canada
| | - Scott J Myers
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig, Germany
| | - Timothy A Benke
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO, USA
| | - Hongjie Yuan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Stephen F Traynelis
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Center for Functional Evaluation of Rare Variants (CFERV), Emory University School of Medicine, Atlanta, GA, 30322, USA.
- Emory Neurodegenerative Disease Center, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| |
Collapse
|
3
|
Houdayer C, Phillips AM, Chabbert M, Bourreau J, Maroofian R, Houlden H, Richards K, Saadi NW, Dad'ová E, Van Bogaert P, Rupin M, Keren B, Charles P, Smol T, Riquet A, Pais L, O'Donnell-Luria A, VanNoy GE, Bayat A, Møller RS, Olofsson K, Abou Jamra R, Syrbe S, Dasouki M, Seaver LH, Sullivan JA, Shashi V, Alkuraya FS, Poss AF, Spence JE, Schnur RE, Forster IC, Mckenzie CE, Simons C, Wang M, Snell P, Kothur K, Buckley M, Roscioli T, Elserafy N, Dauriat B, Procaccio V, Henrion D, Lenaers G, Colin E, Verbeek NE, Van Gassen KL, Legendre C, Bonneau D, Reid CA, Howell KB, Ziegler A, Legros C. Mono and biallelic variants in HCN2 cause severe neurodevelopmental disorders. medRxiv 2024:2024.03.19.24303984. [PMID: 38562733 PMCID: PMC10984036 DOI: 10.1101/2024.03.19.24303984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Hyperpolarization activated Cyclic Nucleotide (HCN) gated channels are crucial for various neurophysiological functions, including learning and sensory functions, and their dysfunction are responsible for brain disorders, such as epilepsy. To date, HCN2 variants have only been associated with mild epilepsy and recently, one monoallelic missense variant has been linked to developmental and epileptic encephalopathy. Here, we expand the phenotypic spectrum of HCN2- related disorders by describing twenty-one additional individuals from fifteen unrelated families carrying HCN2 variants. Seventeen individuals had developmental delay/intellectual disability (DD/ID), two had borderline DD/ID, and one had borderline DD. Ten individuals had epilepsy with DD/ID, with median age of onset of 10 months, and one had epilepsy with normal development. Molecular diagnosis identified thirteen different pathogenic HCN2 variants, including eleven missense variants affecting highly conserved amino acids, one frameshift variant, and one in-frame deletion. Seven variants were monoallelic of which five occurred de novo, one was not maternally inherited, one was inherited from a father with mild learning disabilities, and one was of unknown inheritance. The remaining six variants were biallelic, with four homozygous and two compound heterozygous variants. Functional studies using two-electrode voltage-clamp recordings in Xenopus laevis oocytes were performed on three monoallelic variants, p.(Arg324His), p.(Ala363Val), and p.(Met374Leu), and three biallelic variants, p.(Leu377His), p.(Pro493Leu) and p.(Gly587Asp). The p.(Arg324His) variant induced a strong increase of HCN2 conductance, while p.(Ala363Val) and p.(Met374Leu) displayed dominant negative effects, leading to a partial loss of HCN2 channel function. By confocal imaging, we found that the p.(Leu377His), p.(Pro493Leu) and p.(Gly587Asp) pathogenic variants impaired membrane trafficking, resulting in a complete loss of HCN2 elicited currents in Xenopus oocytes. Structural 3D-analysis in depolarized and hyperpolarized states of HCN2 channels, revealed that the pathogenic variants p.(His205Gln), p.(Ser409Leu), p.(Arg324Cys), p.(Asn369Ser) and p.(Gly460Asp) modify molecular interactions altering HCN2 function. Taken together, our data broadens the clinical spectrum associated with HCN2 variants, and disclose that HCN2 is involved in developmental encephalopathy with or without epilepsy.
Collapse
|
4
|
Schoch K, Ruegg MSG, Fellows BJ, Cao J, Uhrig S, Einsele-Scholz S, Biskup S, Hawarden SRA, Salpietro V, Capra V, Brown CM, Accogli A, Shashi V, Bicknell LS. A second hotspot for pathogenic exon-skipping variants in CDC45. Eur J Hum Genet 2024:10.1038/s41431-024-01583-1. [PMID: 38467731 DOI: 10.1038/s41431-024-01583-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/13/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Biallelic pathogenic variants in CDC45 are associated with Meier-Gorlin syndrome with craniosynostosis (MGORS type 7), which also includes short stature and absent/hypoplastic patellae. Identified variants act through a hypomorphic loss of function mechanism, to reduce CDC45 activity and impact DNA replication initiation. In addition to missense and premature termination variants, several pathogenic synonymous variants have been identified, most of which cause increased exon skipping of exon 4, which encodes an essential part of the RecJ-orthologue's DHH domain. Here we have identified a second cohort of families segregating CDC45 variants, where patients have craniosynostosis and a reduction in height, alongside common facial dysmorphisms, including thin eyebrows, consistent with MGORS7. Skipping of exon 15 is a consequence of two different variants, including a shared synonymous variant that is enriched in individuals of East Asian ancestry, while other variants in trans are predicted to alter key intramolecular interactions in α/β domain II, or cause retention of an intron within the 3'UTR. Our cohort and functional data confirm exon skipping is a relatively common pathogenic mechanism in CDC45, and highlights the need for alternative splicing events, such as exon skipping, to be especially considered for variants initially predicted to be less likely to cause the phenotype, particularly synonymous variants.
Collapse
Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Mischa S G Ruegg
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Bridget J Fellows
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Joseph Cao
- Division of Pediatric Radiology, Department of Radiology Duke University School of Medicine, Durham, NC, USA
| | - Sabine Uhrig
- Institute of Clinical Genetics, Klinikum Stuttgart, Stuttgart, Germany
| | | | - Saskia Biskup
- Center for Human Genetics Tuebingen and CeGaT GmbH, Tuebingen, Germany
| | - Samuel R A Hawarden
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Vincenzo Salpietro
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Valeria Capra
- Genomics and Clinical Genetics, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Andrea Accogli
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
5
|
Li D, Wang Q, Bayat A, Battig MR, Zhou Y, Bosch DG, van Haaften G, Granger L, Petersen AK, Pérez-Jurado LA, Aznar-Laín G, Aneja A, Hancarova M, Bendova S, Schwarz M, Kremlikova Pourova R, Sedlacek Z, Keena BA, March ME, Hou C, O’Connor N, Bhoj EJ, Harr MH, Lemire G, Boycott KM, Towne M, Li M, Tarnopolsky M, Brady L, Parker MJ, Faghfoury H, Parsley LK, Agolini E, Dentici ML, Novelli A, Wright M, Palmquist R, Lai K, Scala M, Striano P, Iacomino M, Zara F, Cooper A, Maarup TJ, Byler M, Lebel RR, Balci TB, Louie R, Lyons M, Douglas J, Nowak C, Afenjar A, Hoyer J, Keren B, Maas SM, Motazacker MM, Martinez-Agosto JA, Rabani AM, McCormick EM, Falk MJ, Ruggiero SM, Helbig I, Møller RS, Tessarollo L, Tomassoni Ardori F, Palko ME, Hsieh TC, Krawitz PM, Ganapathi M, Gelb BD, Jobanputra V, Wilson A, Greally J, Jacquemont S, Jizi K, Bruel AL, Quelin C, Misra VK, Chick E, Romano C, Greco D, Arena A, Morleo M, Nigro V, Seyama R, Uchiyama Y, Matsumoto N, Taira R, Tashiro K, Sakai Y, Yigit G, Wollnik B, Wagner M, Kutsche B, Hurst AC, Thompson ML, Schmidt R, Randolph L, Spillmann RC, Shashi V, Higginbotham EJ, Cordeiro D, Carnevale A, Costain G, Khan T, Funalot B, Tran Mau-Them F, Fernandez Garcia Moya L, García-Miñaúr S, Osmond M, Chad L, Quercia N, Carrasco D, Li C, Sanchez-Valle A, Kelley M, Nizon M, Jensson BO, Sulem P, Stefansson K, Gorokhova S, Busa T, Rio M, Hadj Habdallah H, Lesieur-Sebellin M, Amiel J, Pingault V, Mercier S, Vincent M, Philippe C, Fatus-Fauconnier C, Friend K, Halligan RK, Biswas S, Rosser J, Shoubridge C, Corbett M, Barnett C, Gecz J, Leppig K, Slavotinek A, Marcelis C, Pfundt R, de Vries BB, van Slegtenhorst MA, Brooks AS, Cogne B, Rambaud T, Tümer Z, Zackai EH, Akizu N, Song Y, Hakonarson H. Spliceosome malfunction causes neurodevelopmental disorders with overlapping features. J Clin Invest 2024; 134:e171235. [PMID: 37962958 PMCID: PMC10760965 DOI: 10.1172/jci171235] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/06/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023] Open
Abstract
Pre-mRNA splicing is a highly coordinated process. While its dysregulation has been linked to neurological deficits, our understanding of the underlying molecular and cellular mechanisms remains limited. We implicated pathogenic variants in U2AF2 and PRPF19, encoding spliceosome subunits in neurodevelopmental disorders (NDDs), by identifying 46 unrelated individuals with 23 de novo U2AF2 missense variants (including 7 recurrent variants in 30 individuals) and 6 individuals with de novo PRPF19 variants. Eight U2AF2 variants dysregulated splicing of a model substrate. Neuritogenesis was reduced in human neurons differentiated from human pluripotent stem cells carrying two U2AF2 hyper-recurrent variants. Neural loss of function (LoF) of the Drosophila orthologs U2af50 and Prp19 led to lethality, abnormal mushroom body (MB) patterning, and social deficits, which were differentially rescued by wild-type and mutant U2AF2 or PRPF19. Transcriptome profiling revealed splicing substrates or effectors (including Rbfox1, a third splicing factor), which rescued MB defects in U2af50-deficient flies. Upon reanalysis of negative clinical exomes followed by data sharing, we further identified 6 patients with NDD who carried RBFOX1 missense variants which, by in vitro testing, showed LoF. Our study implicates 3 splicing factors as NDD-causative genes and establishes a genetic network with hierarchy underlying human brain development and function.
Collapse
Affiliation(s)
- Dong Li
- Center for Applied Genomics, and
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Qin Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Allan Bayat
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department for Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | | | - Yijing Zhou
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daniëlle G.M. Bosch
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Leslie Granger
- Department of Genetics and Metabolism, Randall Children’s Hospital at Legacy Emanuel Medical Center, Portland, Oregon, USA
| | - Andrea K. Petersen
- Department of Genetics and Metabolism, Randall Children’s Hospital at Legacy Emanuel Medical Center, Portland, Oregon, USA
| | - Luis A. Pérez-Jurado
- Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
- Genetic Service, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Gemma Aznar-Laín
- Universitat Pompeu Fabra, Barcelona, Spain
- Pediatric Neurology, Hospital del Mar Research Institute (IMIM), Barcelona, Spain
| | - Anushree Aneja
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Miroslava Hancarova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Sarka Bendova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Martin Schwarz
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Radka Kremlikova Pourova
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Zdenek Sedlacek
- Department of Biology and Medical Genetics, Charles University Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Beth A. Keena
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | | | | | - Elizabeth J. Bhoj
- Center for Applied Genomics, and
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Gabrielle Lemire
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Megan Li
- Invitae, San Francisco, California, USA
| | - Mark Tarnopolsky
- Division of Neuromuscular and Neurometabolic Disorders, Department of Paediatrics, McMaster University Children’s Hospital, Hamilton, Ontario, Canada
| | - Lauren Brady
- Division of Neuromuscular and Neurometabolic Disorders, Department of Paediatrics, McMaster University Children’s Hospital, Hamilton, Ontario, Canada
| | - Michael J. Parker
- Department of Clinical Genetics, Sheffield Children’s Hospital, Sheffield, United Kingdom
| | | | - Lea Kristin Parsley
- University of Illinois College of Medicine, Mercy Health Systems, Rockford, Illinois, USA
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Meredith Wright
- Rady Children’s Institute for Genomic Medicine, San Diego, California, USA
| | - Rachel Palmquist
- Division of Pediatric Neurology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Khanh Lai
- Division of Pediatric Pulmonary and Sleep Medicine, University of Utah, Salt Lake City, Utah, USA
| | - Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, and
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università Degli Studi di Genova, Genoa, Italy
- Pediatric Neurology and Muscular Diseases Unit, and
| | - Michele Iacomino
- Medical Genetics Unit, IRCCS, Istituto Giannina Gaslini, Genoa, Italy
| | - Federico Zara
- Medical Genetics Unit, IRCCS, Istituto Giannina Gaslini, Genoa, Italy
| | - Annina Cooper
- Department of Genetics, Southern California Permanente Medical Group, Kaiser Permanente, San Diego, California, USA
| | - Timothy J. Maarup
- Department of Genetics, Kaiser Permanente, Los Angeles, California, USA
| | - Melissa Byler
- Center for Development, Behavior and Genetics, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Robert Roger Lebel
- Center for Development, Behavior and Genetics, SUNY Upstate Medical University, Syracuse, New York, USA
| | - Tugce B. Balci
- Division of Genetics, Department of Paediatrics, London Health Sciences Centre, London, Ontario, Canada
| | - Raymond Louie
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Michael Lyons
- Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Jessica Douglas
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Catherine Nowak
- Division of Genetics and Metabolism, Mass General Hospital for Children, Boston, Massachusetts, USA
| | - Alexandra Afenjar
- APHP. SU, Reference Center for Intellectual Disabilities Caused by Rare Causes, Department of Genetics and Medical Embryology, Hôpital Trousseau, Paris, France
| | - Juliane Hoyer
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Boris Keren
- Department of Genetics, Hospital Pitié-Salpêtrière, Paris, France
| | - Saskia M. Maas
- Department of Human Genetics, Academic Medical Center, and
| | - Mahdi M. Motazacker
- Laboratory of Genome Diagnostics, Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | | | - Ahna M. Rabani
- Division of Medical Genetics, Department of Pediatrics, UCLA, Los Angeles, California, USA
| | - Elizabeth M. McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics
| | - Marni J. Falk
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics
| | - Sarah M. Ruggiero
- Division of Neurology, and
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ingo Helbig
- Division of Neurology, and
- The Epilepsy NeuroGenetics Initiative (ENGIN), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Neurology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biomedical and Health Informatics (DBHi), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Rikke S. Møller
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark
| | - Lino Tessarollo
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Francesco Tomassoni Ardori
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Mary Ellen Palko
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute (NCI), Frederick, Maryland, USA
| | - Tzung-Chien Hsieh
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Peter M. Krawitz
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Mythily Ganapathi
- New York Genome Center, New York, New York, USA
- Department of Pathology, Columbia University Irving Medical Center, New York, New York, USA
| | - Bruce D. Gelb
- Mindich Child Health and Development Institute and the Departments of Pediatrics and Genetics and Genomic Sciences, Icahn School of Medicine, New York, New York, USA
| | - Vaidehi Jobanputra
- New York Genome Center, New York, New York, USA
- Department of Pathology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - John Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Sébastien Jacquemont
- Division of Genetics and Genomics, CHU Ste-Justine Hospital and CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Khadijé Jizi
- Division of Genetics and Genomics, CHU Ste-Justine Hospital and CHU Sainte-Justine Research Centre, University of Montreal, Montreal, Quebec, Canada
| | - Ange-Line Bruel
- INSERM UMR 1231, Genetics of Developmental Anomalies, Université de Bourgogne Franche-Comté, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
- FHU-TRANSLAD, Fédération Hospitalo-Universitaire Translational Medicine in Developmental Anomalies, CHU Dijon Bourgogne, Dijon, France
| | - Chloé Quelin
- Medical Genetics Department, Centre de Référence Maladies Rares CLAD-Ouest, CHU Hôpital Sud, Rennes, France
| | - Vinod K. Misra
- Division of Genetic, Genomic, and Metabolic Disorders, Children’s Hospital of Michigan, Detroit, Michigan, USA
- Central Michigan University College of Medicine, Discipline of Pediatrics, Mount Pleasant, Michigan, USA
| | - Erika Chick
- Division of Genetic, Genomic, and Metabolic Disorders, Children’s Hospital of Michigan, Detroit, Michigan, USA
| | - Corrado Romano
- Research Unit of Rare Diseases and Neurodevelopmental Disorders, Oasi Research Institute-IRCCS, Troina, Italy
- Medical Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | | | | | - Manuela Morleo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Naples, Italy
| | - Rie Seyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Obstetrics and Gynecology, Juntendo University, Tokyo, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ryoji Taira
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Katsuya Tashiro
- Department of Pediatrics, Karatsu Red Cross Hospital, Saga, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, Göttingen, Germany
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), partner site Göttingen, Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Göttingen, Germany
| | - Michael Wagner
- Kinderzentrum Oldenburg, Sozialpädiatrisches Zentrum, Diakonisches Werk Oldenburg, Oldenburg, Germany
| | - Barbara Kutsche
- Kinderzentrum Oldenburg, Sozialpädiatrisches Zentrum, Diakonisches Werk Oldenburg, Oldenburg, Germany
| | - Anna C.E. Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | | | - Ryan Schmidt
- Department of Pathology and Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, California, USA
- Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Linda Randolph
- Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
- Division of Medical Genetics, Children’s Hospital Los Angeles, California, USA
| | - Rebecca C. Spillmann
- Department of Pediatrics–Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Vandana Shashi
- Department of Pediatrics–Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Dawn Cordeiro
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Amanda Carnevale
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tayyaba Khan
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Benoît Funalot
- Department of Genetics, Hôpital Henri-Mondor APHP and CHI Creteil, University Paris Est Creteil, IMRB, Inserm U.955, Creteil, France
| | - Frederic Tran Mau-Them
- INSERM UMR 1231, Genetics of Developmental Anomalies, Université de Bourgogne Franche-Comté, Dijon, France
- UF Innovation en Diagnostic Génomique des Maladies Rares, CHU Dijon Bourgogne, Dijon, France
| | | | - Sixto García-Miñaúr
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, Madrid, Spain
| | - Matthew Osmond
- Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Lauren Chad
- Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Nada Quercia
- Department of Genetic Counselling, Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Ottawa, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Diana Carrasco
- Department of Clinical Genetics, Cook Children’s Hospital, Fort Worth, Texas, USA
| | - Chumei Li
- Division of Genetics, Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Amarilis Sanchez-Valle
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | - Meghan Kelley
- Division of Genetics and Metabolism, Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | - Mathilde Nizon
- Nantes Université, CHU Nantes, Medical Genetics Department, Nantes, France
- Nantes Université, CNRS, INSERM, l’Institut du Thorax, Nantes, France
| | | | | | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Svetlana Gorokhova
- Aix Marseille University, Inserm, U1251-MMG, Marseille Medical Genetics, Marseille, France
- Department of Medical Genetics, Timone Hospital, APHM, Marseille, France
| | - Tiffany Busa
- Department of Medical Genetics, Timone Hospital, APHM, Marseille, France
| | - Marlène Rio
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Hamza Hadj Habdallah
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Marion Lesieur-Sebellin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Jeanne Amiel
- Rare Disease Genetics Department, APHP, Hôpital Necker, Paris, France
- Université Paris Cité, Inserm, Institut Imagine, Embryology and Genetics of Malformations Laboratory, Paris, France
| | - Véronique Pingault
- Rare Disease Genetics Department, APHP, Hôpital Necker, Paris, France
- Université Paris Cité, Inserm, Institut Imagine, Embryology and Genetics of Malformations Laboratory, Paris, France
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France
| | - Sandra Mercier
- Nantes Université, CHU Nantes, Medical Genetics Department, Nantes, France
- Nantes Université, CNRS, INSERM, l’Institut du Thorax, Nantes, France
| | - Marie Vincent
- Nantes Université, CHU Nantes, Medical Genetics Department, Nantes, France
- Nantes Université, CNRS, INSERM, l’Institut du Thorax, Nantes, France
| | - Christophe Philippe
- INSERM UMR 1231, Genetics of Developmental Anomalies, Université de Bourgogne Franche-Comté, Dijon, France
| | | | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, South Australia, Australia
| | | | | | - Jane Rosser
- Department of General Medicine, Women’s and Children’s Hospital, Adelaide, South Australia, Australia
| | - Cheryl Shoubridge
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, South Australia, Australia
| | - Mark Corbett
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, South Australia, Australia
| | - Christopher Barnett
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, South Australia, Australia
- Pediatric and Reproductive Genetics Unit, Women’s and Children’s Hospital, North Adelaide, South Australia, Australia
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Kathleen Leppig
- Genetic Services, Kaiser Permenante of Washington, Seattle, Washington, USA
| | - Anne Slavotinek
- Department of Pediatrics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, USA
| | - Carlo Marcelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bert B.A. de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Benjamin Cogne
- Nantes Université, CHU Nantes, Medical Genetics Department, Nantes, France
- Nantes Université, CNRS, INSERM, l’Institut du Thorax, Nantes, France
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France
| | - Thomas Rambaud
- Laboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr), Paris, France
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Elaine H. Zackai
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Naiara Akizu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yuanquan Song
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, and
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| |
Collapse
|
6
|
Sullivan JA, Spillmann RC, Schoch K, Walley N, Alkelai A, Stong N, Shea PR, Petrovski S, Jobanputra V, McConkie-Rosell A, Shashi V. The best of both worlds: Blending cutting-edge research with clinical processes for a productive exome clinic. Clin Genet 2024; 105:62-71. [PMID: 37853563 DOI: 10.1111/cge.14437] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/11/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023]
Abstract
Genomic medicine has been transformed by next-generation sequencing (NGS), inclusive of exome sequencing (ES) and genome sequencing (GS). Currently, ES is offered widely in clinical settings, with a less prevalent alternative model consisting of hybrid programs that incorporate research ES along with clinical patient workflows. We were among the earliest to implement a hybrid ES clinic, have provided diagnoses to 45% of probands, and have identified several novel candidate genes. Our program is enabled by a cost-effective investment by the health system and is unique in encompassing all the processes that have been variably included in other hybrid/clinical programs. These include careful patient selection, utilization of a phenotype-agnostic bioinformatics pipeline followed by manual curation of variants and phenotype integration by clinicians, close collaborations between the clinicians and the bioinformatician, pursuit of interesting variants, communication of results to patients in categories that are predicated upon the certainty of a diagnosis, and tracking changes in results over time and the underlying mechanisms for such changes. Due to its effectiveness, scalability to GS and its resource efficiency, specific elements of our paradigm can be incorporated into existing clinical settings, or the entire hybrid model can be implemented within health systems that have genomic medicine programs, to provide NGS in a scientifically rigorous, yet pragmatic setting.
Collapse
Affiliation(s)
- Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, New York, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Predictive Sciences, Bristol Myers Squibb, Summit, New Jersey, USA
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Genomics and Bioinformatics Analysis Resource, Columbia University, New York, New York, USA
| | - Slavè Petrovski
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York, USA
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, North Carolina, USA
| |
Collapse
|
7
|
McConkie-Rosell A, Spillmann RC, Schoch K, Sullivan JA, Walley N, McDonald M, Hooper SR, Shashi V. Unraveling non-participation in genomic research: A complex interplay of barriers, facilitators, and sociocultural factors. J Genet Couns 2023; 32:993-1008. [PMID: 37005744 PMCID: PMC10542653 DOI: 10.1002/jgc4.1707] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 11/28/2022] [Revised: 03/15/2023] [Accepted: 03/19/2023] [Indexed: 04/04/2023]
Abstract
Although genomic research offering next-generation sequencing (NGS) has increased the diagnoses of rare/ultra-rare disorders, populations experiencing health disparities infrequently participate in these studies. The factors underlying non-participation would most reliably be ascertained from individuals who have had the opportunity to participate, but decline. We thus enrolled parents of children and adult probands with undiagnosed disorders who had declined genomic research offering NGS with return of results with undiagnosed disorders (Decliners, n = 21) and compared their data to those who participated (Participants, n = 31). We assessed: (1) practical barriers and facilitators, (2) sociocultural factors-genomic knowledge and distrust, and (3) the value placed upon a diagnosis by those who declined participation. The primary findings were that residence in rural and medically underserved areas (MUA) and higher number of barriers were significantly associated with declining participation in the study. Exploratory analyses revealed multiple co-occurring practical barriers, greater emotional exhaustion and research hesitancy in the parents in the Decliner group compared to the Participants, with both groups identifying a similar number of facilitators. The parents in the Decliner group also had lower genomic knowledge, but distrust of clinical research was not different between the groups. Importantly, despite their non-participation, those in the Decliner group indicated an interest in obtaining a diagnosis and expressed confidence in being able to emotionally manage the ensuing results. Study findings support the concept that some families who decline participation in diagnostic genomic research may be experiencing pile-up with exhaustion of family resources - making participation in the genomic research difficult. This study highlights the complexity of the factors that underlie non-participation in clinically relevant NGS research. Thus, approaches to mitigating barriers to NGS research participation by populations experiencing health disparities need to be multi-pronged and tailored so that they can benefit from state-of -the art genomic technologies.
Collapse
Affiliation(s)
- Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, NC, USA
| | - Rebecca C. Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, NC, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, NC, USA
| | - Jennifer A. Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, NC, USA
| | - Nicole Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, NC, USA
| | - Marie McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, NC, USA
| | | | - Stephen R. Hooper
- Department of Allied Health Sciences, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine and Duke Health System, Durham, NC, USA
| |
Collapse
|
8
|
Schoch K, McConkie-Rosell A, Walley N, Bhambhani V, Feyma T, Pizoli CE, Smith EC, Tan QKG, Shashi V. Parental perspectives of episodic irritability in an ultra-rare genetic disorder associated with NACC1. Orphanet J Rare Dis 2023; 18:269. [PMID: 37667351 PMCID: PMC10476425 DOI: 10.1186/s13023-023-02891-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 04/21/2023] [Accepted: 08/25/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND A recurrent de novo variant (c.892C>T) in NACC1 causes a neurodevelopmental disorder with epilepsy, cataracts, feeding difficulties, and delayed brain myelination (NECFM). An unusual and consistently reported feature is episodic extreme irritability and inconsolability. We now characterize these episodes, their impact on the family, and ascertain treatments that may be effective. Parents of 14 affected individuals provided narratives describing the irritability episodes, including triggers, behavioral and physiological changes, and treatments. Simultaneously, parents of 15 children completed the Non-communicating Children's Pain Checklist-Revised (NCCPC-R), a measure to assess pain in non-verbal children. RESULTS The episodes of extreme irritability include a prodromal, peak, and resolving phase, with normal periods in between. The children were rated to have extreme pain-related behaviors on the NCCPC-R scale, although it is unknown whether the physiologic changes described by parents are caused by pain. Attempted treatments included various classes of medications, with psychotropic and sedative medications being most effective (7/15). Nearly all families (13/14) describe how the episodes have a profound impact on their lives. CONCLUSIONS NECFM caused by the recurrent variant c.892C>T is associated with a universal feature of incapacitating episodic irritability of unclear etiology. Further understanding of the pathophysiology can lead to more effective therapeutic strategies.
Collapse
Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Nicole Walley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Vikas Bhambhani
- Division of Genetics and Genomic Medicine, Children's Hospital and Clinics of Minnesota, Minneapolis, MN, USA
| | - Timothy Feyma
- Gillette Children's Specialty Healthcare, Saint Paul, MN, USA
| | - Carolyn E Pizoli
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Edward C Smith
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Queenie K-G Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA.
| |
Collapse
|
9
|
Shashi V, Schoch K, Ganetzky R, Kranz PG, Sondheimer N, Markert ML, Cope H, Sadeghpour A, Roehrs P, Arbogast T, Muraresku C, Tyndall AV, Esser MJ, Woodward KE, Ping-Yee Au B, Parboosingh JS, Lamont RE, Bernier FP, Wright NAM, Benseler SM, Parsons SJ, El-Dairi M, Smith EC, Valdez P, Tennison M, Innes AM, Davis EE. Biallelic variants in ribonuclease inhibitor (RNH1), an inflammasome modulator, are associated with a distinctive subtype of acute, necrotizing encephalopathy. Genet Med 2023; 25:100897. [PMID: 37191094 PMCID: PMC10506156 DOI: 10.1016/j.gim.2023.100897] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 03/13/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
PURPOSE Mendelian etiologies for acute encephalopathies in previously healthy children are poorly understood, with the exception of RAN binding protein 2 (RANBP2)-associated acute necrotizing encephalopathy subtype 1 (ANE1). We provide clinical, genetic, and neuroradiological evidence that biallelic variants in ribonuclease inhibitor (RNH1) confer susceptibility to a distinctive ANE subtype. METHODS This study aimed to evaluate clinical data, neuroradiological studies, genomic sequencing, and protein immunoblotting results in 8 children from 4 families who experienced acute febrile encephalopathy. RESULTS All 8 healthy children became acutely encephalopathic during a viral/febrile illness and received a variety of immune modulation treatments. Long-term outcomes varied from death to severe neurologic deficits to normal outcomes. The neuroradiological findings overlapped with ANE but had distinguishing features. All affected children had biallelic predicted damaging variants in RNH1: a subset that was studied had undetectable RNH1 protein. Incomplete penetrance of the RNH1 variants was evident in 1 family. CONCLUSION Biallelic variants in RNH1 confer susceptibility to a subtype of ANE (ANE2) in previously healthy children. Intensive immunological treatments may alter outcomes. Genomic sequencing in children with unexplained acute febrile encephalopathy can detect underlying genetic etiologies, such as RNH1, and improve outcomes in the probands and at-risk siblings.
Collapse
Affiliation(s)
- Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC.
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Rebecca Ganetzky
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke University Medical Center, Durham, NC
| | | | - M Louise Markert
- Department of Pediatrics, Duke University School of Medicine, Durham, NC; Department of Immunology, Duke University Medical Center, Durham, NC
| | - Heidi Cope
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC
| | - Azita Sadeghpour
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC; Duke Precision Medicine Program, Department of Medicine, Division of General Internal Medicine, Duke University Medical Center, Durham, NC
| | - Philip Roehrs
- Pediatric Stem Cell Transplant and Cellular Therapy, Department of Pediatrics, University of Virginia, Charlottesville, VA
| | - Thomas Arbogast
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL
| | - Colleen Muraresku
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amanda V Tyndall
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Michael J Esser
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Kristine E Woodward
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Billie Ping-Yee Au
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jillian S Parboosingh
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Ryan E Lamont
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Francois P Bernier
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nicola A M Wright
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Susa M Benseler
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Simon J Parsons
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Mays El-Dairi
- Department of Ophthalmology, Duke University Medical Center, Durham, NC
| | - Edward C Smith
- Division of Neurology, Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Purnima Valdez
- Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Michael Tennison
- Department of Neurology, University of North Carolina at Chapel Hill, NC
| | - A Micheil Innes
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Erica E Davis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL; Departments of Pediatrics and Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL.
| |
Collapse
|
10
|
Calame DG, Guo T, Wang C, Garrett L, Jolly A, Dawood M, Kurolap A, Henig NZ, Fatih JM, Herman I, Du H, Mitani T, Becker L, Rathkolb B, Gerlini R, Seisenberger C, Marschall S, Hunter JV, Gerard A, Heidlebaugh A, Challman T, Spillmann RC, Jhangiani SN, Coban-Akdemir Z, Lalani S, Liu L, Revah-Politi A, Iglesias A, Guzman E, Baugh E, Boddaert N, Rondeau S, Ormieres C, Barcia G, Tan QKG, Thiffault I, Pastinen T, Sheikh K, Biliciler S, Mei D, Melani F, Shashi V, Yaron Y, Steele M, Wakeling E, Østergaard E, Nazaryan-Petersen L, Millan F, Santiago-Sim T, Thevenon J, Bruel AL, Thauvin-Robinet C, Popp D, Platzer K, Gawlinski P, Wiszniewski W, Marafi D, Pehlivan D, Posey JE, Gibbs RA, Gailus-Durner V, Guerrini R, Fuchs H, Hrabě de Angelis M, Hölter SM, Cheung HH, Gu S, Lupski JR. Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease. Am J Hum Genet 2023; 110:1394-1413. [PMID: 37467750 PMCID: PMC10432148 DOI: 10.1016/j.ajhg.2023.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 02/23/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/21/2023] Open
Abstract
DExD/H-box RNA helicases (DDX/DHX) are encoded by a large paralogous gene family; in a subset of these human helicase genes, pathogenic variation causes neurodevelopmental disorder (NDD) traits and cancer. DHX9 encodes a BRCA1-interacting nuclear helicase regulating transcription, R-loops, and homologous recombination and exhibits the highest mutational constraint of all DDX/DHX paralogs but remains unassociated with disease traits in OMIM. Using exome sequencing and family-based rare-variant analyses, we identified 20 individuals with de novo, ultra-rare, heterozygous missense or loss-of-function (LoF) DHX9 variant alleles. Phenotypes ranged from NDDs to the distal symmetric polyneuropathy axonal Charcot-Marie-Tooth disease (CMT2). Quantitative Human Phenotype Ontology (HPO) analysis demonstrated genotype-phenotype correlations with LoF variants causing mild NDD phenotypes and nuclear localization signal (NLS) missense variants causing severe NDD. We investigated DHX9 variant-associated cellular phenotypes in human cell lines. Whereas wild-type DHX9 was restricted to the nucleus, NLS missense variants abnormally accumulated in the cytoplasm. Fibroblasts from an individual with an NLS variant also showed abnormal cytoplasmic DHX9 accumulation. CMT2-associated missense variants caused aberrant nucleolar DHX9 accumulation, a phenomenon previously associated with cellular stress. Two NDD-associated variants, p.Gly411Glu and p.Arg761Gln, altered DHX9 ATPase activity. The severe NDD-associated variant p.Arg141Gln did not affect DHX9 localization but instead increased R-loop levels and double-stranded DNA breaks. Dhx9-/- mice exhibited hypoactivity in novel environments, tremor, and sensorineural hearing loss. All together, these results establish DHX9 as a critical regulator of mammalian neurodevelopment and neuronal homeostasis.
Collapse
Affiliation(s)
- Daniel G Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tianyu Guo
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chen Wang
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lillian Garrett
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Alina Kurolap
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Noa Zunz Henig
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Boys Town National Research Hospital, Boys Town, NE, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lore Becker
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Birgit Rathkolb
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Molecular Animal Breeding and Biotechnology, Gene Center, Ludwig-Maximilians University Munich, Munich, Germany; German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Raffaele Gerlini
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Seisenberger
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Susan Marschall
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, TX, USA; E.B. Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, TX, USA
| | - Amanda Gerard
- Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Thomas Challman
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Seema Lalani
- Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lingxiao Liu
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Anya Revah-Politi
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandro Iglesias
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Edwin Guzman
- Division of Clinical Genetics, Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Evan Baugh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Nathalie Boddaert
- Paediatric Radiology Department, AP-HP, Hôpital Necker Enfants Malades, Université Paris Cité, Institut Imagine INSERM U1163, 75015 Paris, France
| | - Sophie Rondeau
- Service de Médecine Génomique des Maladies Rares - APHP, Hôpital Necker Enfants Malades, Université de Paris, Paris, France
| | - Clothide Ormieres
- Service de Médecine Génomique des Maladies Rares - APHP, Hôpital Necker Enfants Malades, Université de Paris, Paris, France
| | - Giulia Barcia
- Service de Médecine Génomique des Maladies Rares - APHP, Hôpital Necker Enfants Malades, Université de Paris, Paris, France
| | - Queenie K G Tan
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, MO, USA; University of Missouri Kansas City School of Medicine, Kansas City, MO, USA
| | - Kazim Sheikh
- Department of Neurology, UT Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Suur Biliciler
- Department of Neurology, UT Health Science Center at Houston, McGovern Medical School, Houston, TX, USA
| | - Davide Mei
- Neuroscience Department, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Federico Melani
- Neuroscience Department, Meyer Children's Hospital IRCCS, Florence, Italy
| | - Vandana Shashi
- Department of Pediatrics, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Yuval Yaron
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Mary Steele
- Lifetime Neurodevelopmental Care, San Francisco, CA, USA
| | - Emma Wakeling
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Elsebet Østergaard
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lusine Nazaryan-Petersen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est, Fédération Hospitalo-Universitaire Médecine TRANSLationnelle et Anomalies du Développement, Centre Hospitalier Universitaire Dijon, Equipe Genetics of Developmental Anomalies-INSERM UMR 1231, Dijon, France
| | - Ange-Line Bruel
- Functional Unit for Diagnostic Innovation in Rare Diseases, FHU-TRANSLAD, Dijon Bourgogne University Hospital, Dijon, France; INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France
| | - Christel Thauvin-Robinet
- INSERM UMR1231 GAD "Génétique des Anomalies du Développement," FHU-TRANSLAD, University of Burgundy, Dijon, France; Department of Genetics and Reference Center for Development Disorders and Intellectual Disabilities, Dijon Bourgogne University Hospital, Dijon, France
| | - Denny Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Pawel Gawlinski
- Institute of Mother and Child, Kasprzaka 17a, 02-211 Warsaw, Poland
| | - Wojciech Wiszniewski
- Oregon Health & Sciences University, 3181 SW Sam Jackson Park Road L103, Portland, OR, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Valerie Gailus-Durner
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Renzo Guerrini
- Neuroscience Department, Meyer Children's Hospital IRCCS, Florence, Italy; University of Florence, Florence, Italy
| | - Helmut Fuchs
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; Chair of Experimental Genetics, TUM School of Life Sciences, Technische Universität München, Alte Akademie 8, 85354 Freising, Germany
| | - Sabine M Hölter
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Technische Universität München, Freising-Weihenstephan, Germany
| | - Hoi-Hung Cheung
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Shen Gu
- School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong SAR, China; Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Hong Kong SAR, China; Kunming Institute of Zoology Chinese Academy of Sciences, the Chinese University of Hong Kong Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Hong Kong SAR, China.
| | - James R Lupski
- Texas Children's Hospital, Houston, TX, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
| |
Collapse
|
11
|
Zhao Y, Wang Y, Shi L, McDonald-McGinn DM, Crowley TB, McGinn DE, Tran OT, Miller D, Lin JR, Zackai E, Johnston HR, Chow EWC, Vorstman JAS, Vingerhoets C, van Amelsvoort T, Gothelf D, Swillen A, Breckpot J, Vermeesch JR, Eliez S, Schneider M, van den Bree MBM, Owen MJ, Kates WR, Repetto GM, Shashi V, Schoch K, Bearden CE, Digilio MC, Unolt M, Putotto C, Marino B, Pontillo M, Armando M, Vicari S, Angkustsiri K, Campbell L, Busa T, Heine-Suñer D, Murphy KC, Murphy D, García-Miñaúr S, Fernández L, Zhang ZD, Goldmuntz E, Gur RE, Emanuel BS, Zheng D, Marshall CR, Bassett AS, Wang T, Morrow BE. Chromatin regulators in the TBX1 network confer risk for conotruncal heart defects in 22q11.2DS. NPJ Genom Med 2023; 8:17. [PMID: 37463940 PMCID: PMC10354062 DOI: 10.1038/s41525-023-00363-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/29/2023] [Indexed: 07/20/2023] Open
Abstract
Congenital heart disease (CHD) affecting the conotruncal region of the heart, occurs in 40-50% of patients with 22q11.2 deletion syndrome (22q11.2DS). This syndrome is a rare disorder with relative genetic homogeneity that can facilitate identification of genetic modifiers. Haploinsufficiency of TBX1, encoding a T-box transcription factor, is one of the main genes responsible for the etiology of the syndrome. We suggest that genetic modifiers of conotruncal defects in patients with 22q11.2DS may be in the TBX1 gene network. To identify genetic modifiers, we analyzed rare, predicted damaging variants in whole genome sequence of 456 cases with conotruncal defects and 537 controls, with 22q11.2DS. We then performed gene set approaches and identified chromatin regulatory genes as modifiers. Chromatin genes with recurrent damaging variants include EP400, KAT6A, KMT2C, KMT2D, NSD1, CHD7 and PHF21A. In total, we identified 37 chromatin regulatory genes, that may increase risk for conotruncal heart defects in 8.5% of 22q11.2DS cases. Many of these genes were identified as risk factors for sporadic CHD in the general population. These genes are co-expressed in cardiac progenitor cells with TBX1, suggesting that they may be in the same genetic network. The genes KAT6A, KMT2C, CHD7 and EZH2, have been previously shown to genetically interact with TBX1 in mouse models. Our findings indicate that disturbance of chromatin regulatory genes impact the TBX1 gene network serving as genetic modifiers of 22q11.2DS and sporadic CHD, suggesting that there are some shared mechanisms involving the TBX1 gene network in the etiology of CHD.
Collapse
Affiliation(s)
- Yingjie Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Yujue Wang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Lijie Shi
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - T Blaine Crowley
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - Daniel E McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - Oanh T Tran
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - Daniella Miller
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Eva W C Chow
- Department of Psychiatry, University of Toronto, Ontario, M5G 0A4, Canada
| | - Jacob A S Vorstman
- Program in Genetics and Genome Biology, Research Institute and Autism Research Unit, The Hospital for Sick Children, Toronto, ON, M5G 0A4, Canada
| | - Claudia Vingerhoets
- Department of Psychiatry and Psychology, Maastricht University, Maastricht, 6200, MD, the Netherlands
| | - Therese van Amelsvoort
- Department of Psychiatry and Psychology, Maastricht University, Maastricht, 6200, MD, the Netherlands
| | - Doron Gothelf
- The Division of Child & Adolescent Psychiatry, Edmond and Lily Sapfra Children's Hospital, Sheba Medical Center and Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Ramat Gan, 5262000, Israel
| | - Ann Swillen
- Center for Human Genetics, University Hospital Leuven, Department of Human Genetics, University of Leuven (KU Leuven), Leuven, 3000, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University Hospital Leuven, Department of Human Genetics, University of Leuven (KU Leuven), Leuven, 3000, Belgium
| | - Joris R Vermeesch
- Center for Human Genetics, University Hospital Leuven, Department of Human Genetics, University of Leuven (KU Leuven), Leuven, 3000, Belgium
| | - Stephan Eliez
- Developmental Imaging and Psychopathology Laboratory, Department of Psychiatry, Faculty of Medicine, University of Geneva, Geneva, 1211, Switzerland
| | - Maude Schneider
- Developmental Imaging and Psychopathology Laboratory, Department of Psychiatry, Faculty of Medicine, University of Geneva, Geneva, 1211, Switzerland
| | - Marianne B M van den Bree
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Wales, CF24 4HQ, UK
| | - Michael J Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Wales, CF24 4HQ, UK
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, 13202, USA
- Program in Neuroscience, SUNY Upstate Medical University, Syracuse, NY, 13202, USA
| | - Gabriela M Repetto
- Center for Genetics and Genomics, Facultad de Medicina Clinica Alemana-Universidad del Desarrollo, Santiago, 7710162, Chile
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC, 27710, USA
| | - Kelly Schoch
- Department of Pediatrics, Duke University, Durham, NC, 27710, USA
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - M Cristina Digilio
- Department of Medical Genetics, Bambino Gesù Hospital, Rome, 00165, Italy
| | - Marta Unolt
- Department of Medical Genetics, Bambino Gesù Hospital, Rome, 00165, Italy
- Department of Pediatrics, Gynecology, and Obstetrics, La Sapienza University of Rome, Rome, 00185, Italy
| | - Carolina Putotto
- Department of Pediatrics, Gynecology, and Obstetrics, La Sapienza University of Rome, Rome, 00185, Italy
| | - Bruno Marino
- Department of Pediatrics, Gynecology, and Obstetrics, La Sapienza University of Rome, Rome, 00185, Italy
| | - Maria Pontillo
- Department of Neuroscience, Bambino Gesù Hospital, Rome, 00165, Italy
| | - Marco Armando
- Department of Neuroscience, Bambino Gesù Hospital, Rome, 00165, Italy
- Developmental Imaging and Psychopathology Lab, University of Geneva, Geneva, 1211, Switzerland
| | - Stefano Vicari
- Department of Life Sciences and Public Health, Catholic University and Child & Adolescent Psychiatry Unit at Bambino Gesù Hospital, Rome, 00165, Italy
| | - Kathleen Angkustsiri
- Developmental Behavioral Pediatrics, MIND Institute, University of California, Davis, CA, 95817, USA
| | - Linda Campbell
- School of Psychology, University of Newcastle, Newcastle, 2258, Australia
| | - Tiffany Busa
- Department of Medical Genetics, Aix-Marseille University, Marseille, 13284, France
| | - Damian Heine-Suñer
- Genomics of Health and Unit of Molecular Diagnosis and Clinical Genetics, Son Espases University Hospital, Balearic Islands Health Research Institute, Palma de Mallorca, 07120, Spain
| | - Kieran C Murphy
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin, 505095, Ireland
| | - Declan Murphy
- Department of Forensic and Neurodevelopmental Sciences, King's College London, Institute of Psychiatry, Psychology, and Neuroscience, London, SE5 8AF, UK
- Behavioral and Developmental Psychiatry Clinical Academic Group, Behavioral Genetics Clinic, National Adult Autism and ADHD Service, South London and Maudsley Foundation National Health Service Trust, London, SE5 8AZ, UK
| | - Sixto García-Miñaúr
- Institute of Medical and Molecular Genetics, University Hospital La Paz, Madrid, 28046, Spain
| | - Luis Fernández
- Institute of Medical and Molecular Genetics, University Hospital La Paz, Madrid, 28046, Spain
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine of the University of Pennsylvania Philadelphia, Philadelphia, PA, 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, 19104, USA
| | - Deyou Zheng
- Department of Genetics, Department of Neurology, Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Christian R Marshall
- Division of Genome Diagnostics, The Hospital for Sick Children and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5T 1R8, Canada
| | - Anne S Bassett
- Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Dalglish Family 22q Clinic, Toronto General Hospital, and Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, M5T 1R8, Canada
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| |
Collapse
|
12
|
Srivastava S, Shaked HM, Gable K, Gupta SD, Pan X, Somashekarappa N, Han G, Mohassel P, Gotkine M, Doney E, Goldenberg P, Tan QKG, Gong Y, Kleinstiver B, Wishart B, Cope H, Pires CB, Stutzman H, Spillmann RC, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM, Dai H, Dhar SU, Emrick LT, Goldman AM, Hanchard NA, Jamal F, Karaviti L, Lalani SR, Lee BH, Lewis RA, Marom R, Moretti PM, Murdock DR, Nicholas SK, Orengo JP, Posey JE, Potocki L, Rosenfeld JA, Samson SL, Scott DA, Tran AA, Vogel TP, Wangler MF, Yamamoto S, Eng CM, Liu P, Ward PA, Behrens E, Deardorff M, Falk M, Hassey K, Sullivan K, Vanderver A, Goldstein DB, Cope H, McConkie-Rosell A, Schoch K, Shashi V, Smith EC, Spillmann RC, Sullivan JA, Tan QKG, Walley NM, Agrawal PB, Beggs AH, Berry GT, Briere LC, Cobban LA, Coggins M, Cooper CM, Fieg EL, High F, Holm IA, Korrick S, Krier JB, Lincoln SA, Loscalzo J, Maas RL, MacRae CA, Pallais JC, Rao DA, Rodan LH, Silverman EK, Stoler JM, Sweetser DA, Walker M, Walsh CA, Esteves C, Kelley EG, Kohane IS, LeBlanc K, McCray AT, Nagy A, Dasari S, Lanpher BC, Lanza IR, Morava E, Oglesbee D, Bademci G, Barbouth D, Bivona S, Carrasquillo O, Chang TCP, Forghani I, Grajewski A, Isasi R, Lam B, Levitt R, Liu XZ, McCauley J, Sacco R, Saporta M, Schaechter J, Tekin M, Telischi F, Thorson W, Zuchner S, Colley HA, Dayal JG, Eckstein DJ, Findley LC, Krasnewich DM, Mamounas LA, Manolio TA, Mulvihill JJ, LaMoure GL, Goldrich MP, Urv TK, Doss AL, Acosta MT, Bonnenmann C, D’Souza P, Draper DD, Ferreira C, Godfrey RA, Groden CA, Macnamara EF, Maduro VV, Markello TC, Nath A, Novacic D, Pusey BN, Toro C, Wahl CE, Baker E, Burke EA, Adams DR, Gahl WA, Malicdan MCV, Tifft CJ, Wolfe LA, Yang J, Power B, Gochuico B, Huryn L, Latham L, Davis J, Mosbrook-Davis D, Rossignol F, Solomon B, MacDowall J, Thurm A, Zein W, Yousef M, Adam M, Amendola L, Bamshad M, Beck A, Bennett J, Berg-Rood B, Blue E, Boyd B, Byers P, Chanprasert S, Cunningham M, Dipple K, Doherty D, Earl D, Glass I, Golden-Grant K, Hahn S, Hing A, Hisama FM, Horike-Pyne M, Jarvik GP, Jarvik J, Jayadev S, Lam C, Maravilla K, Mefford H, Merritt JL, Mirzaa G, Nickerson D, Raskind W, Rosenwasser N, Scott CR, Sun A, Sybert V, Wallace S, Wener M, Wenger T, Ashley EA, Bejerano G, Bernstein JA, Bonner D, Coakley TR, Fernandez L, Fisher PG, Fresard L, Hom J, Huang Y, Kohler JN, Kravets E, Majcherska MM, Martin BA, Marwaha S, McCormack CE, Raja AN, Reuter CM, Ruzhnikov M, Sampson JB, Smith KS, Sutton S, Tabor HK, Tucker BM, Wheeler MT, Zastrow DB, Zhao C, Byrd WE, Crouse AB, Might M, Nakano-Okuno M, Whitlock J, Brown G, Butte MJ, Dell’Angelica EC, Dorrani N, Douine ED, Fogel BL, Gutierrez I, Huang A, Krakow D, Lee H, Loo SK, Mak BC, Martin MG, Martínez-Agosto JA, McGee E, Nelson SF, Nieves-Rodriguez S, Palmer CGS, Papp JC, Parker NH, Renteria G, Signer RH, Sinsheimer JS, Wan J, Wang LK, Perry KW, Woods JD, Alvey J, Andrews A, Bale J, Bohnsack J, Botto L, Carey J, Pace L, Longo N, Marth G, Moretti P, Quinlan A, Velinder M, Viskochi D, Bayrak-Toydemir P, Mao R, Westerfield M, Bican A, Brokamp E, Duncan L, Hamid R, Kennedy J, Kozuira M, Newman JH, PhillipsIII JA, Rives L, Robertson AK, Solem E, Cogan JD, Cole FS, Hayes N, Kiley D, Sisco K, Wambach J, Wegner D, Baldridge D, Pak S, Schedl T, Shin J, Solnica-Krezel L, Sadjadi R, Elpeleg O, Lee CH, Bellen HJ, Edvardson S, Eichler F, Dunn TM. SPTSSA variants alter sphingolipid synthesis and cause a complex hereditary spastic paraplegia. Brain 2023; 146:1420-1435. [PMID: 36718090 PMCID: PMC10319774 DOI: 10.1093/brain/awac460] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 06/17/2022] [Revised: 11/03/2022] [Accepted: 11/19/2022] [Indexed: 02/01/2023] Open
Abstract
Sphingolipids are a diverse family of lipids with critical structural and signalling functions in the mammalian nervous system, where they are abundant in myelin membranes. Serine palmitoyltransferase, the enzyme that catalyses the rate-limiting reaction of sphingolipid synthesis, is composed of multiple subunits including an activating subunit, SPTSSA. Sphingolipids are both essential and cytotoxic and their synthesis must therefore be tightly regulated. Key to the homeostatic regulation are the ORMDL proteins that are bound to serine palmitoyltransferase and mediate feedback inhibition of enzymatic activity when sphingolipid levels become excessive. Exome sequencing identified potential disease-causing variants in SPTSSA in three children presenting with a complex form of hereditary spastic paraplegia. The effect of these variants on the catalytic activity and homeostatic regulation of serine palmitoyltransferase was investigated in human embryonic kidney cells, patient fibroblasts and Drosophila. Our results showed that two different pathogenic variants in SPTSSA caused a hereditary spastic paraplegia resulting in progressive motor disturbance with variable sensorineural hearing loss and language/cognitive dysfunction in three individuals. The variants in SPTSSA impaired the negative regulation of serine palmitoyltransferase by ORMDLs leading to excessive sphingolipid synthesis based on biochemical studies and in vivo studies in Drosophila. These findings support the pathogenicity of the SPTSSA variants and point to excessive sphingolipid synthesis due to impaired homeostatic regulation of serine palmitoyltransferase as responsible for defects in early brain development and function.
Collapse
Affiliation(s)
- Siddharth Srivastava
- Department of Neurology, Rosamund Stone Zander Translational Neuroscience Center, BostonChildren's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hagar Mor Shaked
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Kenneth Gable
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Sita D Gupta
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Xueyang Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Niranjanakumari Somashekarappa
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Gongshe Han
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Payam Mohassel
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20814, USA
| | - Marc Gotkine
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | | | - Paula Goldenberg
- Department of Pediatrics, Section on Medical Genetics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Queenie K G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yi Gong
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Benjamin Kleinstiver
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian Wishart
- Physical Medicine and Rehabilitation, Spaulding Rehabilitation Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Claudia Brito Pires
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hannah Stutzman
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus, Jerusalem 91240, Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.,Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Reza Sadjadi
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Orly Elpeleg
- Department of Genetics, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem , Jerusalem 91120 , Israel
| | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children’s Research Hospital , Memphis, TN 38105 , USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine , Houston, TX 77030 , USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital , Houston, TX 77030 , USA
| | - Simon Edvardson
- Pediatric Neurology Unit, Hadassah University Hospital, Mount Scopus , Jerusalem 91240 , Israel
| | - Florian Eichler
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
- Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114 , USA
| | - Teresa M Dunn
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences , Bethesda, MD 20814 , USA
| | | |
Collapse
|
13
|
Spillmann RC, Tan QKG, Reuter C, Schoch K, Kohler J, Bonner D, Zastrow D, Alkelai A, Baugh E, Cope H, Marwaha S, Wheeler MT, Bernstein JA, Shashi V. A concurrent dual analysis of genomic data augments diagnoses: Experiences of 2 clinical sites in the Undiagnosed Diseases Network. Genet Med 2023; 25:100353. [PMID: 36481303 PMCID: PMC10506157 DOI: 10.1016/j.gim.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/02/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Next-generation sequencing (NGS) has revolutionized the diagnostic process for rare/ultrarare conditions. However, diagnosis rates differ between analytical pipelines. In the National Institutes of Health-Undiagnosed Diseases Network (UDN) study, each individual's NGS data are concurrently analyzed by the UDN sequencing core laboratory and the clinical sites. We examined the outcomes of this practice. METHODS A retrospective review was performed at 2 UDN clinical sites to compare the variants and diagnoses/candidate genes identified with the dual analyses of the NGS data. RESULTS In total, 95 individuals had 100 diagnoses/candidate genes. There was 59% concordance between the UDN sequencing core laboratories and the clinical sites in identifying diagnoses/candidate genes. The core laboratory provided more diagnoses, whereas the clinical sites prioritized more research variants/candidate genes (P < .001). The clinical sites solely identified 15% of the diagnoses/candidate genes. The differences between the 2 pipelines were more often because of variant prioritization disparities than variant detection. CONCLUSION The unique dual analysis of NGS data in the UDN synergistically enhances outcomes. The core laboratory provided a clinical analysis with more diagnoses and the clinical sites prioritized more research variants/candidate genes. Implementing such concurrent dual analyses in other genomic research studies and clinical settings can improve both variant detection and prioritization.
Collapse
Affiliation(s)
- Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Queenie K-G Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Chloe Reuter
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Jennefer Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Diane Zastrow
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Anna Alkelai
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Evan Baugh
- Institute for Genome Medicine, Columbia University Medical Center, New York, NY
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC
| | - Shruti Marwaha
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Matthew T Wheeler
- Stanford Center for Inherited Cardiovascular Disease, Division of Cardiovascular Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, CA; Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, and Department of Pediatrics, Stanford University School of Medicine, Stanford, CA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC.
| |
Collapse
|
14
|
Serey-Gaut M, Cortes M, Makrythanasis P, Suri M, Taylor AMR, Sullivan JA, Asleh AN, Mitra J, Dar MA, McNamara A, Shashi V, Dugan S, Song X, Rosenfeld JA, Cabrol C, Iwaszkiewicz J, Zoete V, Pehlivan D, Akdemir ZC, Roeder ER, Littlejohn RO, Dibra HK, Byrd PJ, Stewart GS, Geckinli BB, Posey J, Westman R, Jungbluth C, Eason J, Sachdev R, Evans CA, Lemire G, VanNoy GE, O'Donnell-Luria A, Mau-Them FT, Juven A, Piard J, Nixon CY, Zhu Y, Ha T, Buckley MF, Thauvin C, Essien Umanah GK, Van Maldergem L, Lupski JR, Roscioli T, Dawson VL, Dawson TM, Antonarakis SE. Bi-allelic TTI1 variants cause an autosomal-recessive neurodevelopmental disorder with microcephaly. Am J Hum Genet 2023; 110:499-515. [PMID: 36724785 PMCID: PMC10027477 DOI: 10.1016/j.ajhg.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 09/19/2022] [Accepted: 01/09/2023] [Indexed: 02/03/2023] Open
Abstract
Telomere maintenance 2 (TELO2), Tel2 interacting protein 2 (TTI2), and Tel2 interacting protein 1 (TTI1) are the three components of the conserved Triple T (TTT) complex that modulates activity of phosphatidylinositol 3-kinase-related protein kinases (PIKKs), including mTOR, ATM, and ATR, by regulating the assembly of mTOR complex 1 (mTORC1). The TTT complex is essential for the expression, maturation, and stability of ATM and ATR in response to DNA damage. TELO2- and TTI2-related bi-allelic autosomal-recessive (AR) encephalopathies have been described in individuals with moderate to severe intellectual disability (ID), short stature, postnatal microcephaly, and a movement disorder (in the case of variants within TELO2). We present clinical, genomic, and functional data from 11 individuals in 9 unrelated families with bi-allelic variants in TTI1. All present with ID, and most with microcephaly, short stature, and a movement disorder. Functional studies performed in HEK293T cell lines and fibroblasts and lymphoblastoid cells derived from 4 unrelated individuals showed impairment of the TTT complex and of mTOR pathway activity which is improved by treatment with Rapamycin. Our data delineate a TTI1-related neurodevelopmental disorder and expand the group of disorders related to the TTT complex.
Collapse
Affiliation(s)
- Margaux Serey-Gaut
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France.
| | - Marisol Cortes
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Periklis Makrythanasis
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland; Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, Athens, Greece; Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Mohnish Suri
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Alexander M R Taylor
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | - Ayat N Asleh
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jaba Mitra
- Department of Biophysics and Biophysical Chemistry, Biophysics and Biomedical Engineering, JHU Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Mohamad A Dar
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amy McNamara
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Sarah Dugan
- Providence Medical Group Genetic Clinics, Spokane, WA, USA
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christelle Cabrol
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France
| | - Justyna Iwaszkiewicz
- Molecular Modeling Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Vincent Zoete
- Molecular Modeling Group, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research Lausanne Branch, University of Lausanne, Lausanne, Switzerland
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; EA481 Integrative and Cognitive Neuroscience Research Unit, University of Franche-Comte, Besancon, France
| | - Zeynep Coban Akdemir
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; University Texas Health Science Center, Houston, TX 77030, USA
| | - Elizabeth R Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca Okashah Littlejohn
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harpreet K Dibra
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Philip J Byrd
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Bilgen B Geckinli
- Department of Medical Genetics, Marmara University School of Medicine, Istanbul 34722, Turkey
| | - Jennifer Posey
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rachel Westman
- Providence Medical Group Genetic Clinics, Spokane, WA, USA
| | | | - Jacqueline Eason
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Carey-Anne Evans
- Neuroscience Research Australia (NeuRA) Institute, Sydney, NSW, Australia
| | - Gabrielle Lemire
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Grace E VanNoy
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Anne O'Donnell-Luria
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Frédéric Tran Mau-Them
- UF6254 Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Aurélien Juven
- UF6254 Innovation en diagnostic génomique des maladies rares, CHU Dijon Bourgogne, Dijon, France
| | - Juliette Piard
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France
| | - Cheng Yee Nixon
- Neuroscience Research Australia (NeuRA) Institute, Sydney, NSW, Australia
| | - Ying Zhu
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Biophysics and Biomedical Engineering, JHU Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Michael F Buckley
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Christel Thauvin
- INSERM UMR1231 GAD, Bourgogne Franche-Comté University, Dijon, France; Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, Dijon, France
| | - George K Essien Umanah
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lionel Van Maldergem
- Centre de génétique humaine, Université de Franche-Comté, Besançon, France; Clinical Investigation Center 1431, National Institute of Health and Medical Research (INSERM), CHU, Besancon, France; EA481 Integrative and Cognitive Neuroscience Research Unit, University of Franche-Comte, Besancon, France
| | - 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
| | - Tony Roscioli
- Centre for Clinical Genetics, Sydney Children's Hospital, Sydney, NSW, Australia; Neuroscience Research Australia (NeuRA) Institute, Sydney, NSW, Australia; New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Valina L Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder, Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stylianos E Antonarakis
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland; Department of Genetic Medicine and Development, University of Geneva Medical Faculty, Geneva 1211, Switzerland; Medigenome, Swiss Institute of Genomic Medicine, 1207 Geneva, Switzerland.
| |
Collapse
|
15
|
Morimoto M, Bhambhani V, Gazzaz N, Davids M, Sathiyaseelan P, Macnamara EF, Lange J, Lehman A, Zerfas PM, Murphy JL, Acosta MT, Wang C, Alderman E, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Cassini T, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fieg EL, Fisher PG, Fogel BL, Forghani I, Glass I, Gochuico B, Goddard PC, Godfrey RA, Golden-Grant K, Grajewski A, Gutierrez I, Hadley D, Hahn S, Halley MC, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Hutchison S, Introne WJ, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jean-Marie O, Jobanputra V, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, LeBlanc K, Lee BH, Levitt R, Lewis RA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacRae CA, Maduro VV, Mahoney R, Mak BC, Mamounas LA, Manolio TA, Mao R, Maravilla K, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti P, Nakano-Okuno M, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Pusey Swerdzewski BN, Quinlan A, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Toro C, Tran AA, Ungar RA, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Weisz Hubshman M, Wener M, Wenger T, Wesseling Perry K, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Worley K, Xiao C, Yamamoto S, Yang J, Zhang Z, Zuchner S, Reichert S, Thurm A, Adams DR, Introne WJ, Gorski SM, Boerkoel CF, Gahl WA, Tifft CJ, Malicdan MCV. Bi-allelic ATG4D variants are associated with a neurodevelopmental disorder characterized by speech and motor impairment. NPJ Genom Med 2023; 8:4. [PMID: 36765070 PMCID: PMC9918471 DOI: 10.1038/s41525-022-00343-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 12/06/2022] [Indexed: 02/12/2023] Open
Abstract
Autophagy regulates the degradation of damaged organelles and protein aggregates, and is critical for neuronal development, homeostasis, and maintenance, yet few neurodevelopmental disorders have been associated with pathogenic variants in genes encoding autophagy-related proteins. We report three individuals from two unrelated families with a neurodevelopmental disorder characterized by speech and motor impairment, and similar facial characteristics. Rare, conserved, bi-allelic variants were identified in ATG4D, encoding one of four ATG4 cysteine proteases important for autophagosome biogenesis, a hallmark of autophagy. Autophagosome biogenesis and induction of autophagy were intact in cells from affected individuals. However, studies evaluating the predominant substrate of ATG4D, GABARAPL1, demonstrated that three of the four ATG4D patient variants functionally impair ATG4D activity. GABARAPL1 is cleaved or "primed" by ATG4D and an in vitro GABARAPL1 priming assay revealed decreased priming activity for three of the four ATG4D variants. Furthermore, a rescue experiment performed in an ATG4 tetra knockout cell line, in which all four ATG4 isoforms were knocked out by gene editing, showed decreased GABARAPL1 priming activity for the two ATG4D missense variants located in the cysteine protease domain required for priming, suggesting that these variants impair the function of ATG4D. The clinical, bioinformatic, and functional data suggest that bi-allelic loss-of-function variants in ATG4D contribute to the pathogenesis of this syndromic neurodevelopmental disorder.
Collapse
Affiliation(s)
- Marie Morimoto
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Vikas Bhambhani
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Nour Gazzaz
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada ,grid.412125.10000 0001 0619 1117Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mariska Davids
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paalini Sathiyaseelan
- grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Ellen F. Macnamara
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | | | - Anna Lehman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Patricia M. Zerfas
- grid.94365.3d0000 0001 2297 5165Diagnostic and Research Services Branch, Office of Research Services, National Institutes of Health, Bethesda, MD 20892 USA
| | - Jennifer L. Murphy
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Maria T. Acosta
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Camille Wang
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA
| | - Emily Alderman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | | | - Sara Reichert
- grid.418506.e0000 0004 0629 5022Department of Medical Genetics, Children’s Hospitals and Clinics of Minnesota, Minneapolis, MN 55404 USA
| | - Audrey Thurm
- grid.94365.3d0000 0001 2297 5165Neurodevelopmental and Behavioral Phenotyping Service, Office of the Clinical Director, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20892 USA
| | - David R. Adams
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Wendy J. Introne
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Sharon M. Gorski
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.434706.20000 0004 0410 5424Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3 Canada ,grid.61971.380000 0004 1936 7494Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6 Canada
| | - Cornelius F. Boerkoel
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V6H 3N1 Canada ,grid.414137.40000 0001 0684 7788Provincial Medical Genetics Program, British Columbia Women’s and Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - William A. Gahl
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - Cynthia J. Tifft
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | - May Christine V. Malicdan
- grid.94365.3d0000 0001 2297 5165National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, Bethesda, MD 20892 USA ,grid.94365.3d0000 0001 2297 5165Human Biochemical Genetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892 USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Abstract
Exome sequencing (ES) and genome sequencing (GS) have radically transformed the diagnostic approach to undiagnosed rare/ultrarare Mendelian diseases. Next-generation sequencing (NGS), the technology integral for ES, GS, and most large (100+) gene panels, has enabled previously unimaginable diagnoses, changes in medical management, new treatments, and accurate reproductive risk assessments for patients, as well as new disease gene discoveries. Yet, challenges remain, as most individuals remain undiagnosed with current NGS. Improved NGS technology has resulted in long-read sequencing, which may resolve diagnoses in some patients who do not obtain a diagnosis with current short-read ES and GS, but its effectiveness is unclear, and it is expensive. Other challenges that persist include the resolution of variants of uncertain significance, the urgent need for patients with ultrarare disorders to have access to therapeutics, the need for equity in patient access to NGS-based testing, and the study of ethical concerns. However, the outlook for undiagnosed disease resolution is bright, due to continual advancements in the field.
Collapse
Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA;
| |
Collapse
|
17
|
Miller IM, Yashar BM, Macnamara EF, Adams DR, Agrawal PB, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Bayrak-Toydemir P, Beck A, Beggs AH, Behrens E, Bejerano G, Bellen HJ, Bennett J, Berg-Rood B, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Boyd B, Briere LC, Brokamp E, Brown G, Burke EA, Burrage LC, Butte MJ, Byers P, Byrd WE, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Coggins M, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Crouse AB, Cunningham M, D’Souza P, Dai H, Dasari S, Davis J, Dayal JG, Dell’Angelica EC, Dipple K, Doherty D, Dorrani N, Doss AL, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Falk M, Fernandez L, Ferreira C, Fieg EL, Findley LC, Fisher PG, Fogel BL, Forghani I, Gahl WA, Glass I, Gochuico B, Godfrey RA, Golden-Grant K, Goldrich MP, Goldstein DB, Grajewski A, Groden CA, Gutierrez I, Hahn S, Hamid R, Hassey K, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang Y, Huang A, Huryn L, Isasi R, Izumi K, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Karaviti L, Kennedy J, Ketkar S, Kiley D, Kilich G, Kobren SN, Kohane IS, Kohler JN, Korrick S, Kozuira M, Krakow D, Krasnewich DM, Kravets E, Krier JB, Lalani SR, Lam B, Lam C, LaMoure GL, Lanpher BC, Lanza IR, Latham L, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, MacDowall J, Macnamara EF, MacRae CA, Maduro VV, Mahoney R, Mak BC, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martfnez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCray AT, McGee E, Mefford H, Merritt JL, Might M, Mirzaa G, Morava E, Moretti PM, Moretti P, Mosbrook-Davis D, Mulvihill JJ, Nakano-Okuno M, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Nieves-Rodriguez S, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CGS, Papp JC, Parker NH, Phillips JA, Posey JE, Potocki L, Power B, Pusey BN, Quinlan A, Raja AN, Rao DA, Raper A, Raskind W, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rosenwasser N, Rossignol F, Ruzhnikov M, Sacco R, Sampson JB, Saporta M, Schaechter J, Schedl T, Schoch K, Scott DA, Scott CR, Shashi V, Shin J, Signer RH, Silverman EK, Sinsheimer JS, Sisco K, Smith EC, Smith KS, Solem E, Solnica-Krezel L, Solomon B, Spillmann RC, Stoler JM, Sullivan K, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tan QKG, Tan ALM, Tekin M, Telischi F, Thorson W, Thurm A, Tifft CJ, Toro C, Tran AA, Tucker BM, Urv TK, Vanderver A, Velinder M, Viskochil D, Vogel TP, Wahl CE, Walker M, Wallace S, Walley NM, Walsh CA, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Hubshman MW, Wener M, Wenger T, Perry KW, Westerfield M, Wheeler MT, Whitlock J, Wolfe LA, Woods JD, Worley K, Yamamoto S, Yang J, Yousef M, Zastrow DB, Zein W, Zhang Z, Zhao C, Zuchner S, Macnamara EF. Continuing a search for a diagnosis: the impact of adolescence and family dynamics. Orphanet J Rare Dis 2023; 18:6. [PMID: 36624503 PMCID: PMC9830697 DOI: 10.1186/s13023-022-02598-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 12/14/2022] [Indexed: 01/11/2023] Open
Abstract
The "diagnostic odyssey" describes the process those with undiagnosed conditions undergo to identify a diagnosis. Throughout this process, families of children with undiagnosed conditions have multiple opportunities to decide whether to continue or stop their search for a diagnosis and accept the lack of a diagnostic label. Previous studies identified factors motivating a family to begin searching, but there is limited information about the decision-making process in a prolonged search and how the affected child impacts a family's decision. This study aimed to understand how families of children with undiagnosed diseases decide whether to continue to pursue a diagnosis after standard clinical testing has failed. Parents who applied to the Undiagnosed Disease Network (UDN) at the National Institutes of Health (NIH) were recruited to participate in semi-structured interviews. The 2015 Supportive Care Needs model by Pelenstov, which defines critical needs in families with rare/undiagnosed diseases, provided a framework for interview guide development and transcript analysis (Pelentsov et al in Disabil Health J 8(4):475-491, 2015. https://doi.org/10.1016/J.DHJO.2015.03.009 ). A deductive, iterative coding approach was used to identify common unifying themes. Fourteen parents from 13 families were interviewed. The average child's age was 11 years (range 3-18) and an average 63% of their life had been spent searching for a diagnosis. Our analysis found that alignment or misalignment of parent and child needs impact the trajectory of the diagnostic search. When needs and desires align, reevaluation of a decision to pursue a diagnosis is limited. However, when there is conflict between parent and child desires, there is reevaluation, and often a pause, in the search. This tension is exacerbated when children are adolescents and attempting to balance their dependence on parents for medical care with a natural desire for independence. Our results provide novel insights into the roles of adolescents in the diagnostic odyssey. The tension between desired and realistic developmental outcomes for parents and adolescents impacts if, and how, the search for a diagnosis progresses.
Collapse
Affiliation(s)
- Ilana M. Miller
- grid.239560.b0000 0004 0482 1586Children’s National Medical Center, Rare Disease Institute, 7125 13th Place NW, DC 20012 Washington, USA ,grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | - Beverly M. Yashar
- grid.214458.e0000000086837370Department of Human Genetics, University of Michigan, 4909 Buhl Building, Catherine St, Ann Arbor, MI 48109 USA
| | | | - Ellen F. Macnamara
- grid.453125.40000 0004 0533 8641National Institutes of Health Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH, Bethesda, MD USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Bainbridge MN, Mazumder A, Ogasawara D, Abou Jamra R, Bernard G, Bertini E, Burglen L, Cope H, Crawford A, Derksen A, Dure L, Gantz E, Koch-Hogrebe M, Hurst ACE, Mahida S, Marshall P, Micalizzi A, Novelli A, Peng H, Rodriguez D, Robbins SL, Rutledge SL, Scalise R, Schließke S, Shashi V, Srivastava S, Thiffault I, Topol S, Qebibo L, Wieczorek D, Cravatt B, Haricharan S, Torkamani A, Friedman J. Endocannabinoid dysfunction in neurological disease: neuro-ocular DAGLA-related syndrome. Brain 2022; 145:3383-3390. [PMID: 35737950 PMCID: PMC9586540 DOI: 10.1093/brain/awac223] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 04/16/2022] [Accepted: 05/30/2022] [Indexed: 11/12/2022] Open
Abstract
The endocannabinoid system is a highly conserved and ubiquitous signalling pathway with broad-ranging effects. Despite critical pathway functions, gene variants have not previously been conclusively linked to human disease. We identified nine children from eight families with heterozygous, de novo truncating variants in the last exon of DAGLA with a neuro-ocular phenotype characterized by developmental delay, ataxia and complex oculomotor abnormality. All children displayed paroxysms of nystagmus or eye deviation accompanied by compensatory head posture and worsened incoordination most frequently after waking. RNA sequencing showed clear expression of the truncated transcript and no differences were found between mutant and wild-type DAGLA activity. Immunofluorescence staining of patient-derived fibroblasts and HEK cells expressing the mutant protein showed distinct perinuclear aggregation not detected in control samples. This report establishes truncating variants in the last DAGLA exon as the cause of a unique paediatric syndrome. Because enzymatic activity was preserved, the observed mislocalization of the truncated protein may account for the observed phenotype. Potential mechanisms include DAGLA haploinsufficiency at the plasma membrane or dominant negative effect. To our knowledge, this is the first report directly linking an endocannabinoid system component with human genetic disease and sets the stage for potential future therapeutic avenues.
Collapse
Affiliation(s)
- Matthew N Bainbridge
- Rady Children's Institute for Genomic Medicine (RCIGM), San Diego, CA 92123, USA
| | - Aloran Mazumder
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Daisuke Ogasawara
- The Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig 04103, Germany
| | - Geneviève Bernard
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada.,Department of Pediatrics and Human Genetics, McGill University, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada.,Department Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences 'Bambino Gesu' Children's Research Hospital, IRCCS, Rome, Italy
| | - Lydie Burglen
- Centre de Référence Malformations et Maladies Congénitales du Cervelet, Département de génétique, AP-HP Sorbonne Université, Hôpital Trousseau, Paris, France.,Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Heidi Cope
- Department of Pediatrics, Division Medical Genetics Durham, Duke University Medical Center, North Carolina, USA
| | | | - Alexa Derksen
- Department of Neurology and Neurosurgery, McGill University, Montreal, Canada.,Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Canada
| | - Leon Dure
- Division of Pediatric Neurology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Emily Gantz
- Division of Pediatric Neurology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | | | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Paige Marshall
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Alessia Micalizzi
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Roma, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Roma, Italy
| | - Hongfan Peng
- The Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Diana Rodriguez
- Sorbonne Université, INSERM UMR 1141, AP-HP.SU, Centre de Référence Maladies Rares Malformations et Maladies Congénitales du Cervelet & Service de Neuropédiatrie, Hôpital Trousseau, Paris, France
| | - Shira L Robbins
- Ratner Children's Eye Center at the Shiley Eye Institute; Viterbi Family Department of Ophthalmology, University of California San Diego, La Jolla, CA 92093, USA
| | - S Lane Rutledge
- Division of Pediatric Neurology, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35233, USA.,Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Roberta Scalise
- Department of Developmental Neuroscience, IRCCS Stella Maris Foundation, Pisa, Italy.,Tuscan PhD Program of Neuroscience, University of Florence, Pisa and Siena, Florence, Italy
| | - Sophia Schließke
- Institute of Human Genetics, University Medical Center Leipzig, Leipzig 04103, Germany
| | - Vandana Shashi
- Department of Pediatrics, Division Medical Genetics Durham, Duke University Medical Center, North Carolina, USA
| | | | - Isabella Thiffault
- Genomic Medicine Center, Children's Mercy Hospital, Kansas City, Missouri, USA.,Faculty of Medicine, University of Missouri Kansas City, Kansas City, Missouri, USA.,Department of Pathology, Children's Mercy Hospital, Kansas City, Missouri, USA
| | - Sarah Topol
- The Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Leila Qebibo
- Centre de Référence Malformations et Maladies Congénitales du Cervelet, Département de génétique, AP-HP Sorbonne Université, Hôpital Trousseau, Paris, France
| | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, 40225, Düsseldorf, Germany
| | - Benjamin Cravatt
- The Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Svasti Haricharan
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Ali Torkamani
- The Scripps Research Translational Institute, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jennifer Friedman
- Rady Children's Institute for Genomic Medicine (RCIGM), San Diego, CA 92123, USA.,Division of Neurology, Rady Children's Hospital San Diego, CA 92123, USA.,Department of Neurosciences, University of California La Jolla, CA 92037, USA.,Department of Pediatrics, University of California La Jolla, CA 92037, USA
| |
Collapse
|
19
|
Barish S, Senturk M, Schoch K, Minogue AL, Lopergolo D, Fallerini C, Harland J, Seemann JH, Stong N, Kranz PG, Kansagra S, Mikati MA, Jasien J, El-Dairi M, Galluzzi P, Ariani F, Renieri A, Mari F, Wangler MF, Arur S, Jiang YH, Yamamoto S, Shashi V, Bellen HJ. The microRNA processor DROSHA is a candidate gene for a severe progressive neurological disorder. Hum Mol Genet 2022; 31:2934-2950. [PMID: 35405010 PMCID: PMC9433733 DOI: 10.1093/hmg/ddac085] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/14/2022] [Accepted: 04/05/2022] [Indexed: 11/15/2022] Open
Abstract
DROSHA encodes a ribonuclease that is a subunit of the Microprocessor complex and is involved in the first step of microRNA (miRNA) biogenesis. To date, DROSHA has not yet been associated with a Mendelian disease. Here, we describe two individuals with profound intellectual disability, epilepsy, white matter atrophy, microcephaly and dysmorphic features, who carry damaging de novo heterozygous variants in DROSHA. DROSHA is constrained for missense variants and moderately intolerant to loss-of-function (o/e = 0.24). The loss of the fruit fly ortholog drosha causes developmental arrest and death in third instar larvae, a severe reduction in brain size and loss of imaginal discs in the larva. Loss of drosha in eye clones causes small and rough eyes in adult flies. One of the identified DROSHA variants (p.Asp1219Gly) behaves as a strong loss-of-function allele in flies, while another variant (p.Arg1342Trp) is less damaging in our assays. In worms, a knock-in that mimics the p.Asp1219Gly variant at a worm equivalent residue causes loss of miRNA expression and heterochronicity, a phenotype characteristic of the loss of miRNA. Together, our data show that the DROSHA variants found in the individuals presented here are damaging based on functional studies in model organisms and likely underlie the severe phenotype involving the nervous system.
Collapse
Affiliation(s)
- Scott Barish
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Mumine Senturk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda L Minogue
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Diego Lopergolo
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
| | - Jake Harland
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Jacob H Seemann
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, NC 27710, USA
| | - Sujay Kansagra
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Joan Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mays El-Dairi
- Department of Ophthalmology, Duke Health, Durham, NC 27710, USA
| | - Paolo Galluzzi
- Department of Medical Genetics, NeuroImaging and NeuroInterventional Unit, Azienda Ospedaliera e Universitaria, Senese, Siena 53100, Italy
| | - Francesca Ariani
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Francesca Mari
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Swathi Arur
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yong-Hui Jiang
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
- Yale School of Medicine, New Haven, CT 06510, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
20
|
Fiksinski AM, Bearden CE, Bassett AS, Kahn RS, Zinkstok JR, Hooper SR, Tempelaar W, McDonald-McGinn D, Swillen A, Emanuel B, Morrow B, Gur R, Chow E, van den Bree M, Vermeesch J, Warren S, Owen M, van Amelsvoort T, Eliez S, Gothelf D, Arango C, Kates W, Simon T, Murphy K, Repetto G, Suner DH, Vicari S, Cubells J, Armando M, Philip N, Campbell L, Garcia-Minaur S, Schneider M, Shashi V, Vorstman J, Breetvelt EJ. A normative chart for cognitive development in a genetically selected population. Neuropsychopharmacology 2022; 47:1379-1386. [PMID: 33782512 PMCID: PMC9117666 DOI: 10.1038/s41386-021-00988-6] [Citation(s) in RCA: 10] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/12/2021] [Accepted: 01/30/2021] [Indexed: 02/03/2023]
Abstract
Certain pathogenic genetic variants impact neurodevelopment and cause deviations from typical cognitive trajectories. Understanding variant-specific cognitive trajectories is clinically important for informed monitoring and identifying patients at risk for comorbid conditions. Here, we demonstrate a variant-specific normative chart for cognitive development for individuals with 22q11.2 deletion syndrome (22q11DS). We used IQ data from 1365 individuals with 22q11DS to construct variant-specific normative charts for cognitive development (Full Scale, Verbal, and Performance IQ). This allowed us to calculate Z-scores for each IQ datapoint. Then, we calculated the change between first and last available IQ assessments (delta Z-IQ-scores) for each individual with longitudinal IQ data (n = 708). We subsequently investigated whether using the variant-specific IQ-Z-scores would decrease required sample size to detect an effect with schizophrenia risk, as compared to standard IQ-scores. The mean Z-IQ-scores for FSIQ, VIQ, and PIQ were close to 0, indicating that participants had IQ-scores as predicted by the normative chart. The mean delta-Z-IQ-scores were equally close to 0, demonstrating a good fit of the normative chart and indicating that, as a group, individuals with 22q11DS show a decline in IQ-scores as they grow into adulthood. Using variant-specific IQ-Z-scores resulted in 30% decrease of required sample size, as compared to the standard IQ-based approach, to detect the association between IQ-decline and schizophrenia (p < 0.01). Our findings suggest that using variant-specific normative IQ data significantly reduces required sample size in a research context, and may facilitate a more clinically informative interpretation of IQ data. This approach allows identification of individuals that deviate from their expected, variant-specific, trajectory. This group may be at increased risk for comorbid conditions, such as schizophrenia in the case of 22q11DS.
Collapse
Affiliation(s)
- Ania M Fiksinski
- Wilhelmina Children's Hospital & University Medical Center Utrecht, Brain Center, Utrecht, The Netherlands.
- Centre for Addiction and Mental Health, Toronto, ON, Canada.
- The Dalglish Family 22q Clinic for 22q11.2 Deletion Syndrome, Toronto General Hospital, University Health Network, Toronto, ON, Canada.
- Department of Psychiatry and Neuropsychology, Division of Mental Health, MHeNS, Maastricht University, Maastricht, The Netherlands.
| | - Carrie E Bearden
- Departments of Psychiatry and Biobehavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, USA
| | - Anne S Bassett
- The Dalglish Family 22q Clinic, Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - René S Kahn
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Janneke R Zinkstok
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stephen R Hooper
- Department of Allied Health Sciences, School of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Wanda Tempelaar
- Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Donna McDonald-McGinn
- Division of Human Genetics, 22q and You Center, Clinical Genetics Center, and Section of Genetic Counseling, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ann Swillen
- Center for Human Genetics, University Hospital Gasthuisberg, Leuven, Belgium
- Department of Human Genetics KU Leuven, Leuven, Belgium
| | - Beverly Emanuel
- Division of Human Genetics, 22q and You Center, Clinical Genetics Center, and Section of Genetic Counseling, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Bernice Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Raquel Gur
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Eva Chow
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Marianne van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Joris Vermeesch
- Center for Human Genetics, University Hospital Gasthuisberg, Leuven, Belgium
| | - Stephen Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Therese van Amelsvoort
- Department of Psychiatry and Neuropsychology, Division of Mental Health, MHeNS, Maastricht University, Maastricht, The Netherlands
| | - Stephan Eliez
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Doron Gothelf
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Wendy Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Tony Simon
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis, Sacramento, CA, USA
| | - Kieran Murphy
- Department of Psychiatry, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Gabriela Repetto
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Damian Heine Suner
- Genomics of Health Group and Molecular Diagnostics and Clinical Genetics Unit (UDMGC), Health Research Institute of the Balearic Islands (IdISBa), Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Stefano Vicari
- Department of Life Sciences and Public Health, Catholic University; Child and Adolescent Psychiatry Unit, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Joseph Cubells
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Autism Center, Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Marco Armando
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Nicole Philip
- Département de Génétique Médicale, APHM, CHU Timone Enfants, Marseille, France
- Aix Marseille Université, MMG, INSERM, Marseille, France
| | - Linda Campbell
- School of Psychology, University of Newcastle, Newcastle, Australia
| | - Sixto Garcia-Minaur
- Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | - Maude Schneider
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Jacob Vorstman
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Psychiatry, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elemi J Breetvelt
- Department of Psychiatry, The Hospital for Sick Children, Toronto, Ontario, Canada
| |
Collapse
|
21
|
Ritter AL, Gold J, Hayashi H, Ackermann AM, Hanke S, Skraban C, Cuddapah S, Bhoj E, Li D, Kuroda Y, Wen J, Takeda R, Bibb A, El Chehadeh S, Piton A, Ohl J, Kukolich MK, Nagasaki K, Kato K, Ogi T, Bhatti T, Russo P, Krock B, Murrell JR, Sullivan JA, Shashi V, Stong N, Hakonarson H, Sawano K, Torti E, Willaert R, Si Y, Wilcox WR, Wirgenes KV, Thomassen K, Carlotti K, Erwin A, Lazier J, Marquardt T, He M, Edmondson AC, Izumi K. Expanding the phenotypic spectrum of ARCN1-related syndrome. Genet Med 2022; 24:1227-1237. [PMID: 35300924 PMCID: PMC9923403 DOI: 10.1016/j.gim.2022.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 12/10/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 01/18/2023] Open
Abstract
PURPOSE This study aimed to describe the phenotypic and molecular characteristics of ARCN1-related syndrome. METHODS Patients with ARCN1 variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. RESULTS In total, we identified 14 cases of ARCN1-related syndrome, (9 pediatrics, and 5 fetal cases from 3 families). The clinical features these newly identified cases were compared to 6 previously reported cases for a total of 20 cases. Intrauterine growth restriction, micrognathia, and short stature were present in all patients. Other common features included prematurity (11/15, 73.3%), developmental delay (10/14, 71.4%), genitourinary malformations in males (6/8, 75%), and microcephaly (12/15, 80%). Novel features of ARCN1-related syndrome included transient liver dysfunction and specific glycosylation abnormalities during illness, giant cell hepatitis, hepatoblastoma, cataracts, and lethal skeletal manifestations. Developmental delay was seen in 73% of patients, but only 3 patients had intellectual disability, which is less common than previously reported. CONCLUSION ARCN1-related syndrome presents with a wide clinical spectrum ranging from a severe embryonic lethal syndrome to a mild syndrome with intrauterine growth restriction, micrognathia, and short stature without intellectual disability. Patients with ARCN1-related syndrome should be monitored for liver dysfunction during illness, cataracts, and hepatoblastoma. Additional research to further define the phenotypic spectrum and possible genotype-phenotype correlations are required.
Collapse
Affiliation(s)
- Alyssa L Ritter
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jessica Gold
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Hiroshi Hayashi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amanda M Ackermann
- Division of Endocrinology and Diabetes, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Stephanie Hanke
- Division of Endocrinology and Diabetes, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Cara Skraban
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Sanmati Cuddapah
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Elizabeth Bhoj
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Dong Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Yukiko Kuroda
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jessica Wen
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Ryojun Takeda
- Division of Genetics, Nagano Children's Hospital, Nagano, Japan
| | - Audrey Bibb
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Laboratoire de Génétique Médicale, UMR_S1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg et INSERM, Strasbourg, France
| | - Amélie Piton
- Department of Translational Medicine and Neurogenetics, Institut Génétique Biologie Moléculaire Cellulaire, IGBMC - CNRS UMR 7104 - Inserm U 1258, Illkirch, France; Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jeanine Ohl
- Service d'assistance Médicale à la Procréation, Centre médico-chirurgical et obstétrical (CMCO), Schiltigheim, France
| | - Mary K Kukolich
- Department of Genetics, Cook Children's Medical Center, Cook Children's Health Care System, Fort Worth, TX
| | - Keisuke Nagasaki
- Department of Pediatrics, Niigata University Medical & Dental Hospital, Niigata, Japan
| | - Kohji Kato
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Tricia Bhatti
- Division of Anatomic Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Pierre Russo
- Division of Anatomic Pathology, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Bryan Krock
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jill R Murrell
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Durham, NC
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Duke University School of Medicine, Durham, NC
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kentaro Sawano
- Department of Pediatrics, Niigata University Medical & Dental Hospital, Niigata, Japan
| | | | | | | | - William Ross Wilcox
- Department of Human Genetics, Emory University School of Medicine, Emory University, Atlanta, GA
| | - Katrine Verena Wirgenes
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Kristian Thomassen
- Department of Radiology and Nuclear Medicine, Oslo University Hospital, Oslo, Norway
| | | | - Angelika Erwin
- Genomic Medicine Institute, Cleveland Clinic Foundation, Cleveland, OH
| | - Joanna Lazier
- Department of Medical Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Thorsten Marquardt
- Department of Pediatrics, University Hospital of Muenster, Muenster, Germany
| | - Miao He
- Metabolic and Advanced Diagnostics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrew C Edmondson
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kosuke Izumi
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA.
| |
Collapse
|
22
|
Küry S, Ebstein F, Mollé A, Besnard T, Lee MK, Vignard V, Hery T, Nizon M, Mancini GM, Giltay JC, Cogné B, McWalter K, Deb W, Mor-Shaked H, Li H, Schnur RE, Wentzensen IM, Denommé-Pichon AS, Fourgeux C, Verheijen FW, Faurie E, Schot R, Stevens CA, Smits DJ, Barr E, Sheffer R, Bernstein JA, Stimach CL, Kovitch E, Shashi V, Schoch K, Smith W, van Jaarsveld RH, Hurst AC, Smith K, Baugh EH, Bohm SG, Vyhnálková E, Ryba L, Delnatte C, Neira J, Bonneau D, Toutain A, Rosenfeld JA, Audebert-Bellanger S, Gilbert-Dussardier B, Odent S, Laumonnier F, Berger SI, Smith AC, Bourdeaut F, Stern MH, Redon R, Krüger E, Margueron R, Bézieau S, Poschmann J, Isidor B, Isidor B. Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder. Am J Hum Genet 2022; 109:361-372. [PMID: 35051358 DOI: 10.1016/j.ajhg.2021.12.011] [Citation(s) in RCA: 3] [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: 07/22/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Nuclear deubiquitinase BAP1 (BRCA1-associated protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a neurodevelopmental disorder (NDD) or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic NDD. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France.
| |
Collapse
|
23
|
McConkie-Rosell A, Schoch K, Sullivan J, Spillmann RC, Cope H, Tan QKG, Palmer CGS, Hooper SR, Shashi V. Clinical application of a scale to assess genomic healthcare empowerment (GEmS): Process and illustrative case examples. J Genet Couns 2022; 31:59-70. [PMID: 34115423 PMCID: PMC8664895 DOI: 10.1002/jgc4.1451] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/04/2021] [Accepted: 05/09/2021] [Indexed: 02/03/2023]
Abstract
The Genome Empowerment Scale (GEmS), developed as a research tool, assesses perspectives of parents of children with undiagnosed disorders about to undergo exome or genome sequencing related to the process of empowerment. We defined genomic healthcare empowerment as follows: perceived ability to understand and seek new information related to the genomic sequencing, manage emotions related to the diagnostic process and outcomes, and utilize genomic sequencing information to the betterment of the individual/child and family. The GEmS consists of four scales, two are primarily emotion-focused (Meaning of a Diagnosis, and Emotional Management of the Process) and two are action-oriented (Seeking Information and Support, and Implications and Planning). The purpose of this research was to provide a strategy for interpreting results from the GEmS and present illustrative cases. These illustrations should serve to facilitate use of the GEmS in the clinical and research arena, particularly with respect to guiding genetic counseling processes for parents of children with undiagnosed conditions.
Collapse
Affiliation(s)
- Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Jennifer Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Rebecca C. Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Queenie K.-G. Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Christina G. S. Palmer
- Department of Psychiatry and Biobehavioral Sciences, Department of Human Genetics, Institute for Society and Genetics, UCLA, Los Angeles, CA, USA
| | | | - Stephen R. Hooper
- Department of Allied Health Sciences, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| |
Collapse
|
24
|
Rodan LH, Spillmann RC, Kurata HT, Lamothe SM, Maghera J, Jamra RA, Alkelai A, Antonarakis SE, Atallah I, Bar-Yosef O, Bilan F, Bjorgo K, Blanc X, Van Bogaert P, Bolkier Y, Burrage LC, Christ BU, Granadillo JL, Dickson P, Donald KA, Dubourg C, Eliyahu A, Emrick L, Engleman K, Gonfiantini MV, Good JM, Kalser J, Kloeckner C, Lachmeijer G, Macchiaiolo M, Nicita F, Odent S, O'Heir E, Ortiz-Gonzalez X, Pacio-Miguez M, Palomares-Bralo M, Pena L, Platzer K, Quinodoz M, Ranza E, Rosenfeld JA, Roulet-Perez E, Santani A, Santos-Simarro F, Pode-Shakked B, Skraban C, Slaugh R, Superti-Furga A, Thiffault I, van Jaabrsveld RH, Vincent M, Wang HG, Zacher P, Rush E, Pitt GS, Au PYB, Shashi V. Correction: Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations. Genet Med 2021; 23:2016. [PMID: 34522029 DOI: 10.1038/s41436-021-01306-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Lance H Rodan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Harley T Kurata
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Shawn M Lamothe
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Jasmine Maghera
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Omer Bar-Yosef
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Frédéric Bilan
- CHU de Poitiers, Service de Génétique, EA3808 NEUVACOD, Poitiers, France
| | - Kathrine Bjorgo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | | | - Yoav Bolkier
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Pediatric Cardiology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lindsay C Burrage
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Björn U Christ
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
- University of Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Danek Gertner Insitute of Human Genetics, Sheba Medical Center, Tel-Hahsomer, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lisa Emrick
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kendra Engleman
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Jean-Marc Good
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Judith Kalser
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Chiara Kloeckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Guus Lachmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marina Macchiaiolo
- Rare Diseases and Medical Genetic Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neurosciences and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de référence "Maladies Rares" Anomalies du développement CLAD-Ouest, Hôpital SUD, Échirolles, France
| | - Emily O'Heir
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xilma Ortiz-Gonzalez
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marta Pacio-Miguez
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - María Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Loren Pena
- Cincinnati Children's Hospital and Medical Center Cincinnati, Cincinnati, OH, USA
- University of Cincinnati College of Medicine Cincinnati, Cincinnati, OH, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Cara Skraban
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, Nantes, France
| | - Hong-Gang Wang
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Eric Rush
- The Children's Mercy Hospital, Kansas City, MO, USA
- Department of Pediatrics University of Missouri-Kansas City, Kansas City, MO, USA
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Geoffrey S Pitt
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ping Yee Billie Au
- Alberta Children's Hospital Research Institute, Department of Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA.
| |
Collapse
|
25
|
Rodan LH, Spillmann RC, Kurata HT, Lamothe SM, Maghera J, Jamra RA, Alkelai A, Antonarakis SE, Atallah I, Bar-Yosef O, Bilan F, Bjorgo K, Blanc X, Van Bogaert P, Bolkier Y, Burrage LC, Christ BU, Granadillo JL, Dickson P, Donald KA, Dubourg C, Eliyahu A, Emrick L, Engleman K, Gonfiantini MV, Good JM, Kalser J, Kloeckner C, Lachmeijer G, Macchiaiolo M, Nicita F, Odent S, O'Heir E, Ortiz-Gonzalez X, Pacio-Miguez M, Palomares-Bralo M, Pena L, Platzer K, Quinodoz M, Ranza E, Rosenfeld JA, Roulet-Perez E, Santani A, Santos-Simarro F, Pode-Shakked B, Skraban C, Slaugh R, Superti-Furga A, Thiffault I, van Jaabrsveld RH, Vincent M, Wang HG, Zacher P, Rush E, Pitt GS, Au PYB, Shashi V. Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations. Genet Med 2021; 23:1922-1932. [PMID: 34163037 PMCID: PMC8488020 DOI: 10.1038/s41436-021-01232-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/14/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE CACNA1C encodes the alpha-1-subunit of a voltage-dependent L-type calcium channel expressed in human heart and brain. Heterozygous variants in CACNA1C have previously been reported in association with Timothy syndrome and long QT syndrome. Several case reports have suggested that CACNA1C variation may also be associated with a primarily neurological phenotype. METHODS We describe 25 individuals from 22 families with heterozygous variants in CACNA1C, who present with predominantly neurological manifestations. RESULTS Fourteen individuals have de novo, nontruncating variants and present variably with developmental delays, intellectual disability, autism, hypotonia, ataxia, and epilepsy. Functional studies of a subgroup of missense variants via patch clamp experiments demonstrated differential effects on channel function in vitro, including loss of function (p.Leu1408Val), neutral effect (p.Leu614Arg), and gain of function (p.Leu657Phe, p.Leu614Pro). The remaining 11 individuals from eight families have truncating variants in CACNA1C. The majority of these individuals have expressive language deficits, and half have autism. CONCLUSION We expand the phenotype associated with CACNA1C variants to include neurodevelopmental abnormalities and epilepsy, in the absence of classic features of Timothy syndrome or long QT syndrome.
Collapse
Affiliation(s)
- Lance H Rodan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Harley T Kurata
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Shawn M Lamothe
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Jasmine Maghera
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Omer Bar-Yosef
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Frédéric Bilan
- CHU de Poitiers, Service de Génétique, EA3808 NEUVACOD, Poitiers, France
| | - Kathrine Bjorgo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | | | - Yoav Bolkier
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Pediatric Cardiology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lindsay C Burrage
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Björn U Christ
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
- University of Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Danek Gertner Insitute of Human Genetics, Sheba Medical Center, Tel-Hahsomer, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lisa Emrick
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kendra Engleman
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Jean-Marc Good
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Judith Kalser
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Chiara Kloeckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Guus Lachmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marina Macchiaiolo
- Rare Diseases and Medical Genetic Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neurosciences and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de référence "Maladies Rares" Anomalies du développement CLAD-Ouest, Hôpital SUD, Échirolles, France
| | - Emily O'Heir
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xilma Ortiz-Gonzalez
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marta Pacio-Miguez
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - María Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Loren Pena
- Cincinnati Children's Hospital and Medical Center Cincinnati, Cincinnati, OH, USA
- University of Cincinnati College of Medicine Cincinnati, Cincinnati, OH, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Cara Skraban
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, Nantes, France
| | - Hong-Gang Wang
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Eric Rush
- The Children's Mercy Hospital, Kansas City, MO, USA
- Department of Pediatrics University of Missouri-Kansas City, Kansas City, MO, USA
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Geoffrey S Pitt
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ping Yee Billie Au
- Alberta Children's Hospital Research Institute, Department of Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA.
| |
Collapse
|
26
|
Cleynen I, Engchuan W, Hestand MS, Heung T, Holleman AM, Johnston HR, Monfeuga T, McDonald-McGinn DM, Gur RE, Morrow BE, Swillen A, Vorstman JAS, Bearden CE, Chow EWC, van den Bree M, Emanuel BS, Vermeesch JR, Warren ST, Owen MJ, Chopra P, Cutler DJ, Duncan R, Kotlar AV, Mulle JG, Voss AJ, Zwick ME, Diacou A, Golden A, Guo T, Lin JR, Wang T, Zhang Z, Zhao Y, Marshall C, Merico D, Jin A, Lilley B, Salmons HI, Tran O, Holmans P, Pardinas A, Walters JTR, Demaerel W, Boot E, Butcher NJ, Costain GA, Lowther C, Evers R, van Amelsvoort TAMJ, van Duin E, Vingerhoets C, Breckpot J, Devriendt K, Vergaelen E, Vogels A, Crowley TB, McGinn DE, Moss EM, Sharkus RJ, Unolt M, Zackai EH, Calkins ME, Gallagher RS, Gur RC, Tang SX, Fritsch R, Ornstein C, Repetto GM, Breetvelt E, Duijff SN, Fiksinski A, Moss H, Niarchou M, Murphy KC, Prasad SE, Daly EM, Gudbrandsen M, Murphy CM, Murphy DG, Buzzanca A, Fabio FD, Digilio MC, Pontillo M, Marino B, Vicari S, Coleman K, Cubells JF, Ousley OY, Carmel M, Gothelf D, Mekori-Domachevsky E, Michaelovsky E, Weinberger R, Weizman A, Kushan L, Jalbrzikowski M, Armando M, Eliez S, Sandini C, Schneider M, Béna FS, Antshel KM, Fremont W, Kates WR, Belzeaux R, Busa T, Philip N, Campbell LE, McCabe KL, Hooper SR, Schoch K, Shashi V, Simon TJ, Tassone F, Arango C, Fraguas D, García-Miñaúr S, Morey-Canyelles J, Rosell J, Suñer DH, Raventos-Simic J, Epstein MP, Williams NM, Bassett AS. Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion. Mol Psychiatry 2021; 26:4496-4510. [PMID: 32015465 PMCID: PMC7396297 DOI: 10.1038/s41380-020-0654-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/01/2019] [Accepted: 01/16/2020] [Indexed: 12/17/2022]
Abstract
Schizophrenia occurs in about one in four individuals with 22q11.2 deletion syndrome (22q11.2DS). The aim of this International Brain and Behavior 22q11.2DS Consortium (IBBC) study was to identify genetic factors that contribute to schizophrenia, in addition to the ~20-fold increased risk conveyed by the 22q11.2 deletion. Using whole-genome sequencing data from 519 unrelated individuals with 22q11.2DS, we conducted genome-wide comparisons of common and rare variants between those with schizophrenia and those with no psychotic disorder at age ≥25 years. Available microarray data enabled direct comparison of polygenic risk for schizophrenia between 22q11.2DS and independent population samples with no 22q11.2 deletion, with and without schizophrenia (total n = 35,182). Polygenic risk for schizophrenia within 22q11.2DS was significantly greater for those with schizophrenia (padj = 6.73 × 10-6). Novel reciprocal case-control comparisons between the 22q11.2DS and population-based cohorts showed that polygenic risk score was significantly greater in individuals with psychotic illness, regardless of the presence of the 22q11.2 deletion. Within the 22q11.2DS cohort, results of gene-set analyses showed some support for rare variants affecting synaptic genes. No common or rare variants within the 22q11.2 deletion region were significantly associated with schizophrenia. These findings suggest that in addition to the deletion conferring a greatly increased risk to schizophrenia, the risk is higher when the 22q11.2 deletion and common polygenic risk factors that contribute to schizophrenia in the general population are both present.
Collapse
Affiliation(s)
| | - Worrawat Engchuan
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada
| | - Matthew S Hestand
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | | | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas Monfeuga
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Donna M McDonald-McGinn
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Raquel E Gur
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Jacob A S Vorstman
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Carrie E Bearden
- Departments of Psychiatry and Biobehavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Eva W C Chow
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Marianne van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Beverly S Emanuel
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard Duncan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alex V Kotlar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Anna J Voss
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alexander Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aaron Golden
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tingwei Guo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhengdong Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yingjie Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Christian Marshall
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Daniele Merico
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada
- Deep Genomics Inc., Toronto, ON, Canada
| | - Andrea Jin
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brenna Lilley
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Harold I Salmons
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Oanh Tran
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Antonio Pardinas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Erik Boot
- Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Nancy J Butcher
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Gregory A Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Hospital for Sick Children, Toronto, ON, Canada
| | - Chelsea Lowther
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Rens Evers
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | | | - Esther van Duin
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Claudia Vingerhoets
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Jeroen Breckpot
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Koen Devriendt
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Elfi Vergaelen
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Annick Vogels
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - T Blaine Crowley
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel E McGinn
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Edward M Moss
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert J Sharkus
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marta Unolt
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elaine H Zackai
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Monica E Calkins
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert S Gallagher
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruben C Gur
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Sunny X Tang
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Elemi Breetvelt
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, Hospital for Sick Children, Toronto, ON, Canada
| | - Sasja N Duijff
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ania Fiksinski
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hayley Moss
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Maria Niarchou
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | | | - Eileen M Daly
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Maria Gudbrandsen
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Clodagh M Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Declan G Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Antonio Buzzanca
- Department of Human Neurosciences, University Sapienza of Rome, Rome, Italy
| | - Fabio Di Fabio
- Department of Human Neurosciences, University Sapienza of Rome, Rome, Italy
| | | | - Maria Pontillo
- Child and Adolescence Neuropsychiatry Unit, Department of Neuroscience, IRCSS Bambino Gesù Children's Hospital of Rome, Rome, Italy
| | | | - Stefano Vicari
- Child and Adolescence Neuropsychiatry Unit, Department of Neuroscience, IRCSS Bambino Gesù Children's Hospital of Rome, Rome, Italy
| | - Karlene Coleman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Joseph F Cubells
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Opal Y Ousley
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Miri Carmel
- Felsenstein Medical Research Center, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Doron Gothelf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Ehud Mekori-Domachevsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Elena Michaelovsky
- Felsenstein Medical Research Center, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronnie Weinberger
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Abraham Weizman
- Felsenstein Medical Research Center, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Geha Mental Health Center, Petach Tikva, Israel
| | - Leila Kushan
- Departments of Psychiatry and Biobehavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Maria Jalbrzikowski
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marco Armando
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Stéphan Eliez
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Corrado Sandini
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Maude Schneider
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | | | - Kevin M Antshel
- Department of Psychology, Syracuse University, Syracuse, NY, USA
| | - Wanda Fremont
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Raoul Belzeaux
- Pôle de psychiatrie, Hopital Sainte Marguerite, Batiment Solaris, APHM, Marseille, France
| | - Tiffany Busa
- Departement de Genetique Medicale Hôpital d'Enfants de la Timone, APHM, Marseille, France
| | - Nicole Philip
- Departement de Genetique Medicale Aix Marseille Univ, INSERM, GMGF, APHM, Marseille, France
| | | | - Kathryn L McCabe
- University of Newcastle, Callaghan, Australia
- University of California Davis, Davis, CA, USA
| | - Stephen R Hooper
- Department of Allied Health Sciences, School of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC, USA
| | - Tony J Simon
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis, Davis, CA, USA
| | - Flora Tassone
- Department of Microbiology and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - David Fraguas
- Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Sixto García-Miñaúr
- Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | | | | | - Damià H Suñer
- Laboratorio Unidad de Diagnóstico Molecular y Genética Clínica, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | | | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Nigel M Williams
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
27
|
Cope H, Barseghyan H, Bhattacharya S, Fu Y, Hoppman N, Marcou C, Walley N, Rehder C, Deak K, Alkelai A, Vilain E, Shashi V. Detection of a mosaic CDKL5 deletion and inversion by optical genome mapping ends an exhaustive diagnostic odyssey. Mol Genet Genomic Med 2021; 9:e1665. [PMID: 33955715 PMCID: PMC8372083 DOI: 10.1002/mgg3.1665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Currently available structural variant (SV) detection methods do not span the complete spectrum of disease-causing SVs. Optical genome mapping (OGM), an emerging technology with the potential to resolve diagnostic dilemmas, was performed to investigate clinically-relevant SVs in a 4-year-old male with an epileptic encephalopathy of undiagnosed molecular origin. METHODS OGM was utilized to image long, megabase-size DNA molecules, fluorescently labeled at specific sequence motifs throughout the genome with high sensitivity for detection of SVs greater than 500 bp in size. OGM results were confirmed in a CLIA-certified laboratory via mate-pair sequencing. RESULTS OGM identified a mosaic, de novo 90 kb deletion and inversion on the X chromosome disrupting the CDKL5 gene. Detection of the mosaic deletion, which had been previously undetected by chromosomal microarray, an infantile epilepsy panel including exon-level microarray for CDKL5, exome sequencing as well as genome sequencing, resulted in a diagnosis of X-linked dominant early infantile epileptic encephalopathy-2. CONCLUSION OGM affords an effective technology for the detection of SVs, especially those that are mosaic, since these remain difficult to detect with current NGS technologies and with conventional chromosomal microarrays. Further research in undiagnosed populations with OGM is warranted.
Collapse
Affiliation(s)
- Heidi Cope
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Hayk Barseghyan
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
- Bionano Genomics IncSan DiegoCAUSA
| | | | - Yulong Fu
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
| | - Nicole Hoppman
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Cherisse Marcou
- Division of Laboratory Genetics and GenomicsDepartment of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
| | - Nicole Walley
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| | - Catherine Rehder
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Kristen Deak
- Department of PathologyDuke University Medical CenterDurhamNCUSA
| | - Anna Alkelai
- Institute for Genomic MedicineColumbia University Medical CenterNew YorkNYUSA
| | - Eric Vilain
- Center for Genetic Medicine ResearchChildren’s National HospitalWashingtonDCUSA
- Department of genomics and Precision MedicineSchool of Medicine and Health SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Vandana Shashi
- Division of Medical GeneticsDepartment of PediatricsDuke University Medical CenterDurhamNCUSA
| |
Collapse
|
28
|
Parenti I, Lehalle D, Nava C, Torti E, Leitão E, Person R, Mizuguchi T, Matsumoto N, Kato M, Nakamura K, de Man SA, Cope H, Shashi V, Friedman J, Joset P, Steindl K, Rauch A, Muffels I, van Hasselt PM, Petit F, Smol T, Le Guyader G, Bilan F, Sorlin A, Vitobello A, Philippe C, van de Laar IMBH, van Slegtenhorst MA, Campeau PM, Au PYB, Nakashima M, Saitsu H, Yamamoto T, Nomura Y, Louie RJ, Lyons MJ, Dobson A, Plomp AS, Motazacker MM, Kaiser FJ, Timberlake AT, Fuchs SA, Depienne C, Mignot C. Missense and truncating variants in CHD5 in a dominant neurodevelopmental disorder with intellectual disability, behavioral disturbances, and epilepsy. Hum Genet 2021; 140:1109-1120. [PMID: 33944996 PMCID: PMC8197709 DOI: 10.1007/s00439-021-02283-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [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: 01/29/2021] [Accepted: 04/15/2021] [Indexed: 12/27/2022]
Abstract
Located in the critical 1p36 microdeletion region, the chromodomain helicase DNA-binding protein 5 (CHD5) gene encodes a subunit of the nucleosome remodeling and deacetylation (NuRD) complex required for neuronal development. Pathogenic variants in six of nine chromodomain (CHD) genes cause autosomal dominant neurodevelopmental disorders, while CHD5-related disorders are still unknown. Thanks to GeneMatcher and international collaborations, we assembled a cohort of 16 unrelated individuals harboring heterozygous CHD5 variants, all identified by exome sequencing. Twelve patients had de novo CHD5 variants, including ten missense and two splice site variants. Three familial cases had nonsense or missense variants segregating with speech delay, learning disabilities, and/or craniosynostosis. One patient carried a frameshift variant of unknown inheritance due to unavailability of the father. The most common clinical features included language deficits (81%), behavioral symptoms (69%), intellectual disability (64%), epilepsy (62%), and motor delay (56%). Epilepsy types were variable, with West syndrome observed in three patients, generalized tonic-clonic seizures in two, and other subtypes observed in one individual each. Our findings suggest that, in line with other CHD-related disorders, heterozygous CHD5 variants are associated with a variable neurodevelopmental syndrome that includes intellectual disability with speech delay, epilepsy, and behavioral problems as main features.
Collapse
Affiliation(s)
- Ilaria Parenti
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Daphné Lehalle
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Caroline Nava
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013, Paris, France
| | | | - Elsa Leitão
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | - Takeshi Mizuguchi
- 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
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, 142-8666, Japan
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University Faculty of Medicine, Yamagata, 990-9585, Japan
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer Friedman
- Departments of Neuroscience and Pediatrics, Division of Neurology, Rady Children's Hospital, UCSD, San Diego and Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
- Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases University of Zurich, 8032, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
- Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases University of Zurich, 8032, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
- Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases University of Zurich, 8032, Zurich, Switzerland
| | - Irena Muffels
- Department of Metabolic Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Peter M van Hasselt
- Department of Metabolic Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | | | - Thomas Smol
- Institut de Génétique Médicale, CHRU Lille, Université de Lille, Lille, France
| | - Gwenaël Le Guyader
- Service de Génétique Médicale, CHU de Poitiers, Poitiers, France
- EA3808 NEUVACOD, University of Poitiers, Poitiers, France
| | - Frédéric Bilan
- Service de Génétique Médicale, CHU de Poitiers, Poitiers, France
- EA3808 NEUVACOD, University of Poitiers, Poitiers, France
| | - Arthur Sorlin
- Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
- Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs », Centre de Génétique, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
| | - Christophe Philippe
- Unité Fonctionnelle d'Innovation Diagnostique des Maladies Rares, FHU-TRANSLAD, France Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Centre Hospitalier Universitaire Dijon Bourgogne, CHU Dijon Bourgogne, Dijon, France
- INSERM-Université de Bourgogne UMR1231 GAD « Génétique Des Anomalies du Développement », FHU-TRANSLAD, UFR Des Sciences de Santé, Dijon, France
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marjon A van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Philippe M Campeau
- CHU Sainte-Justine Research Center, Montreal, QC, H3T 1C5, Canada
- Sainte-Justine Hospital, University of Montreal, Montreal, QC, H3T 1C5, Canada
| | - Ping Yee Billie Au
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
| | - Tatsuya Yamamoto
- Department of Pediatrics, Hirosaki University Graduate School of Medicine and School of Medicine, Hirosaki, 036-8562, Japan
| | - Yumiko Nomura
- Department of Pediatrics, Hirosaki National Hospital, Hirosaki, 036-8545, Japan
- Aomori City Health Center, Aomori, 030-0962, Japan
| | | | | | - Amy Dobson
- Greenwood Genetic Center, Greenwood, SC, 29646, USA
| | - Astrid S Plomp
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - M Mahdi Motazacker
- Laboratory of Genome Diagnostics, Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Frank J Kaiser
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Andrew T Timberlake
- Hansjörg Wyss Department of Plastic Surgery, NYU Langone Health, New York, NY, USA
| | - Sabine A Fuchs
- Department of Metabolic Diseases, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany.
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013, Paris, France.
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière and Hôpital Trousseau, APHP, Sorbonne Université, Paris, France.
- Institut du Cerveau (ICM), UMR S 1127, Inserm U1127, CNRS UMR 7225, Sorbonne Université, 75013, Paris, France.
| |
Collapse
|
29
|
Luo X, Schoch K, Jangam SV, Bhavana VH, Graves HK, Kansagra S, Jasien JM, Stong N, Keren B, Mignot C, Ravelli C, Bellen HJ, Wangler MF, Shashi V, Yamamoto S. Rare deleterious de novo missense variants in Rnf2/Ring2 are associated with a neurodevelopmental disorder with unique clinical features. Hum Mol Genet 2021; 30:1283-1292. [PMID: 33864376 PMCID: PMC8255132 DOI: 10.1093/hmg/ddab110] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 01/16/2023] Open
Abstract
The Polycomb group (PcG) gene RNF2 (RING2) encodes a catalytic subunit of the Polycomb repressive complex 1 (PRC1), an evolutionarily conserved machinery that post-translationally modifies chromatin to maintain epigenetic transcriptional repressive states of target genes including Hox genes. Here, we describe two individuals, each with rare de novo missense variants in RNF2. Their phenotypes include intrauterine growth retardation, severe intellectual disabilities, behavioral problems, seizures, feeding difficulties and dysmorphic features. Population genomics data suggest that RNF2 is highly constrained for loss-of-function (LoF) and missense variants, and both p.R70H and p.S82R variants have not been reported to date. Structural analyses of the two alleles indicate that these changes likely impact the interaction between RNF2 and BMI1, another PRC1 subunit or its substrate Histone H2A, respectively. Finally, we provide functional data in Drosophila that these two missense variants behave as LoF alleles in vivo. The evidence provide support for deleterious alleles in RNF2 being associated with a new and recognizable genetic disorder. This tentative gene-disease association in addition to the 12 previously identified disorders caused by PcG genes attests to the importance of these chromatin regulators in Mendelian disorders.
Collapse
Affiliation(s)
- Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Sharayu V Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Venkata Hemanjani Bhavana
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hillary K Graves
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Sujay Kansagra
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Joan M Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Boris Keren
- Département de Génétique, Hospitalier Pitié-Salpêtrière, APHP, Paris 75013, France
- Sorbonne Université, Paris 75006, France
| | - Cyril Mignot
- Sorbonne Université, Paris 75006, France
- APHP, Sorbonne Université, Département de Génétique et Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière et Hôpital Trousseau, Paris 75013, France
| | - Claudia Ravelli
- Sorbonne Université, Paris 75006, France
- Département de Neuropédiatrie, Hôpital Armand Trousseau, APHP, Paris 75012, France
| | | | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, BCM, Houston, TX 77030, USA
- Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, BCM, Houston, TX 77030, USA
| |
Collapse
|
30
|
Bowles B, Ferrer A, Nishimura CJ, Pinto E Vairo F, Rey T, Leheup B, Sullivan J, Schoch K, Stong N, Agolini E, Cocciadiferro D, Williams A, Cummings A, Loddo S, Genovese S, Roadhouse C, McWalter K, Wentzensen IM, Li C, Babovic-Vuksanovic D, Lanpher BC, Dentici ML, Ankala A, Hamm JA, Dallapiccola B, Radio FC, Shashi V, Gérard B, Bloch-Zupan A, Smith RJ, Klee EW. TSPEAR variants are primarily associated with ectodermal dysplasia and tooth agenesis but not hearing loss: A novel cohort study. Am J Med Genet A 2021; 185:2417-2433. [PMID: 34042254 PMCID: PMC8361973 DOI: 10.1002/ajmg.a.62347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 10/21/2020] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 12/30/2022]
Abstract
Biallelic loss‐of‐function variants in the thrombospondin‐type laminin G domain and epilepsy‐associated repeats (TSPEAR) gene have recently been associated with ectodermal dysplasia and hearing loss. The first reports describing a TSPEAR disease association identified this gene is a cause of nonsyndromic hearing loss, but subsequent reports involving additional affected families have questioned this evidence and suggested a stronger association with ectodermal dysplasia. To clarify genotype–phenotype associations for TSPEAR variants, we characterized 13 individuals with biallelic TSPEAR variants. Individuals underwent either exome sequencing or panel‐based genetic testing. Nearly all of these newly reported individuals (11/13) have phenotypes that include tooth agenesis or ectodermal dysplasia, while three newly reported individuals have hearing loss. Of the individuals displaying hearing loss, all have additional variants in other hearing‐loss‐associated genes, specifically TMPRSS3, GJB2, and GJB6, that present competing candidates for their hearing loss phenotype. When presented alongside previous reports, the overall evidence supports the association of TSPEAR variants with ectodermal dysplasia and tooth agenesis features but creates significant doubt as to whether TSPEAR variants are a monogenic cause of hearing loss. Further functional evidence is needed to evaluate this phenotypic association.
Collapse
Affiliation(s)
- Bradley Bowles
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Alejandro Ferrer
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Carla J Nishimura
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Filippo Pinto E Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Tristan Rey
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Bruno Leheup
- Département de Médecine Infantile, CHRU de Nancy, Nancy, France
| | - Jennifer Sullivan
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Kelly Schoch
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA.,Brystol Myers Squibb, New York, New York, USA
| | - Emanuele Agolini
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Abigail Williams
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Alex Cummings
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA.,University of Wisconsin Hospitals and Clinics, Madison, Wisconsin, USA
| | - Sara Loddo
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chelsea Roadhouse
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | | | | | - Chumei Li
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Dusica Babovic-Vuksanovic
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Brendan C Lanpher
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota, USA
| | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Arun Ankala
- EGL Genetics LLC, Tucker, Georgia, USA.,Emory University School of Medicine, Atlanta, Georgia, USA
| | - J Austin Hamm
- Department of Pediatrics, East Tennessee Children's Hospital, Knoxville, Tennessee, USA
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesca Clementina Radio
- Genetics and Rare Diseases Research Division, Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Benedicte Gérard
- Laboratoires de Diagnostic génétique, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
| | - Agnes Bloch-Zupan
- Faculté de Chirurgie Dentaire, Université de Strasbourg, Strasbourg, France.,Centre de référence des maladies rares orales et dentaires O-Rares, Filière Santé Maladies rares TETE COU, European Reference Network CRANIO, Pôle de Médecine et Chirurgie Bucco-dentaires, Hôpital Civil, Hôpitaux Universitaires de Strasbourg (HUS), Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Illkirch, France
| | - Richard J Smith
- Molecular Otolaryngology and Renal Research Laboratories, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
31
|
Dias C, Pfundt R, Kleefstra T, Shuurs-Hoeijmakers J, Boon EMJ, van Hagen JM, Zwijnenburg P, Weiss MM, Keren B, Mignot C, Isapof A, Weiss K, Hershkovitz T, Iascone M, Maitz S, Feichtinger RG, Kotzot D, Mayr JA, Ben-Omran T, Mahmoud L, Pais LS, Walsh CA, Shashi V, Sullivan JA, Stong N, Lecoquierre F, Guerrot AM, Charollais A, Rodan LH. De novo variants in TCF7L2 are associated with a syndromic neurodevelopmental disorder. Am J Med Genet A 2021; 185:2384-2390. [PMID: 34003604 DOI: 10.1002/ajmg.a.62254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 01/18/2021] [Revised: 03/25/2021] [Accepted: 04/24/2021] [Indexed: 01/21/2023]
Abstract
TCF7L2 encodes transcription factor 7-like 2 (OMIM 602228), a key mediator of the evolutionary conserved canonical Wnt signaling pathway. Although several large-scale sequencing studies have implicated TCF7L2 in intellectual disability and autism, both the genetic mechanism and clinical phenotype have remained incompletely characterized. We present here a comprehensive genetic and phenotypic description of 11 individuals who have been identified to carry de novo variants in TCF7L2, both truncating and missense. Missense variation is clustered in or near a high mobility group box domain, involving this region in these variants' pathogenicity. All affected individuals present with developmental delays in childhood, but most ultimately achieved normal intelligence or had only mild intellectual disability. Myopia was present in approximately half of the individuals, and some individuals also possessed dysmorphic craniofacial features, orthopedic abnormalities, or neuropsychiatric comorbidities including autism and attention-deficit/hyperactivity disorder (ADHD). We thus present an initial clinical and genotypic spectrum associated with variation in TCF7L2, which will be important in informing both medical management and future research.
Collapse
Affiliation(s)
- Caroline Dias
- Division of Developmental Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rolph Pfundt
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Tjitske Kleefstra
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, Netherlands.,Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | | | - Elles M J Boon
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Petra Zwijnenburg
- Department of Clinical Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Marjan M Weiss
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Boris Keren
- Département de Génétique, hôpital Pitié-Salpêtrière, APHP.Sorbonne Université, Paris, France
| | - Cyril Mignot
- Département de Génétique, hôpital Pitié-Salpêtrière, APHP.Sorbonne Université, Paris, France
| | - Arnaud Isapof
- Service de Neurologie Pédiatrique, Hôpital Armand Trousseau, APHP, Sorbonne Université, Paris, France
| | - Karin Weiss
- Genetics Institute, Rambam Health Care Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Tova Hershkovitz
- Genetics Institute, Rambam Health Care Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Silvia Maitz
- Clinical Pediatric Genetic Unit, Pediatric Clinic, Fondazione MBBM, San Gerardo Hospital, Monza, Italy
| | - René G Feichtinger
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Dieter Kotzot
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Johannes A Mayr
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU) Salzburg, Salzburg, Austria
| | - Tawfeg Ben-Omran
- Department of Pediatrics, Sidra Medicine, Department of Medical Genetics, Hamad Medical Corporation, Weill Cornell Medical College, Doha, Qatar
| | - Laila Mahmoud
- Department of Pediatrics, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Lynn S Pais
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Francois Lecoquierre
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Univ, UNIROUEN, Inserm U1245, Rouen, France
| | - Anne-Marie Guerrot
- Department of Genetics and Reference Center for Developmental Disorders, Normandy Center for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Univ, UNIROUEN, Inserm U1245, Rouen, France
| | - Aude Charollais
- Reference Centre for Learning Disorders, Rouen University Hospital, F-76031 Rouen Cedex, Rouen, France.,Department of Neonatology and Paediatric Intensive Care, Rouen University Hospital, F-76031 Cedex, Rouen, France
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
32
|
Cappuccio G, Ceccatelli Berti C, Baruffini E, Sullivan J, Shashi V, Jewett T, Stamper T, Maitz S, Canonico F, Revah-Politi A, Kupchik GS, Anyane-Yeboa K, Aggarwal V, Benneche A, Bratland E, Berland S, D'Arco F, Alves CA, Vanderver A, Longo D, Bertini E, Torella A, Nigro V, D'Amico A, van der Knaap MS, Goffrini P, Brunetti-Pierri N. Bi-allelic KARS1 pathogenic variants affecting functions of cytosolic and mitochondrial isoforms are associated with a progressive and multisystem disease. Hum Mutat 2021; 42:745-761. [PMID: 33942428 PMCID: PMC8251883 DOI: 10.1002/humu.24210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/09/2020] [Revised: 03/10/2021] [Accepted: 04/07/2021] [Indexed: 12/12/2022]
Abstract
KARS1 encodes a lysyl‐transfer RNA synthetase (LysRS) that links lysine to its cognate transfer RNA. Two different KARS1 isoforms exert functional effects in cytosol and mitochondria. Bi‐allelic pathogenic variants in KARS1 have been associated to sensorineural hearing and visual loss, neuropathy, seizures, and leukodystrophy. We report the clinical, biochemical, and neuroradiological features of nine individuals with KARS1‐related disorder carrying 12 different variants with nine of them being novel. The consequences of these variants on the cytosol and/or mitochondrial LysRS were functionally validated in yeast mutants. Most cases presented with severe neurological features including congenital and progressive microcephaly, seizures, developmental delay/intellectual disability, and cerebral atrophy. Oculo‐motor dysfunction and immuno‐hematological problems were present in six and three cases, respectively. A yeast growth defect of variable severity was detected for most variants on both cytosolic and mitochondrial isoforms. The detrimental effects of two variants on yeast growth were partially rescued by lysine supplementation. Congenital progressive microcephaly, oculo‐motor dysfunction, and immuno‐hematological problems are emerging phenotypes in KARS1‐related disorder. The data in yeast emphasize the role of both mitochondrial and cytosolic isoforms in the pathogenesis of KARS1‐related disorder and supports the therapeutic potential of lysine supplementation at least in a subset of patients.
Collapse
Affiliation(s)
- Gerarda Cappuccio
- Department of Translational Medicine, Federico II University, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| | - Camilla Ceccatelli Berti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Enrico Baruffini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Jennifer Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Tamison Jewett
- Department of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Tara Stamper
- Department of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Silvia Maitz
- Clinical Pediatric Genetics Unit, Pediatrics Clinics, MBBM Foundation, Hospital San Gerardo, Monza, Italy
| | - Francesco Canonico
- Department of Neuroradiology, San Gerardo Hospital, ASST di Monza, Università degli Studi di Milano Bicocca, Monza, Italy
| | - Anya Revah-Politi
- Department of Pathology and Cell Biology, Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Gabriel S Kupchik
- Division of Medical Genetics, Maimonides Children's Hospital of Brooklyn at Maimonides Medical Center, Downstate Medical Center, State University of New York, New York, New York, USA
| | - Kwame Anyane-Yeboa
- Department of Pediatrics, Institute for Genomic Medicine Columbia University Medical Center, New York, New York, USA
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | - Andreas Benneche
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Eirik Bratland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Siren Berland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Felice D'Arco
- Department of Paediatric Neuroradiology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Cesar A Alves
- Division of Neuroradiology, Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Adeline Vanderver
- Division of Neurology, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniela Longo
- Department of Diagnostic Imaging, Pediatric Hospital Bambino Gesù, Rome, Italy
| | - Enrico Bertini
- Department of Neuroscience, Unit of Neuromuscular and Neurodegenerative Diseases, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy.,Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy.,Department of Precision Medicine, University of Campania Luigi Vanvitelli, Naples, Italy
| | | | - Alessandra D'Amico
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
| | - Marjo S van der Knaap
- Department of Child Neurology, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam University Medical Centers and Amsterdam Neuroscience, Amsterdam, The Netherlands.,Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Paola Goffrini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy
| |
Collapse
|
33
|
Rehder C, Bean LJH, Bick D, Chao E, Chung W, Das S, O'Daniel J, Rehm H, Shashi V, Vincent LM. Next-generation sequencing for constitutional variants in the clinical laboratory, 2021 revision: a technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1399-1415. [PMID: 33927380 DOI: 10.1038/s41436-021-01139-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technologies are now established in clinical laboratories as a primary testing modality in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude. It is now cost-effective to analyze an individual with disease-targeted gene panels, exome sequencing, or genome sequencing to assist in the diagnosis of a wide array of clinical scenarios. While clinical validation and use of NGS in many settings is established, there are continuing challenges as technologies and the associated informatics evolve. To assist clinical laboratories with the validation of NGS methods and platforms, the ongoing monitoring of NGS testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics (ACMG) has developed the following technical standards.
Collapse
Affiliation(s)
| | - Lora J H Bean
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Elizabeth Chao
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, CA, USA
| | - Wendy Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Julianne O'Daniel
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Heidi Rehm
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC, USA
| | - Lisa M Vincent
- Division of Pathology & Laboratory Medicine, Children's National Health System, Washington, DC, USA.,Departments of Pathology and Pediatrics, George Washington University, Washington, DC, USA
| | | |
Collapse
|
34
|
Moya-Mendez ME, Mueller DM, Pratt M, Bonner M, Elliott C, Hunanyan A, Kucera G, Bock C, Prange L, Jasien J, Keough K, Shashi V, McDonald M, Mikati MA. Early onset severe ATP1A2 epileptic encephalopathy: Clinical characteristics and underlying mutations. Epilepsy Behav 2021; 116:107732. [PMID: 33493807 PMCID: PMC7940561 DOI: 10.1016/j.yebeh.2020.107732] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 11/09/2020] [Accepted: 12/20/2020] [Indexed: 01/26/2023]
Abstract
BACKGROUND ATP1A2 mutations cause hemiplegic migraine with or without epilepsy or acute reversible encephalopathy. Typical onset is in adulthood or older childhood without subsequent severe long-term developmental impairments. AIM We aimed to describe the manifestations of early onset severe ATP1A2-related epileptic encephalopathy and its underlying mutations in a cohort of seven patients. METHODS A retrospective chart review of a cohort of seven patients was conducted. Response to open-label memantine therapy, used off-label due to its NMDA receptor antagonist effects, was assessed by the Global Rating Scale of Change (GRSC) and Clinical Global Impression Scale of Improvement (CGI-I) methodologies. Molecular modeling was performed using PyMol program. RESULTS Patients (age 2.5-20 years) had symptom onset at an early age (6 days-1 year). Seizures were either focal or generalized. Common features were: drug resistance, recurrent status epilepticus, etc., severe developmental delay with episodes of acute severe encephalopathy often with headaches, dystonias, hemiplegias, seizures, and developmental regression. All had variants predicted to be disease causing (p.Ile293Met, p.Glu1000Lys, c.1017+5G>A, p.Leu809Arg, and 3 patients with p.Met813Lys). Modeling revealed that mutations interfered with ATP1A2 ion binding and translocation sites. Memantine, given to five, was tolerated in all (mean treatment: 2.3 years, range 6 weeks-4.8 years) with some improvements reported in all five. CONCLUSIONS Our observations describe a distinctive clinical profile of seven unrelated probands with early onset severe ATP1A2-related epileptic encephalopathy, provide insights into structure-function relationships of ATP1A2 mutations, and support further studies of NMDAR antagonist therapy in ATP1A2-encephalopathy.
Collapse
Affiliation(s)
- Mary E. Moya-Mendez
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Medicine, Duke University, Durham, NC, United States
| | - David M. Mueller
- Center for Genetic Diseases, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, Chicago, IL, United States
| | - Milton Pratt
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Medicine, Duke University, Durham, NC, United States
| | - Melanie Bonner
- Department of Psychiatry, Duke University, Durham, NC, United States
| | - Courtney Elliott
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Medicine, Duke University, Durham, NC, United States
| | - Arsen Hunanyan
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Medicine, Duke University, Durham, NC, United States
| | - Gary Kucera
- Duke Cancer Institute Rodent Cancer Models Shared Resource, Duke University Medical Center, Durham, NC, United States
| | - Cheryl Bock
- Duke Cancer Institute Rodent Cancer Models Shared Resource, Duke University Medical Center, Durham, NC, United States
| | - Lyndsey Prange
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Medicine, Duke University, Durham, NC, United States
| | - Joan Jasien
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Medicine, Duke University, Durham, NC, United States
| | - Karen Keough
- Dell Medical School at the University of Texas, Austin TX, United States
| | - Vandana Shashi
- Dell Medical School at the University of Texas, Austin TX, United States
| | - Marie McDonald
- Dell Medical School at the University of Texas, Austin TX, United States
| | - Mohamad A. Mikati
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Medicine, Duke University, Durham, NC, United States,Department of Neurobiology, Duke University, Durham, NC, United States,Corresponding Author: Mohamad Mikati, MD, Children Health Center, T913J, Duke University Medical Center, 2301 Erwin Road, Durham, NC 27710, Phone: 919-668-4073, Fax: 919-681-8943,
| |
Collapse
|
35
|
Weng PL, Majmundar AJ, Khan K, Lim TY, Shril S, Jin G, Musgrove J, Wang M, Ahram DF, Aggarwal VS, Bier LE, Heinzen EL, Onuchic-Whitford AC, Mann N, Buerger F, Schneider R, Deutsch K, Kitzler TM, Klämbt V, Kolb A, Mao Y, Moufawad El Achkar C, Mitrotti A, Martino J, Beck BB, Altmüller J, Benz MR, Yano S, Mikati MA, Gunduz T, Cope H, Shashi V, Trachtman H, Bodria M, Caridi G, Pisani I, Fiaccadori E, AbuMaziad AS, Martinez-Agosto JA, Yadin O, Zuckerman J, Kim A, John-Kroegel U, Tyndall AV, Parboosingh JS, Innes AM, Bierzynska A, Koziell AB, Muorah M, Saleem MA, Hoefele J, Riedhammer KM, Gharavi AG, Jobanputra V, Pierce-Hoffman E, Seaby EG, O'Donnell-Luria A, Rehm HL, Mane S, D'Agati VD, Pollak MR, Ghiggeri GM, Lifton RP, Goldstein DB, Davis EE, Hildebrandt F, Sanna-Cherchi S. De novo TRIM8 variants impair its protein localization to nuclear bodies and cause developmental delay, epilepsy, and focal segmental glomerulosclerosis. Am J Hum Genet 2021; 108:357-367. [PMID: 33508234 PMCID: PMC7895901 DOI: 10.1016/j.ajhg.2021.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 07/27/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
Focal segmental glomerulosclerosis (FSGS) is the main pathology underlying steroid-resistant nephrotic syndrome (SRNS) and a leading cause of chronic kidney disease. Monogenic forms of pediatric SRNS are predominantly caused by recessive mutations, while the contribution of de novo variants (DNVs) to this trait is poorly understood. Using exome sequencing (ES) in a proband with FSGS/SRNS, developmental delay, and epilepsy, we discovered a nonsense DNV in TRIM8, which encodes the E3 ubiquitin ligase tripartite motif containing 8. To establish whether TRIM8 variants represent a cause of FSGS, we aggregated exome/genome-sequencing data for 2,501 pediatric FSGS/SRNS-affected individuals and 48,556 control subjects, detecting eight heterozygous TRIM8 truncating variants in affected subjects but none in control subjects (p = 3.28 × 10-11). In all six cases with available parental DNA, we demonstrated de novo inheritance (p = 2.21 × 10-15). Reverse phenotyping revealed neurodevelopmental disease in all eight families. We next analyzed ES from 9,067 individuals with epilepsy, yielding three additional families with truncating TRIM8 variants. Clinical review revealed FSGS in all. All TRIM8 variants cause protein truncation clustering within the last exon between residues 390 and 487 of the 551 amino acid protein, indicating a correlation between this syndrome and loss of the TRIM8 C-terminal region. Wild-type TRIM8 overexpressed in immortalized human podocytes and neuronal cells localized to nuclear bodies, while constructs harboring patient-specific variants mislocalized diffusely to the nucleoplasm. Co-localization studies demonstrated that Gemini and Cajal bodies frequently abut a TRIM8 nuclear body. Truncating TRIM8 DNVs cause a neuro-renal syndrome via aberrant TRIM8 localization, implicating nuclear bodies in FSGS and developmental brain disease.
Collapse
Affiliation(s)
- Patricia L Weng
- Division of Pediatric Nephrology, UCLA, Los Angeles, CA 90095, USA
| | - Amar J Majmundar
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Kamal Khan
- Center for Disease Modeling, Duke University, Durham, NC 27701, USA; Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Tze Y Lim
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Shirlee Shril
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Gina Jin
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - John Musgrove
- Center for Disease Modeling, Duke University, Durham, NC 27701, USA; Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27705, USA
| | - Minxian Wang
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Dina F Ahram
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Vimla S Aggarwal
- Institute of Genomic Medicine, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Louise E Bier
- Institute of Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Erin L Heinzen
- Institute of Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Ana C Onuchic-Whitford
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nina Mann
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Florian Buerger
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ronen Schneider
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Konstantin Deutsch
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Thomas M Kitzler
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Verena Klämbt
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Amy Kolb
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Youying Mao
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christelle Moufawad El Achkar
- Division of Epilepsy and Clinical Neurophysiology, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Adele Mitrotti
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Jeremiah Martino
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Bodo B Beck
- Institute of Human Genetics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Janine Altmüller
- Center for Molecular Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | | | - Shoji Yano
- Genetics Division, Department of Pediatrics, LAC+USC Medical Center, Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology and Developmental Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Talha Gunduz
- Division of Pediatric Neurology and Developmental Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics. Duke University Medical Center, Durham, NC 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics. Duke University Medical Center, Durham, NC 27710, USA
| | - Howard Trachtman
- Department of Pediatrics, Division of Nephrology, New York University Langone Health, New York, NY 10016, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis and Transplantation, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Giannina Gaslini, 16147 Genova GE, Italy
| | - Gianluca Caridi
- Division of Nephrology, Dialysis and Transplantation, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Giannina Gaslini, 16147 Genova GE, Italy
| | - Isabella Pisani
- U.O. Nefrologia, Azienda Ospedaliero-Universitaria di Parma and Dipartimento di Medicina e Chirurgia, Università di Parma, 43126 Parma PR, Italy
| | - Enrico Fiaccadori
- U.O. Nefrologia, Azienda Ospedaliero-Universitaria di Parma and Dipartimento di Medicina e Chirurgia, Università di Parma, 43126 Parma PR, Italy
| | - Asmaa S AbuMaziad
- Division of Pediatric Nephrology, University of Arizona-Tucson, AZ 85724, USA
| | - Julian A Martinez-Agosto
- Department of Pediatrics, Division of Medical Genetics, UCLA, Los Angeles, CA 90095, USA; Department of Human Genetics, UCLA, Los Angeles, CA 90095, USA; Department of Psychiatry, UCLA, Los Angeles, CA 90095, USA
| | - Ora Yadin
- Division of Pediatric Nephrology, UCLA, Los Angeles, CA 90095, USA
| | - Jonathan Zuckerman
- Department of Pathology and Laboratory Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Arang Kim
- Department of Pediatrics, Division of Medical Genetics, UCLA, Los Angeles, CA 90095, USA
| | | | - Amanda V Tyndall
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Jillian S Parboosingh
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Agnieszka Bierzynska
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol BS2 8BJ, UK
| | - Ania B Koziell
- Department of Paediatric Nephrology, Evelina London, London SE1 7EH, UK; Faculty of Life Sciences, King's College London SE1 9RT, UK
| | - Mordi Muorah
- Renal Unit, Birmingham Children's Hospital, Birmingham, B4 6NH, UK
| | - Moin A Saleem
- Bristol Renal, University of Bristol and Bristol Royal Hospital for Children, Bristol BS2 8BJ, UK
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany; Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Vaidehi Jobanputra
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA; New York Genome Center, New York, NY 10013, USA
| | - Emma Pierce-Hoffman
- Broad Center for Mendelian Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Eleanor G Seaby
- Broad Center for Mendelian Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Anne O'Donnell-Luria
- Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Broad Center for Mendelian Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Heidi L Rehm
- Broad Center for Mendelian Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Vivette D D'Agati
- Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Martin R Pollak
- Division of Nephrology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, Istituto di Ricovero e Cura a Carattere Scientifico, Istituto Giannina Gaslini, 16147 Genova GE, Italy
| | - Richard P Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA; Yale Center for Mendelian Genomics, Yale University School of Medicine, New Haven, CT 06520, USA; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - David B Goldstein
- Institute of Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Erica E Davis
- Center for Disease Modeling, Duke University, Durham, NC 27701, USA; Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | | | | |
Collapse
|
36
|
Schoch K, Esteves C, Bican A, Spillmann R, Cope H, McConkie-Rosell A, Walley N, Fernandez L, Kohler JN, Bonner D, Reuter C, Stong N, Mulvihill JJ, Novacic D, Wolfe L, Abdelbaki A, Toro C, Tifft C, Malicdan M, Gahl W, Liu P, Newman J, Goldstein DB, Hom J, Sampson J, Wheeler MT, Cogan J, Bernstein JA, Adams DR, McCray AT, Shashi V. Clinical sites of the Undiagnosed Diseases Network: unique contributions to genomic medicine and science. Genet Med 2021; 23:259-271. [PMID: 33093671 PMCID: PMC7867619 DOI: 10.1038/s41436-020-00984-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE The NIH Undiagnosed Diseases Network (UDN) evaluates participants with disorders that have defied diagnosis, applying personalized clinical and genomic evaluations and innovative research. The clinical sites of the UDN are essential to advancing the UDN mission; this study assesses their contributions relative to standard clinical practices. METHODS We analyzed retrospective data from four UDN clinical sites, from July 2015 to September 2019, for diagnoses, new disease gene discoveries and the underlying investigative methods. RESULTS Of 791 evaluated individuals, 231 received 240 diagnoses and 17 new disease-gene associations were recognized. Straightforward diagnoses on UDN exome and genome sequencing occurred in 35% (84/240). We considered these tractable in standard clinical practice, although genome sequencing is not yet widely available clinically. The majority (156/240, 65%) required additional UDN-driven investigations, including 90 diagnoses that occurred after prior nondiagnostic exome sequencing and 45 diagnoses (19%) that were nongenetic. The UDN-driven investigations included complementary/supplementary phenotyping, innovative analyses of genomic variants, and collaborative science for functional assays and animal modeling. CONCLUSION Investigations driven by the clinical sites identified diagnostic and research paradigms that surpass standard diagnostic processes. The new diagnoses, disease gene discoveries, and delineation of novel disorders represent a model for genomic medicine and science.
Collapse
Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Cecilia Esteves
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Anna Bican
- Vanderbilt Center for Undiagnosed Disease, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Division of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Nicole Walley
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Liliana Fernandez
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Jennefer N Kohler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Devon Bonner
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Chloe Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - John J Mulvihill
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Donna Novacic
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Lynne Wolfe
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Ayat Abdelbaki
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Camilo Toro
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
| | - Cyndi Tifft
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
- Office of the Clinical Director, NHGRI, NIH, Bethesda, MD, USA
| | - May Malicdan
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
- Medical Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - William Gahl
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
- Medical Genetics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - John Newman
- Vanderbilt Center for Undiagnosed Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | - Jason Hom
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Jacinda Sampson
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Department of Neurology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew T Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joy Cogan
- Vanderbilt Center for Undiagnosed Disease, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pediatrics, Division of Medical Genetics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan A Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - David R Adams
- Undiagnosed Diseases Program, Common Fund, NIH Office of the Director, NIH, Bethesda, MD, USA
- Office of the Clinical Director, NHGRI, NIH, Bethesda, MD, USA
| | - Alexa T McCray
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA.
| |
Collapse
|
37
|
Klöckner C, Sticht H, Zacher P, Popp B, Babcock HE, Bakker DP, Barwick K, Bonfert MV, Bönnemann CG, Brilstra EH, Chung WK, Clarke AJ, Devine P, Donkervoort S, Fraser JL, Friedman J, Gates A, Ghoumid J, Hobson E, Horvath G, Keller-Ramey J, Keren B, Kurian MA, Lee V, Leppig KA, Lundgren J, McDonald MT, McLaughlin HM, McTague A, Mefford HC, Mignot C, Mikati MA, Nava C, Raymond FL, Sampson JR, Sanchis-Juan A, Shashi V, Shieh JTC, Shinawi M, Slavotinek A, Stödberg T, Stong N, Sullivan JA, Taylor AC, Toler TL, van den Boogaard MJ, van der Crabben SN, van Gassen KLI, van Jaarsveld RH, Van Ziffle J, Wadley AF, Wagner M, Wigby K, Wortmann SB, Zarate YA, Møller RS, Lemke JR, Platzer K. De novo variants in SNAP25 cause an early-onset developmental and epileptic encephalopathy. Genet Med 2020; 23:653-660. [PMID: 33299146 DOI: 10.1038/s41436-020-01020-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE This study aims to provide a comprehensive description of the phenotypic and genotypic spectrum of SNAP25 developmental and epileptic encephalopathy (SNAP25-DEE) by reviewing newly identified and previously reported individuals. METHODS Individuals harboring heterozygous missense or loss-of-function variants in SNAP25 were assembled through collaboration with international colleagues, matchmaking platforms, and literature review. For each individual, detailed phenotyping, classification, and structural modeling of the identified variant were performed. RESULTS The cohort comprises 23 individuals with pathogenic or likely pathogenic de novo variants in SNAP25. Intellectual disability and early-onset epilepsy were identified as the core symptoms of SNAP25-DEE, with recurrent findings of movement disorders, cerebral visual impairment, and brain atrophy. Structural modeling for all variants predicted possible functional defects concerning SNAP25 or impaired interaction with other components of the SNARE complex. CONCLUSION We provide a comprehensive description of SNAP25-DEE with intellectual disability and early-onset epilepsy mostly occurring before the age of two years. These core symptoms and additional recurrent phenotypes show an overlap to genes encoding other components or associated proteins of the SNARE complex such as STX1B, STXBP1, or VAMP2. Thus, these findings advance the concept of a group of neurodevelopmental disorders that may be termed "SNAREopathies."
Collapse
Affiliation(s)
- Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Holly E Babcock
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Dewi P Bakker
- Department of Child Neurology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Katy Barwick
- Institute of Child Health, University Collge London, London, UK
| | - Michaela V Bonfert
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU - University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Angus J Clarke
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Wales, UK
| | - Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jamie L Fraser
- Rare Disease Institute, Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California San Diego and Division of Neurology, Rady Children's Hospital, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Alyssa Gates
- Department of Genetic Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Jamal Ghoumid
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - Emma Hobson
- Yorkshire Clinical Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Gabriella Horvath
- Department of Pediatrics, Division of Biochemical Diseases, University of British Columbia, Vancouver, Canada
| | | | - Boris Keren
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Manju A Kurian
- Institute of Child Health, University Collge London, London, UK
| | - Virgina Lee
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen A Leppig
- Department of Genetic Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Johan Lundgren
- Institute of Clinical Sciences, Skane University Hospital, Lund, Sweden
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - Amy McTague
- Institute of Child Health, University Collge London, London, UK
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière et Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Caroline Nava
- Sorbonne University, Paris Brain Institute, Inserm U1127, CNRS UMR 7225, AP-HP, Pitié Salpêtrière Hospital, Department of Genetics, Paris, France
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Julian R Sampson
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Wales, UK
| | - Alba Sanchis-Juan
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Joseph T C Shieh
- Division of Medical Genetics, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Slavotinek
- Division of Medical Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Tommy Stödberg
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Ashley C Taylor
- Section of Genetics, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Tomi L Toler
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Saskia N van der Crabben
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Jessica Van Ziffle
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | | | - Matias Wagner
- Institute of Neurogenomics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Kristen Wigby
- Department of Pediatrics, Division of Genetics, University of California, San Diego and Rady Children's Hospital-San Diego, San Diego, CA, USA
| | - Saskia B Wortmann
- Amalia Children's Hospital, Radboud University Nijmegen, Nijmegen, The Netherlands.,University Childrens Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Rikke S Møller
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark.,Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
| |
Collapse
|
38
|
Davies RW, Fiksinski AM, Breetvelt EJ, Williams NM, Hooper SR, Monfeuga T, Bassett AS, Owen MJ, Gur RE, Morrow BE, McDonald-McGinn DM, Swillen A, Chow EWC, van den Bree M, Emanuel BS, Vermeesch JR, van Amelsvoort T, Arango C, Armando M, Campbell LE, Cubells JF, Eliez S, Garcia-Minaur S, Gothelf D, Kates WR, Murphy KC, Murphy CM, Murphy DG, Philip N, Repetto GM, Shashi V, Simon TJ, Suñer DH, Vicari S, Scherer SW, Bearden CE, Vorstman JAS. Using common genetic variation to examine phenotypic expression and risk prediction in 22q11.2 deletion syndrome. Nat Med 2020; 26:1912-1918. [PMID: 33169016 PMCID: PMC7975627 DOI: 10.1038/s41591-020-1103-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 09/14/2020] [Indexed: 02/06/2023]
Abstract
The 22q11.2 deletion syndrome (22q11DS) is associated with a 20-25% risk of schizophrenia. In a cohort of 962 individuals with 22q11DS, we examined the shared genetic basis between schizophrenia and schizophrenia-related early trajectory phenotypes: sub-threshold symptoms of psychosis, low baseline intellectual functioning and cognitive decline. We studied the association of these phenotypes with two polygenic scores, derived for schizophrenia and intelligence, and evaluated their use for individual risk prediction in 22q11DS. Polygenic scores were not only associated with schizophrenia and baseline intelligence quotient (IQ), respectively, but schizophrenia polygenic score was also significantly associated with cognitive (verbal IQ) decline and nominally associated with sub-threshold psychosis. Furthermore, in comparing the tail-end deciles of the schizophrenia and IQ polygenic score distributions, 33% versus 9% of individuals with 22q11DS had schizophrenia, and 63% versus 24% of individuals had intellectual disability. Collectively, these data show a shared genetic basis for schizophrenia and schizophrenia-related phenotypes and also highlight the future potential of polygenic scores for risk stratification among individuals with highly, but incompletely, penetrant genetic variants.
Collapse
Affiliation(s)
- Robert W Davies
- Program in Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Statistics, University of Oxford, Oxford, UK
| | - Ania M Fiksinski
- Department of Psychiatry, Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Elemi J Breetvelt
- Department of Psychiatry, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nigel M Williams
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Stephen R Hooper
- Department of Allied Health Sciences, School of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Thomas Monfeuga
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- The Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Raquel E Gur
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Donna M McDonald-McGinn
- Division of Human Genetics, 22q and You Center, Clinical Genetics Center, and Section of Genetic Counseling, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA
| | - Ann Swillen
- Center for Human Genetics, University Hospital Gasthuisberg, Leuven, Belgium
- Department of Human Genetics KU Leuven, Leuven, Belgium
| | - Eva W C Chow
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Marianne van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Beverly S Emanuel
- Division of Human Genetics, 22q and You Center, Clinical Genetics Center, and Section of Genetic Counseling, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joris R Vermeesch
- Center for Human Genetics, University Hospital Gasthuisberg, Leuven, Belgium
| | - Therese van Amelsvoort
- Department of Psychiatry and Neuropsychology, Maastricht University, Maastricht, the Netherlands
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Marco Armando
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Linda E Campbell
- School of Psychology, University of Newcastle, Newcastle, Australia
| | - Joseph F Cubells
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Emory Autism Center, Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Stephan Eliez
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Sixto Garcia-Minaur
- Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | - Doron Gothelf
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Kieran C Murphy
- Department of Psychiatry, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Clodagh M Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Declan G Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Nicole Philip
- Département de Génétique Médicale, APHM, CHU Timone Enfants, Marseille, France
- Aix Marseille Université, MMG, INSERM, Marseille, France
| | - Gabriela M Repetto
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC, USA
| | - Tony J Simon
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis, Sacramento, CA, USA
| | - Damiàn Heine Suñer
- Genomics of Health Group and Molecular Diagnostics and Clinical Genetics Unit (UDMGC), Health Research Institute of the Balearic Islands (IdISBa), Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | - Stefano Vicari
- Department of Life Sciences and Public Health, Catholic University; Child and Adolescent Psychiatry Unit, Bambino Gesù Children's Hospital, IRCSS, Rome, Italy
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada
| | - Carrie E Bearden
- Departments of Psychiatry and Biobehavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Jacob A S Vorstman
- Department of Psychiatry, Brain Center, University Medical Center Utrecht, Utrecht, The Netherlands.
- Program in Genetics and Genome Biology, SickKids Research Institute, Toronto, Ontario, Canada.
- Department of Psychiatry, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
39
|
Brunet T, McWalter K, Mayerhanser K, Anbouba GM, Armstrong-Javors A, Bader I, Baugh E, Begtrup A, Bupp CP, Callewaert BL, Cereda A, Cousin MA, Del Rey Jimenez JC, Demmer L, Dsouza NR, Fleischer N, Gavrilova RH, Ghate S, Graf E, Green A, Green SR, Iascone M, Kdissa A, Klee D, Klee EW, Lancaster E, Lindstrom K, Mayr JA, McEntagart M, Meeks NJL, Mittag D, Moore H, Olsen AK, Ortiz D, Parsons G, Pena LDM, Person RE, Punj S, Ramos-Rivera GA, Sacoto MJG, Bradley Schaefer G, Schnur RE, Scott TM, Scott DA, Serbinski CR, Shashi V, Siu VM, Stadheim BF, Sullivan JA, Švantnerová J, Velsher L, Wargowski DS, Wentzensen IM, Wieczorek D, Winkelmann J, Yap P, Zech M, Zimmermann MT, Meitinger T, Distelmaier F, Wagner M. Defining the genotypic and phenotypic spectrum of X-linked MSL3-related disorder. Genet Med 2020; 23:384-395. [PMID: 33173220 PMCID: PMC7862064 DOI: 10.1038/s41436-020-00993-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/16/2020] [Accepted: 09/23/2020] [Indexed: 12/01/2022] Open
Abstract
Purpose We sought to delineate the genotypic and phenotypic spectrum of female and male individuals with X-linked, MSL3-related disorder (Basilicata–Akhtar syndrome). Methods Twenty-five individuals (15 males, 10 females) with causative variants in MSL3 were ascertained through exome or genome sequencing at ten different sequencing centers. Results We identified multiple variant types in MSL3 (ten nonsense, six frameshift, four splice site, three missense, one in-frame-deletion, one multi-exon deletion), most proven to be de novo, and clustering in the terminal eight exons suggesting that truncating variants in the first five exons might be compensated by an alternative MSL3 transcript. Three-dimensional modeling of missense and splice variants indicated that these have a deleterious effect. The main clinical findings comprised developmental delay and intellectual disability ranging from mild to severe. Autism spectrum disorder, muscle tone abnormalities, and macrocephaly were common as well as hearing impairment and gastrointestinal problems. Hypoplasia of the cerebellar vermis emerged as a consistent magnetic resonance image (MRI) finding. Females and males were equally affected. Using facial analysis technology, a recognizable facial gestalt was determined. Conclusion Our aggregated data illustrate the genotypic and phenotypic spectrum of X-linked, MSL3-related disorder (Basilicata–Akhtar syndrome). Our cohort improves the understanding of disease related morbidity and allows us to propose detailed surveillance guidelines for affected individuals.
Collapse
Affiliation(s)
- Theresa Brunet
- Institute of Human Genetics, Technical University Munich, Munich, Germany.
| | | | | | - Grace M Anbouba
- Division of Genetics and Metabolism, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Amy Armstrong-Javors
- Department of Pediatric Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Ingrid Bader
- Department of Clinical Genetics, University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Evan Baugh
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | | | - Caleb P Bupp
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI, USA.,Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Bert L Callewaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Anna Cereda
- Department of Pediatrics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Margot A Cousin
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Laurie Demmer
- Medical Genetics, Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Nikita R Dsouza
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Ralitza H Gavrilova
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.,Department of Neurology, Mayo Clinic, Rochester, MN, USA
| | - Sumedha Ghate
- St Vincent Hospital Medical Genetics Clinic, Green Bay, WI, USA
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Sarah R Green
- University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Springdale, AR, USA
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | | | - Dirk Klee
- Department of Diagnostic and Interventional Radiology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.,Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Emily Lancaster
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kristin Lindstrom
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg, Austria
| | - Meriel McEntagart
- Medical Genetics, St George's University Hospitals NHS FT, London, UK
| | - Naomi J L Meeks
- Department of Pediatrics, Section of Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dana Mittag
- Medical Genetics, Atrium Health Levine Children's Hospital, Charlotte, NC, USA
| | - Harrison Moore
- INTEGRIS Pediatric Specialties/Medical Genetics, Oklahoma City, OK, USA
| | - Anne K Olsen
- Department of Pediatric, Soerlandet Sykehus Kristiansand, Kristiansand, Norway
| | - Damara Ortiz
- UPMC Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Gretchen Parsons
- Medical Genetics, Spectrum Health and Helen DeVos Children's Hospital, Grand Rapids, MI, USA
| | - Loren D M Pena
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | | | | | | | - G Bradley Schaefer
- University of Arkansas for Medical Sciences, Arkansas Children's Hospital, Springdale, AR, USA
| | | | - Tiana M Scott
- Texas Children's Hospital, Houston, TX, USA.,Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Daryl A Scott
- Texas Children's Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Carolyn R Serbinski
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Victoria M Siu
- Department of Pediatrics, Western University, London, ON, Canada
| | | | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Jana Švantnerová
- Second Department of Neurology, Faculty of Medicine, Comenius University, University Hospital Bratislava, Bratislava, Slovakia
| | - Lea Velsher
- Genetics Program, North York General Hospital, Toronto, ON, Canada
| | - David S Wargowski
- Division of Genetics and Metabolism, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.,St Vincent Hospital Medical Genetics Clinic, Green Bay, WI, USA
| | | | - Dagmar Wieczorek
- Institute of Human Genetics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Juliane Winkelmann
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Neurogenetics, Technische Universität München, Munich, Germany
| | - Patrick Yap
- Genetic Health Service New Zealand (Northern Hub), Auckland, New Zealand.,Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Michael Zech
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomics Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Thomas Meitinger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Heinrich-Heine-University, Düsseldorf, Germany
| | - Matias Wagner
- Institute of Human Genetics, Technical University Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| |
Collapse
|
40
|
Lenaerts L, Reynhout S, Verbinnen I, Laumonnier F, Toutain A, Bonnet-Brilhault F, Hoorne Y, Joss S, Chassevent AK, Smith-Hicks C, Loeys B, Joset P, Steindl K, Rauch A, Mehta SG, Chung WK, Devriendt K, Holder SE, Jewett T, Baldwin LM, Wilson WG, Towner S, Srivastava S, Johnson HF, Daumer-Haas C, Baethmann M, Ruiz A, Gabau E, Jain V, Varghese V, Al-Beshri A, Fulton S, Wechsberg O, Orenstein N, Prescott K, Childs AM, Faivre L, Moutton S, Sullivan JA, Shashi V, Koudijs SM, Heijligers M, Kivuva E, McTague A, Male A, van Ierland Y, Plecko B, Maystadt I, Hamid R, Hannig VL, Houge G, Janssens V. The broad phenotypic spectrum of PPP2R1A-related neurodevelopmental disorders correlates with the degree of biochemical dysfunction. Genet Med 2020; 23:352-362. [PMID: 33106617 PMCID: PMC7862067 DOI: 10.1038/s41436-020-00981-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 06/09/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
Purpose Neurodevelopmental disorders (NDD) caused by protein phosphatase 2A (PP2A) dysfunction have mainly been associated with de novo variants in PPP2R5D and PPP2CA, and more rarely in PPP2R1A. Here, we aimed to better understand the latter by characterizing 30 individuals with de novo and often recurrent variants in this PP2A scaffolding Aα subunit. Methods Most cases were identified through routine clinical diagnostics. Variants were biochemically characterized for phosphatase activity and interaction with other PP2A subunits. Results We describe 30 individuals with 16 different variants in PPP2R1A, 21 of whom had variants not previously reported. The severity of developmental delay ranged from mild learning problems to severe intellectual disability (ID) with or without epilepsy. Common features were language delay, hypotonia, and hypermobile joints. Macrocephaly was only seen in individuals without B55α subunit-binding deficit, and these patients had less severe ID and no seizures. Biochemically more disruptive variants with impaired B55α but increased striatin binding were associated with profound ID, epilepsy, corpus callosum hypoplasia, and sometimes microcephaly. Conclusion We significantly expand the phenotypic spectrum of PPP2R1A-related NDD, revealing a broader clinical presentation of the patients and that the functional consequences of the variants are more diverse than previously reported.
Collapse
Affiliation(s)
- Lisa Lenaerts
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Sara Reynhout
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium.,KU Leuven Brain Institute (LBI), Leuven, Belgium
| | - Iris Verbinnen
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Frédéric Laumonnier
- UMR1253, iBrain, University of Tours, INSERM, Tours, France.,Service de Génétique, Centre Hospitalier Régional Universitaire, Tours, France
| | - Annick Toutain
- UMR1253, iBrain, University of Tours, INSERM, Tours, France.,Service de Génétique, Centre Hospitalier Régional Universitaire, Tours, France
| | - Frédérique Bonnet-Brilhault
- UMR1253, iBrain, University of Tours, INSERM, Tours, France.,Excellence Center in Autism and Neurodevelopmental Disorders, Centre Hospitalier Régional Universitaire, Tours, France
| | - Yana Hoorne
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium
| | - Shelagh Joss
- West of Scotland Centre for Genomic Medicine, Queen Elizabeth University Hospital, Glasgow, UK
| | | | | | - Bart Loeys
- Center for Medical Genetics, University of Antwerp/Antwerp University Hospital, Antwerp, Belgium
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, Zurich, Switzerland
| | - Sarju G Mehta
- East Anglian Regional Medical Genetics Service, Addenbrookes Hospital, Cambridge, UK
| | - Wendy K Chung
- Columbia University Medical Center, New York, NY, USA
| | - Koenraad Devriendt
- Department of Human Genetics, University of Leuven (KU Leuven), Leuven, Belgium
| | - Susan E Holder
- North West Thames Regional Genetics Service, Harrow, London, UK
| | - Tamison Jewett
- Wake Forest School of Medicine, Wake Forest University, Winston-Salem, NC, USA
| | - Lauren M Baldwin
- Wake Forest School of Medicine, Wake Forest University, Winston-Salem, NC, USA
| | - William G Wilson
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Shelley Towner
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | | | - Hannah F Johnson
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | | | - Martina Baethmann
- Pediatric Neurology, Sozialpädiatrisches Zentrum, Klinikum Dritter Orden München, Munich, Germany
| | - Anna Ruiz
- Genetics Laboratory, UDIAT-Centre Diagnòstic, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Elisabeth Gabau
- Paediatric Unit, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Vani Jain
- All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Vinod Varghese
- All Wales Medical Genomics Service, University Hospital of Wales, Cardiff, UK
| | - Ali Al-Beshri
- Internal Medicine & Medical Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Oded Wechsberg
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Maccabi Healthcare Services, Tel Aviv, Israel
| | - Naama Orenstein
- Pediatric Genetics Unit, Schneider Children's Medical Center of Israel, Petach Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katrina Prescott
- Yorkshire Regional Genetics Department, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Anne-Marie Childs
- Department of Neurology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Laurence Faivre
- Centre de référence Anomalies du Développement et Syndromes malformatifs, FHU TRANSLAD, UMR1231 GAD, CHU Dijon et Université de Bourgogne, Dijon, France
| | - Sébastien Moutton
- CPDPN, Pôle mère enfant, Maison de Santé Bordeaux Bagatelle, Talence, France
| | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, NC, USA
| | | | - Malou Heijligers
- Department of Clinical Genetics, Maastricht UMC+, Maastricht, The Netherlands
| | - Emma Kivuva
- Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | - Amy McTague
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
| | - Alison Male
- Developmental Neurosciences, UCL Great Ormond Street Institute of Child Health, London, UK.,Department of Neurology, Great Ormond Street Hospital, London, UK
| | | | - Barbara Plecko
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Isabelle Maystadt
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Rizwan Hamid
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation & Proteomics, Department of Cellular & Molecular Medicine, University of Leuven (KU Leuven), Leuven, Belgium. .,KU Leuven Brain Institute (LBI), Leuven, Belgium.
| |
Collapse
|
41
|
Prange L, Pratt M, Herman K, Schiffmann R, Mueller DM, McLean M, Mendez MM, Walley N, Heinzen EL, Goldstein D, Shashi V, Hunanyan A, Pagadala V, Mikati MA. D-DEMØ, a distinct phenotype caused by ATP1A3 mutations. Neurol Genet 2020; 6:e466. [PMID: 32802951 PMCID: PMC7413631 DOI: 10.1212/nxg.0000000000000466] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/18/2020] [Indexed: 11/15/2022]
Abstract
Objective To describe a phenotype caused by ATP1A3 mutations, which manifests as dystonia, dysmorphism of the face, encephalopathy with developmental delay, brain MRI abnormalities always including cerebellar hypoplasia, no hemiplegia (Ø) (D-DEMØ), and neonatal onset. Methods Review and analysis of clinical and genetic data. Results Patients shared the above traits and had whole-exome sequencing that showed de novo variants of the ATP1A3 gene, predicted to be disease causing and occurring in regions of the protein critical for pump function. Patient 1 (c.1079C>G, p.Thr360Arg), an 8-year-old girl, presented on day 1 of life with episodic dystonia, complex partial seizures, and facial dysmorphism. MRI of the brain revealed cerebellar hypoplasia. Patient 2 (c.420G>T, p.Gln140His), an 18-year-old man, presented on day 1 of life with hypotonia, tremor, and facial dysmorphism. He later developed dystonia. MRI of the brain revealed cerebellar hypoplasia and, later, further cerebellar volume loss (atrophy). Patient 3 (c.974G>A, Gly325Asp), a 13-year-old girl, presented on day 1 of life with tremor, episodic dystonia, and facial dysmorphism. MRI of the brain showed severe cerebellar hypoplasia. Patient 4 (c.971A>G, p.Glu324Gly), a 14-year-old boy, presented on day 1 of life with tremor, hypotonia, dystonia, nystagmus, facial dysmorphism, and later seizures. MRI of the brain revealed moderate cerebellar hypoplasia. Conclusions D-DEMØ represents an ATP1A3-related phenotype, the observation of which should trigger investigation for ATP1A3 mutations. Our findings, and the presence of multiple distinct ATP1A3-related phenotypes, support the possibility that there are differences in the underlying mechanisms.
Collapse
Affiliation(s)
- Lyndsey Prange
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Milton Pratt
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Kristin Herman
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Raphael Schiffmann
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - David M Mueller
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Melissa McLean
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Mary Moya Mendez
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Nicole Walley
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Erin L Heinzen
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - David Goldstein
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Vandana Shashi
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Arsen Hunanyan
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Vijay Pagadala
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| | - Mohamad A Mikati
- Duke University (L.P., M.P., M.M.M., N.W., V.S., A.H., M.A.M.), Durham, NC; UC Davis Health (K.H.), Sacramento; Baylor Scott & White Health (R.S.), Dallas, TX; Rosalind Franklin University of Medicine and Science (D.M.M.), Chicago, IL; University of North Carolina at Chapel Hill (E.L.H.); Columbia University (D.G.), New York City, NY; and Glycan Therapeutics, LLC (V.P.), Chapel Hill, NC
| |
Collapse
|
42
|
Cope H, Spillmann R, Rosenfeld JA, Brokamp E, Signer R, Schoch K, Kelley EG, Sullivan JA, Macnamara E, Lincoln S, Golden-Grant K, Orengo JP, Clark G, Burrage LC, Posey JE, Punetha J, Robertson A, Cogan J, Phillips JA, Martinez-Agosto J, Shashi V. Missed diagnoses: Clinically relevant lessons learned through medical mysteries solved by the Undiagnosed Diseases Network. Mol Genet Genomic Med 2020; 8:e1397. [PMID: 32730690 PMCID: PMC7549585 DOI: 10.1002/mgg3.1397] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background Resources within the Undiagnosed Diseases Network (UDN), such as genome sequencing (GS) and model organisms aid in diagnosis and identification of new disease genes, but are currently difficult to access by clinical providers. While these resources do contribute to diagnoses in many cases, they are not always necessary to reach diagnostic resolution. The UDN experience has been that participants can also receive diagnoses through the thoughtful and customized application of approaches and resources that are readily available in clinical settings. Methods The UDN Genetic Counseling and Testing Working Group collected case vignettes that illustrated how clinically available methods resulted in diagnoses. The case vignettes were classified into three themes; phenotypic considerations, selection of genetic testing, and evaluating exome/GS variants and data. Results We present 12 participants that illustrate how clinical practices such as phenotype‐driven genomic investigations, consideration of variable expressivity, selecting the relevant tissue of interest for testing, utilizing updated testing platforms, and recognition of alternate transcript nomenclature resulted in diagnoses. Conclusion These examples demonstrate that when a diagnosis is elusive, an iterative patient‐specific approach utilizing assessment options available to clinical providers may solve a portion of cases. However, this does require increased provider time commitment, a particular challenge in the current practice of genomics.
Collapse
Affiliation(s)
- Heidi Cope
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Rebecca Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elly Brokamp
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rebecca Signer
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Emily G Kelley
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Ellen Macnamara
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, NIH, Bethesda, MD, USA
| | - Sharyn Lincoln
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Katie Golden-Grant
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | -
- Undiagnosed Diseases Program, Common Fund, Office of the Director, National Institutes of Health, NIH, Bethesda, MD, USA
| | - James P Orengo
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Gary Clark
- Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy Robertson
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Joy Cogan
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| |
Collapse
|
43
|
Del Dotto V, Ullah F, Di Meo I, Magini P, Gusic M, Maresca A, Caporali L, Palombo F, Tagliavini F, Baugh EH, Macao B, Szilagyi Z, Peron C, Gustafson MA, Khan K, La Morgia C, Barboni P, Carbonelli M, Valentino ML, Liguori R, Shashi V, Sullivan J, Nagaraj S, El-Dairi M, Iannaccone A, Cutcutache I, Bertini E, Carrozzo R, Emma F, Diomedi-Camassei F, Zanna C, Armstrong M, Page M, Stong N, Boesch S, Kopajtich R, Wortmann S, Sperl W, Davis EE, Copeland WC, Seri M, Falkenberg M, Prokisch H, Katsanis N, Tiranti V, Pippucci T, Carelli V. SSBP1 mutations cause mtDNA depletion underlying a complex optic atrophy disorder. J Clin Invest 2020; 130:108-125. [PMID: 31550240 DOI: 10.1172/jci128514] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/19/2019] [Indexed: 01/07/2023] Open
Abstract
Inherited optic neuropathies include complex phenotypes, mostly driven by mitochondrial dysfunction. We report an optic atrophy spectrum disorder, including retinal macular dystrophy and kidney insufficiency leading to transplantation, associated with mitochondrial DNA (mtDNA) depletion without accumulation of multiple deletions. By whole-exome sequencing, we identified mutations affecting the mitochondrial single-strand binding protein (SSBP1) in 4 families with dominant and 1 with recessive inheritance. We show that SSBP1 mutations in patient-derived fibroblasts variably affect the amount of SSBP1 protein and alter multimer formation, but not the binding to ssDNA. SSBP1 mutations impaired mtDNA, nucleoids, and 7S-DNA amounts as well as mtDNA replication, affecting replisome machinery. The variable mtDNA depletion in cells was reflected in severity of mitochondrial dysfunction, including respiratory efficiency, OXPHOS subunits, and complex amount and assembly. mtDNA depletion and cytochrome c oxidase-negative cells were found ex vivo in biopsies of affected tissues, such as kidney and skeletal muscle. Reduced efficiency of mtDNA replication was also reproduced in vitro, confirming the pathogenic mechanism. Furthermore, ssbp1 suppression in zebrafish induced signs of nephropathy and reduced optic nerve size, the latter phenotype complemented by WT mRNA but not by SSBP1 mutant transcripts. This previously unrecognized disease of mtDNA maintenance implicates SSBP1 mutations as a cause of human pathology.
Collapse
Affiliation(s)
- Valentina Del Dotto
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
| | - Farid Ullah
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Ivano Di Meo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Pamela Magini
- Medical Genetics Unit, Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Mirjana Gusic
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Francesca Tagliavini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Evan Harris Baugh
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Bertil Macao
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Zsolt Szilagyi
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Camille Peron
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Margaret A Gustafson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Chiara La Morgia
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Piero Barboni
- Department of Ophthalmology, Studio Oculistico d'Azeglio, Bologna, Italy
| | - Michele Carbonelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Maria Lucia Valentino
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Rocco Liguori
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | | | | | - Shashi Nagaraj
- Division of Nephrology, Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Alessandro Iannaccone
- Center for Retinal Degenerations and Ophthalmic Genetic Diseases and Visual Function Diagnostic Laboratory, Duke Eye Center, Duke University School of Medicine, Durham, North Carolina, USA
| | | | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Diseases, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Diseases, Department of Neurosciences, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Francesco Emma
- Division of Nephrology, Department of Pediatric Subspecialties, Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Claudia Zanna
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, Bologna, Italy
| | | | - Matthew Page
- Translational Medicine, UCB Pharma, Slough, United Kingdom
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Sylvia Boesch
- Department of Neurology, Medical University Innsbruck, Innsbruck, Austria
| | - Robert Kopajtich
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Saskia Wortmann
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany.,Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Wolfgang Sperl
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University Salzburg, Salzburg, Austria
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Marco Seri
- Medical Genetics Unit, Sant'Orsola-Malpighi University Hospital, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, North Carolina, USA.,Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Departments of Pediatrics and Cellular and Molecular Biology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Valeria Tiranti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico C. Besta, Milan, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Valerio Carelli
- Unit of Neurology, Department of Biomedical and NeuroMotor Sciences (DIBINEM), University of Bologna, Bologna, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| |
Collapse
|
44
|
Sullivan JA, Stong N, Baugh EH, McDonald MT, Takeuchi A, Shashi V. A pathogenic variant in the SETBP1 hotspot results in a forme-fruste Schinzel-Giedion syndrome. Am J Med Genet A 2020; 182:1947-1951. [PMID: 32445275 DOI: 10.1002/ajmg.a.61630] [Citation(s) in RCA: 6] [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: 03/05/2020] [Revised: 04/25/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022]
Abstract
Schinzel-Giedion syndrome (SGS; OMIM 269150) is an ultra-rare genetic disorder associated with a distinctive facial gestalt, congenital malformations, severe intellectual disability, and a progressive neurological course. The prognosis for SGS is poor, with survival beyond the first decade rare. Germline, de novo heterozygous variants in the SETBP1 gene cause SGS with the pathogenic variants associated with the SGS phenotype missense and confined to exon 4 of the gene, clustered in a four amino acid (12 bp) hotspot in the SKI homologous region of the SETBP1 protein. We report a patient with a de novo I871S variant within the SKI homologous region, which has been associated with the severe phenotype previously; but our patient has fewer features of SGS and a milder course. This is the first report of a forme-fruste phenotype in a patient with a pathogenic variant within the SGS hotspot on the SETBP1 gene and it highlights the importance of considering atypical clinical presentations in the context of severe ultra-rare genetic disorders.
Collapse
Affiliation(s)
- Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Evan H Baugh
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| | - Akihito Takeuchi
- Department of Neonatology, Okayama Medical Center, National Hospital Organization, Okayama, Japan
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, North Carolina, USA
| |
Collapse
|
45
|
Schoch K, Tan QKG, Stong N, Deak KL, McConkie-Rosell A, McDonald MT, Goldstein DB, Jiang YH, Shashi V. Alternative transcripts in variant interpretation: the potential for missed diagnoses and misdiagnoses. Genet Med 2020; 22:1269-1275. [PMID: 32366967 PMCID: PMC7335342 DOI: 10.1038/s41436-020-0781-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [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: 02/03/2020] [Revised: 03/04/2020] [Accepted: 03/10/2020] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Guidelines by professional organizations for assessing variant pathogenicity include the recommendation to utilize biologically relevant transcripts; however, there is variability in transcript selection by laboratories. METHODS We describe three patients whose genomic results were incorrect, because alternative transcripts and tissue expression patterns were not considered by the commercial laboratories. RESULTS In individual 1, a pathogenic coding variant in a brain-expressed isoform of CKDL5 was missed twice on sequencing, because the variant was intronic in the transcripts considered in analysis. In individual 2, a microdeletion affecting KMT2C was not reported on microarray, since deletions of proximal exons in this gene are seen in healthy individuals; however, this individual had a more distal deletion involving the brain-expressed KMT2C isoform, giving her a diagnosis of Kleefstra syndrome. Individual 3 was reported to have a pathogenic variant in exon 10 of OFD1 on exome, but had no typical features of the OFD1-related disorders. Since exon 10 is spliced from the more biologically relevant transcripts of OFD1, it was determined that he did not have an OFD1 disorder. CONCLUSION These examples illustrate the importance of considering alternative transcripts as a potential confounder when genetic results are negative or discordant with the phenotype.
Collapse
Affiliation(s)
- Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Queenie K-G Tan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Nicholas Stong
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Kristen L Deak
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - David B Goldstein
- Institute of Genomic Medicine, Columbia University, New York, NY, USA
| | - Yong-Hui Jiang
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA.
| |
Collapse
|
46
|
Mao D, Reuter CM, Ruzhnikov MR, Beck AE, Farrow EG, Emrick LT, Rosenfeld JA, Mackenzie KM, Robak L, Wheeler MT, Burrage LC, Jain M, Liu P, Calame D, Küry S, Sillesen M, Schmitz-Abe K, Tonduti D, Spaccini L, Iascone M, Genetti CA, Koenig MK, Graf M, Tran A, Alejandro M, Lee BH, Thiffault I, Agrawal PB, Bernstein JA, Bellen HJ, Chao HT, Acosta MT, Adam M, Adams DR, Agrawal PB, Alejandro ME, Allard P, Alvey J, Amendola L, Andrews A, Ashley EA, Azamian MS, Bacino CA, Bademci G, Baker E, Balasubramanyam A, Baldridge D, Bale J, Bamshad M, Barbouth D, Batzli GF, Bayrak-Toydemir P, Beck A, Beggs AH, Bejerano G, Bellen HJ, Bennet J, Berg-Rood B, Bernier R, Bernstein JA, Berry GT, Bican A, Bivona S, Blue E, Bohnsack J, Bonnenmann C, Bonner D, Botto L, Briere LC, Brokamp E, Burke EA, Burrage LC, Butte MJ, Byers P, Carey J, Carrasquillo O, Chang TCP, Chanprasert S, Chao HT, Clark GD, Coakley TR, Cobban LA, Cogan JD, Cole FS, Colley HA, Cooper CM, Cope H, Craigen WJ, Cunningham M, D’Souza P, Dai H, Dasari S, Davids M, Dayal JG, Dell’Angelica EC, Dhar SU, Dipple K, Doherty D, Dorrani N, Douine ED, Draper DD, Duncan L, Earl D, Eckstein DJ, Emrick LT, Eng CM, Esteves C, Estwick T, Fernandez L, Ferreira C, Fieg EL, Fisher PG, Fogel BL, Forghani I, Fresard L, Gahl WA, Glass I, Godfrey RA, Golden-Grant K, Goldman AM, Goldstein DB, Grajewski A, Groden CA, Gropman AL, Hahn S, Hamid R, Hanchard NA, Hayes N, High F, Hing A, Hisama FM, Holm IA, Hom J, Horike-Pyne M, Huang A, Huang Y, Isasi R, Jamal F, Jarvik GP, Jarvik J, Jayadev S, Jiang YH, Johnston JM, Karaviti L, Kelley EG, Kiley D, Kohane IS, Kohler JN, Krakow D, Krasnewich DM, Korrick S, Koziura M, Krier JB, Lalani SR, Lam B, Lam C, Lanpher BC, Lanza IR, Lau CC, LeBlanc K, Lee BH, Lee H, Levitt R, Lewis RA, Lincoln SA, Liu P, Liu XZ, Longo N, Loo SK, Loscalzo J, Maas RL, Macnamara EF, MacRae CA, Maduro VV, Majcherska MM, Malicdan MCV, Mamounas LA, Manolio TA, Mao R, Maravilla K, Markello TC, Marom R, Marth G, Martin BA, Martin MG, Martínez-Agosto JA, Marwaha S, McCauley J, McConkie-Rosell A, McCormack CE, McCray AT, Mefford H, Merritt JL, Might M, Mirzaa G, Morava-Kozicz E, Moretti PM, Morimoto M, Mulvihill JJ, Murdock DR, Nath A, Nelson SF, Newman JH, Nicholas SK, Nickerson D, Novacic D, Oglesbee D, Orengo JP, Pace L, Pak S, Pallais JC, Palmer CG, Papp JC, Parker NH, Phillips JA, Posey JE, Postlethwait JH, Potocki L, Pusey BN, Quinlan A, Raskind W, Raja AN, Renteria G, Reuter CM, Rives L, Robertson AK, Rodan LH, Rosenfeld JA, Rowley RK, Ruzhnikov M, Sacco R, Sampson JB, Samson SL, Saporta M, Scott CR, Schaechter J, Schedl T, Schoch K, Scott DA, Shakachite L, Sharma P, Shashi V, Shin J, Signer R, Sillari CH, Silverman EK, Sinsheimer JS, Sisco K, Smith KS, Solnica-Krezel L, Spillmann RC, Stoler JM, Stong N, Sullivan JA, Sun A, Sutton S, Sweetser DA, Sybert V, Tabor HK, Tamburro CP, Tan QKG, Tekin M, Telischi F, Thorson W, Tifft CJ, Toro C, Tran AA, Urv TK, Velinder M, Viskochil D, Vogel TP, Wahl CE, Wallace S, Walley NM, Walsh CA, Walker M, Wambach J, Wan J, Wang LK, Wangler MF, Ward PA, Wegner D, Wener M, Westerfield M, Wheeler MT, Wise AL, Wolfe LA, Woods JD, Yamamoto S, Yang J, Yoon AJ, Yu G, Zastrow DB, Zhao C, Zuchner S. De novo EIF2AK1 and EIF2AK2 Variants Are Associated with Developmental Delay, Leukoencephalopathy, and Neurologic Decompensation. Am J Hum Genet 2020; 106:570-583. [PMID: 32197074 PMCID: PMC7118694 DOI: 10.1016/j.ajhg.2020.02.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 02/28/2020] [Indexed: 02/03/2023] Open
Abstract
EIF2AK1 and EIF2AK2 encode members of the eukaryotic translation initiation factor 2 alpha kinase (EIF2AK) family that inhibits protein synthesis in response to physiologic stress conditions. EIF2AK2 is also involved in innate immune response and the regulation of signal transduction, apoptosis, cell proliferation, and differentiation. Despite these findings, human disorders associated with deleterious variants in EIF2AK1 and EIF2AK2 have not been reported. Here, we describe the identification of nine unrelated individuals with heterozygous de novo missense variants in EIF2AK1 (1/9) or EIF2AK2 (8/9). Features seen in these nine individuals include white matter alterations (9/9), developmental delay (9/9), impaired language (9/9), cognitive impairment (8/9), ataxia (6/9), dysarthria in probands with verbal ability (6/9), hypotonia (7/9), hypertonia (6/9), and involuntary movements (3/9). Individuals with EIF2AK2 variants also exhibit neurological regression in the setting of febrile illness or infection. We use mammalian cell lines and proband-derived fibroblasts to further confirm the pathogenicity of variants in these genes and found reduced kinase activity. EIF2AKs phosphorylate eukaryotic translation initiation factor 2 subunit 1 (EIF2S1, also known as EIF2α), which then inhibits EIF2B activity. Deleterious variants in genes encoding EIF2B proteins cause childhood ataxia with central nervous system hypomyelination/vanishing white matter (CACH/VWM), a leukodystrophy characterized by neurologic regression in the setting of febrile illness and other stressors. Our findings indicate that EIF2AK2 missense variants cause a neurodevelopmental syndrome that may share phenotypic and pathogenic mechanisms with CACH/VWM.
Collapse
|
47
|
Baldridge D, Spillmann RC, Wegner DJ, Wambach JA, White FV, Sisco K, Toler TL, Dickson PI, Cole FS, Shashi V, Grange DK. Phenotypic expansion of KMT2D-related disorder: Beyond Kabuki syndrome. Am J Med Genet A 2020; 182:1053-1065. [PMID: 32083401 DOI: 10.1002/ajmg.a.61518] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [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: 10/10/2019] [Revised: 01/29/2020] [Accepted: 01/29/2020] [Indexed: 12/13/2022]
Abstract
Pathogenic variants in KMT2D, which encodes lysine specific methyltransferase 2D, cause autosomal dominant Kabuki syndrome, associated with distinctive dysmorphic features including arched eyebrows, long palpebral fissures with eversion of the lower lid, large protuberant ears, and fetal finger pads. Most disease-causing variants identified to date are putative loss-of-function alleles, although 15-20% of cases are attributed to missense variants. We describe here four patients (including one previously published patient) with de novo KMT2D missense variants and with shared but unusual clinical findings not typically seen in Kabuki syndrome, including athelia (absent nipples), choanal atresia, hypoparathyroidism, delayed or absent pubertal development, and extreme short stature. These individuals also lack the typical dysmorphic facial features found in Kabuki syndrome. Two of the four patients had severe interstitial lung disease. All of these variants cluster within a 40-amino-acid region of the protein that is located just N-terminal of an annotated coiled coil domain. These findings significantly expand the phenotypic spectrum of features associated with variants in KMT2D beyond those seen in Kabuki syndrome and suggest a possible new underlying disease mechanism for these patients.
Collapse
Affiliation(s)
- Dustin Baldridge
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Rebecca C Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Daniel J Wegner
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennifer A Wambach
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Frances V White
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kathleen Sisco
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tomi L Toler
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Patricia I Dickson
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - F Sessions Cole
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina, USA
| | - Dorothy K Grange
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
48
|
Baloh C, Markert ML, Shashi V, Sleasman J. Predicting Autoimmunity Development in 22q11.2DS. J Allergy Clin Immunol 2020. [DOI: 10.1016/j.jaci.2019.12.679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
49
|
Johnson BV, Kumar R, Oishi S, Alexander S, Kasherman M, Vega MS, Ivancevic A, Gardner A, Domingo D, Corbett M, Parnell E, Yoon S, Oh T, Lines M, Lefroy H, Kini U, Van Allen M, Grønborg S, Mercier S, Küry S, Bézieau S, Pasquier L, Raynaud M, Afenjar A, Billette de Villemeur T, Keren B, Désir J, Van Maldergem L, Marangoni M, Dikow N, Koolen DA, VanHasselt PM, Weiss M, Zwijnenburg P, Sa J, Reis CF, López-Otín C, Santiago-Fernández O, Fernández-Jaén A, Rauch A, Steindl K, Joset P, Goldstein A, Madan-Khetarpal S, Infante E, Zackai E, Mcdougall C, Narayanan V, Ramsey K, Mercimek-Andrews S, Pena L, Shashi V, Schoch K, Sullivan JA, Pinto E Vairo F, Pichurin PN, Ewing SA, Barnett SS, Klee EW, Perry MS, Koenig MK, Keegan CE, Schuette JL, Asher S, Perilla-Young Y, Smith LD, Rosenfeld JA, Bhoj E, Kaplan P, Li D, Oegema R, van Binsbergen E, van der Zwaag B, Smeland MF, Cutcutache I, Page M, Armstrong M, Lin AE, Steeves MA, Hollander ND, Hoffer MJV, Reijnders MRF, Demirdas S, Koboldt DC, Bartholomew D, Mosher TM, Hickey SE, Shieh C, Sanchez-Lara PA, Graham JM, Tezcan K, Schaefer GB, Danylchuk NR, Asamoah A, Jackson KE, Yachelevich N, Au M, Pérez-Jurado LA, Kleefstra T, Penzes P, Wood SA, Burne T, Pierson TM, Piper M, Gécz J, Jolly LA. Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor β Signaling. Biol Psychiatry 2020; 87:100-112. [PMID: 31443933 PMCID: PMC6925349 DOI: 10.1016/j.biopsych.2019.05.028] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/23/2019] [Accepted: 05/30/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND The X-chromosome gene USP9X encodes a deubiquitylating enzyme that has been associated with neurodevelopmental disorders primarily in female subjects. USP9X escapes X inactivation, and in female subjects de novo heterozygous copy number loss or truncating mutations cause haploinsufficiency culminating in a recognizable syndrome with intellectual disability and signature brain and congenital abnormalities. In contrast, the involvement of USP9X in male neurodevelopmental disorders remains tentative. METHODS We used clinically recommended guidelines to collect and interrogate the pathogenicity of 44 USP9X variants associated with neurodevelopmental disorders in males. Functional studies in patient-derived cell lines and mice were used to determine mechanisms of pathology. RESULTS Twelve missense variants showed strong evidence of pathogenicity. We define a characteristic phenotype of the central nervous system (white matter disturbances, thin corpus callosum, and widened ventricles); global delay with significant alteration of speech, language, and behavior; hypotonia; joint hypermobility; visual system defects; and other common congenital and dysmorphic features. Comparison of in silico and phenotypical features align additional variants of unknown significance with likely pathogenicity. In support of partial loss-of-function mechanisms, using patient-derived cell lines, we show loss of only specific USP9X substrates that regulate neurodevelopmental signaling pathways and a united defect in transforming growth factor β signaling. In addition, we find correlates of the male phenotype in Usp9x brain-specific knockout mice, and further resolve loss of hippocampal-dependent learning and memory. CONCLUSIONS Our data demonstrate the involvement of USP9X variants in a distinctive neurodevelopmental and behavioral syndrome in male subjects and identify plausible mechanisms of pathogenesis centered on disrupted transforming growth factor β signaling and hippocampal function.
Collapse
Affiliation(s)
- Brett V Johnson
- University of Adelaide and Robinson Research Institute, Adelaide, Australia
| | - Raman Kumar
- University of Adelaide and Robinson Research Institute, Adelaide, Australia
| | - Sabrina Oishi
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Suzy Alexander
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia; Queensland Centre for Mental Health Research, Wacol, Queensland, Australia
| | - Maria Kasherman
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia; Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | | | - Atma Ivancevic
- University of Adelaide and Robinson Research Institute, Adelaide, Australia; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado
| | - Alison Gardner
- University of Adelaide and Robinson Research Institute, Adelaide, Australia
| | - Deepti Domingo
- University of Adelaide and Robinson Research Institute, Adelaide, Australia
| | - Mark Corbett
- University of Adelaide and Robinson Research Institute, Adelaide, Australia
| | - Euan Parnell
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Sehyoun Yoon
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Tracey Oh
- Department of Medical Genetics, British Columbia Women's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew Lines
- Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Henrietta Lefroy
- Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Services Foundation Trust, Oxford, United Kingdom
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals National Health Services Foundation Trust, Oxford, United Kingdom
| | - Margot Van Allen
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sabine Grønborg
- Center for Rare Diseases, Department of Pediatrics and Department of Clinical Genetics, University Hospital Copenhagen, Copenhagen, Denmark
| | - Sandra Mercier
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes and l'Institut du Thorax, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Nantes, Nantes, France
| | - Sébastien Küry
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes and l'Institut du Thorax, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Nantes, Nantes, France
| | - Stéphane Bézieau
- Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes and l'Institut du Thorax, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université de Nantes, Nantes, France
| | - Laurent Pasquier
- Service de Génétique Clinique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Centre Hospitalier Universitaire Hôpital Sud, Rennes, France
| | - Martine Raynaud
- Centre Hospitalier Régional Universitaire de Tours, Service de Génétique, Unité Nixte de Recherche 1253, iBrain, Université de Tours, Institut National de la Santé et de la Recherche Médicale, Tours, France
| | - Alexandra Afenjar
- Groupe de Recherche Clinique No. 19, ConCer-LD, Département de Génétique, Assistance Publique-Hôpitaux de Paris, Hôpital Armand Trousseau, Centres de Référence Maladies Rares des Déficits Intellectuels de Causes Rares, Paris, France
| | - Thierry Billette de Villemeur
- Sorbonne Université, Groupe de Recherche Clinique No. 19, ConCer-LD, Neuropédiatrie, Centres de Référence Maladies Rares Neurogénétique, Institut National de la Santé et de la Recherche Médicale, Assistance Publique-Hôpitaux de Paris, Hôpital Armand Trousseau, Paris, France
| | - Boris Keren
- Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Julie Désir
- Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Martina Marangoni
- Erasme University Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicola Dikow
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - David A Koolen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter M VanHasselt
- Department of Metabolic Diseases, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marjan Weiss
- Department of Clinical Genetics, Vrije Universiteit University Medical Center, Amsterdam, The Netherlands
| | - Petra Zwijnenburg
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Joaquim Sa
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Claudia Falcao Reis
- Medical Genetics Unit, Hospital Pediátrico, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitário de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain; Centro de Investigación Biomédica en Red de Cáncer, Spain
| | - Olaya Santiago-Fernández
- Departamento de Bioquímica y Biología Molecular, Instituto Universitário de Oncología del Principado de Asturias, Universidad de Oviedo, Oviedo, Spain
| | | | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren, Switzerland
| | - Amy Goldstein
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Elena Infante
- Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | - Elaine Zackai
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Carey Mcdougall
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Saadet Mercimek-Andrews
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Loren Pena
- Division of Human Genetics, Cincinnati Children's Hospital; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina
| | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University Medical Center, Durham, North Carolina
| | - Filippo Pinto E Vairo
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota; Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Pavel N Pichurin
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Sarah A Ewing
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - Sarah S Barnett
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Eric W Klee
- Department of Clinical Genomics, Mayo Clinic, Rochester, Minnesota
| | - M Scott Perry
- Jane and John Justin Neuroscience Center, Cook Children's Medical Center, Fort Worth, Texas
| | - Mary Kay Koenig
- Department of Pediatrics, University of Texas Medical School at Houston, Houston, Texas
| | - Catherine E Keegan
- Division of Genetics, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Jane L Schuette
- Division of Genetics, Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Stephanie Asher
- Translational Medicine & Human Genetics, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Yezmin Perilla-Young
- Division of Pediatric Genetics and Metabolism, University of North Carolina, Chapel Hill, North Carolina
| | - Laurie D Smith
- Division of Pediatric Genetics and Metabolism, University of North Carolina, Chapel Hill, North Carolina
| | | | - Elizabeth Bhoj
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Paige Kaplan
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Dong Li
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Renske Oegema
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bert van der Zwaag
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Matthew Page
- Translational Medicine, UCB Pharma, Braine-l'Alleud, Belgium
| | | | - Angela E Lin
- Medical Genetics Unit, Mass General Hospital for Children, Boston, Massachusetts
| | - Marcie A Steeves
- Medical Genetics Unit, Mass General Hospital for Children, Boston, Massachusetts
| | | | - Mariëtte J V Hoffer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Margot R F Reijnders
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Serwet Demirdas
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | | | - Scott E Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio
| | - Christine Shieh
- David Geffen School of Medicine, University of California-Los Angeles, California
| | | | - John M Graham
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Kamer Tezcan
- Department of Genetics, Kaiser Permanente, Sacramento, California
| | - G B Schaefer
- Section of Genetics and Metabolism, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Noelle R Danylchuk
- Department of Genetic Counseling, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Alexander Asamoah
- Department of Pediatrics, University of Louisville School of Medicine, Louisville, Kentucky
| | - Kelly E Jackson
- Department of Pediatrics, University of Louisville School of Medicine, Louisville, Kentucky
| | - Naomi Yachelevich
- Clinical Genetics Services, Department of Pediatrics, New York University School of Medicine, New York, New York
| | - Margaret Au
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Luis A Pérez-Jurado
- University of Adelaide and Robinson Research Institute, Adelaide, Australia; Women's and Children's Hospital, Adelaide, Australia; South Australian Health and Medical Research Institute, Adelaide, South Australia; Hospital del Mar Research Institute, Network Research Centre for Rare Diseases and Universitat Pompeu Fabra, Barcelona, Spain
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter Penzes
- Department of Physiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Stephen A Wood
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Thomas Burne
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia; Queensland Centre for Mental Health Research, Wacol, Queensland, Australia
| | - Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California; Department of Neurology and the Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Michael Piper
- School of Biomedical Sciences, The University of Queensland, Brisbane, Australia; Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Jozef Gécz
- University of Adelaide and Robinson Research Institute, Adelaide, Australia; South Australian Health and Medical Research Institute, Adelaide, South Australia.
| | - Lachlan A Jolly
- University of Adelaide and Robinson Research Institute, Adelaide, Australia.
| |
Collapse
|
50
|
Zhao Y, Diacou A, Johnston HR, Musfee FI, McDonald-McGinn DM, McGinn D, Crowley TB, Repetto GM, Swillen A, Breckpot J, Vermeesch JR, Kates WR, Digilio MC, Unolt M, Marino B, Pontillo M, Armando M, Di Fabio F, Vicari S, van den Bree M, Moss H, Owen MJ, Murphy KC, Murphy CM, Murphy D, Schoch K, Shashi V, Tassone F, Simon TJ, Shprintzen RJ, Campbell L, Philip N, Heine-Suñer D, García-Miñaúr S, Fernández L, Bearden CE, Vingerhoets C, van Amelsvoort T, Eliez S, Schneider M, Vorstman JAS, Gothelf D, Zackai E, Agopian AJ, Gur RE, Bassett AS, Emanuel BS, Goldmuntz E, Mitchell LE, Wang T, Morrow BE. Complete Sequence of the 22q11.2 Allele in 1,053 Subjects with 22q11.2 Deletion Syndrome Reveals Modifiers of Conotruncal Heart Defects. Am J Hum Genet 2020; 106:26-40. [PMID: 31870554 PMCID: PMC7077921 DOI: 10.1016/j.ajhg.2019.11.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [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: 08/28/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
The 22q11.2 deletion syndrome (22q11.2DS) results from non-allelic homologous recombination between low-copy repeats termed LCR22. About 60%-70% of individuals with the typical 3 megabase (Mb) deletion from LCR22A-D have congenital heart disease, mostly of the conotruncal type (CTD), whereas others have normal cardiac anatomy. In this study, we tested whether variants in the hemizygous LCR22A-D region are associated with risk for CTDs on the basis of the sequence of the 22q11.2 region from 1,053 22q11.2DS individuals. We found a significant association (FDR p < 0.05) of the CTD subset with 62 common variants in a single linkage disequilibrium (LD) block in a 350 kb interval harboring CRKL. A total of 45 of the 62 variants were associated with increased risk for CTDs (odds ratio [OR) ranges: 1.64-4.75). Associations of four variants were replicated in a meta-analysis of three genome-wide association studies of CTDs in affected individuals without 22q11.2DS. One of the replicated variants, rs178252, is located in an open chromatin region and resides in the double-elite enhancer, GH22J020947, that is predicted to regulate CRKL (CRK-like proto-oncogene, cytoplasmic adaptor) expression. Approximately 23% of patients with nested LCR22C-D deletions have CTDs, and inactivation of Crkl in mice causes CTDs, thus implicating this gene as a modifier. Rs178252 and rs6004160 are expression quantitative trait loci (eQTLs) of CRKL. Furthermore, set-based tests identified an enhancer that is predicted to target CRKL and is significantly associated with CTD risk (GH22J020946, sequence kernal association test (SKAT) p = 7.21 × 10-5) in the 22q11.2DS cohort. These findings suggest that variance in CTD penetrance in the 22q11.2DS population can be explained in part by variants affecting CRKL expression.
Collapse
Affiliation(s)
- Yingjie Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Alexander Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Fadi I Musfee
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas 77225, USA
| | - Donna M McDonald-McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - Daniel McGinn
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - T Blaine Crowley
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - Gabriela M Repetto
- Center for Genetics and Genomics, Facultad de Medicina Clinica Alemana-Universidad del Desarrollo, Santiago 7710162, Chile
| | - Ann Swillen
- Center for Human Genetics, University of Leuven (KU Leuven), Leuven 3000, Belgium
| | - Jeroen Breckpot
- Center for Human Genetics, University of Leuven (KU Leuven), Leuven 3000, Belgium
| | - Joris R Vermeesch
- Center for Human Genetics, University of Leuven (KU Leuven), Leuven 3000, Belgium
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY 13202, USA; Program in Neuroscience, SUNY Upstate Medical University, Syracuse, NY 13202, USA
| | - M Cristina Digilio
- Department of Medical Genetics, Bambino Gesù Hospital, Rome 00165, Italy
| | - Marta Unolt
- Department of Medical Genetics, Bambino Gesù Hospital, Rome 00165, Italy; Department of Pediatrics, Gynecology, and Obstetrics, La Sapienza University of Rome, Rome 00185, Italy
| | - Bruno Marino
- Department of Pediatrics, Gynecology, and Obstetrics, La Sapienza University of Rome, Rome 00185, Italy
| | - Maria Pontillo
- Department of Neuroscience, Bambino Gesù Hospital, Rome 00165, Italy
| | - Marco Armando
- Department of Neuroscience, Bambino Gesù Hospital, Rome 00165, Italy; Developmental Imaging and Psychopathology Lab, University of Geneva, Geneva 1211, Switzerland
| | - Fabio Di Fabio
- Department of Pediatrics, Gynecology, and Obstetrics, La Sapienza University of Rome, Rome 00185, Italy
| | - Stefano Vicari
- Department of Neuroscience, Bambino Gesù Hospital, Rome 00165, Italy; Department of Psychiatry, Catholic University, Rome 00153, Italy
| | - Marianne van den Bree
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Wales CF24 4HQ, UK
| | - Hayley Moss
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Wales CF24 4HQ, UK
| | - Michael J Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Wales CF24 4HQ, UK
| | - Kieran C Murphy
- Department of Psychiatry, Royal College of Surgeons in Ireland, Dublin 505095, Ireland
| | - Clodagh M Murphy
- Department of Forensic and Neurodevelopmental Sciences, King's College London, Institute of Psychiatry, Psychology, and Neuroscience, London SE5 8AF, UK; Behavioural and Developmental Psychiatry Clinical Academic Group, Behavioural Genetics Clinic, National Adult Autism and ADHD Service, South London and Maudsley Foundation National Health Service Trust, London SE5 8AZ, UK
| | - Declan Murphy
- Department of Forensic and Neurodevelopmental Sciences, King's College London, Institute of Psychiatry, Psychology, and Neuroscience, London SE5 8AF, UK; Behavioural and Developmental Psychiatry Clinical Academic Group, Behavioural Genetics Clinic, National Adult Autism and ADHD Service, South London and Maudsley Foundation National Health Service Trust, London SE5 8AZ, UK
| | - Kelly Schoch
- Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Vandana Shashi
- Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Flora Tassone
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California, Davis, CA 95817, USA
| | - Tony J Simon
- Department of Psychiatry and Behavioral Sciences, MIND Institute, University of California, Davis, CA 95817, USA
| | | | - Linda Campbell
- School of Psychology, University of Newcastle, Newcastle 2258, Australia
| | - Nicole Philip
- Department of Medical Genetics, Aix-Marseille University, Marseille 13284, France
| | - Damian Heine-Suñer
- Genomics of Health and Unit of Molecular Diagnosis and Clinical Genetics, Son Espases University Hospital, Balearic Islands Health Research Institute, Palma de Mallorca 07120, Spain
| | - Sixto García-Miñaúr
- Institute of Medical and Molecular Genetics, University Hospital La Paz, Madrid 28046, Spain
| | - Luis Fernández
- Institute of Medical and Molecular Genetics, University Hospital La Paz, Madrid 28046, Spain
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Claudia Vingerhoets
- Department of Psychiatry and Psychology, Maastricht University, Maastricht, 6200 MD, the Netherlands
| | - Therese van Amelsvoort
- Department of Psychiatry and Psychology, Maastricht University, Maastricht, 6200 MD, the Netherlands
| | - Stephan Eliez
- Developmental Imaging and Psychopathology Lab, University of Geneva, Geneva 1211, Switzerland
| | - Maude Schneider
- Developmental Imaging and Psychopathology Lab, University of Geneva, Geneva 1211, Switzerland
| | - Jacob A S Vorstman
- Program in Genetics and Genome Biology, Research Institute, Toronto, Ontario, Canada; Department of Psychiatry, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, M5S 1A1, Canada; Department of Psychiatry, University Medical Center Utrecht Brain Center, Utrecht, 3584 CG, the Netherlands
| | - Doron Gothelf
- The Child Psychiatry Unit, Edmond and Lily Sapfra Children's Hospital, Sackler Faculty of Medicine, Tel Aviv University and Sheba Medical Center, Tel Aviv, 52621, Israel
| | - Elaine Zackai
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - A J Agopian
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas 77225, USA
| | - Raquel E Gur
- Department of Psychiatry, Perelman School of Medicine of the University of Pennsylvania Philadelphia, PA 19104, USA; Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anne S Bassett
- Dalglish Family 22q Clinic, Clinical Genetics Research Program, Toronto M5T 1L8, Ontario Canada; Toronto General Hospital, Centre for Addiction and Mental Health, Toronto M5T 1L8, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto M5T 1L8, Ontario, Canada
| | - Beverly S Emanuel
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
| | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Laura E Mitchell
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth School of Public Health, Houston, Texas 77225, USA
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| |
Collapse
|