1
|
María Del Rocío PB, Palomares Bralo M, Vanhooydonck M, Hamerlinck L, D'haene E, Leimbacher S, Jacobs EZ, De Cock L, D'haenens E, Dheedene A, Malfait Z, Vantomme L, Silva A, Rooney K, Santos-Simarro F, Lleuger-Pujol R, García-Miñaúr S, Losantos-García I, Menten B, Gestri G, Ragge N, Sadikovic B, Bogaert E, Syx D, Callewaert B, Vergult S. Loss-of-function of the Zinc Finger Homeobox 4 ( ZFHX4) gene underlies a neurodevelopmental disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.07.24311381. [PMID: 39148819 PMCID: PMC11326360 DOI: 10.1101/2024.08.07.24311381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
8q21.11 microdeletions encompassing the gene encoding transcription factor ZFHX4, have previously been associated by us with a syndromic form of intellectual disability, hypotonia, decreased balance and hearing loss. Here, we report on 57 individuals, 52 probands and 5 affected family members, with protein truncating variants (n=36), (micro)deletions (n=20) or an inversion (n=1) affecting ZFHX4 with variable developmental delay and intellectual disability, distinctive facial characteristics, morphological abnormalities of the central nervous system, behavioral alterations, short stature, hypotonia, and occasionally cleft palate and anterior segment dysgenesis. The phenotypes associated with 8q21.11 microdeletions and ZFHX4 intragenic loss-of-function variants largely overlap, identifying ZFHX4 as the main driver for the microdeletion syndrome, although leukocyte-derived DNA shows a mild common methylation profile for (micro)deletions only. We identify ZFHX4 as a transcription factor that is increasingly expressed during human brain development and neuronal differentiation. Furthermore, ZFHX4 interacting factors identified via IP-MS in neural progenitor cells, suggest an important role for ZFHX4 in cellular and developmental pathways, especially during histone modifications, cytosolic transport and development. Additionally, using CUT&RUN, we observed that ZFHX4 binds with the promoter regions of genes with crucial roles in embryonic, neuron and axon development. Since loss-of-function variants in ZFHX4 are found with consistent dysmorphic facial features, we investigated whether the disruption of zfhx4 causes craniofacial abnormalities in zebrafish. First-generation (F0) zfhx4 crispant zebrafish, (mosaic) mutant for zfhx4 loss-of-function variants, have significantly shorter Meckel's cartilages and smaller ethmoid plates compared to control zebrafish. Furthermore, behavioral assays show a decreased movement frequency in the zfhx4 crispant zebrafish in comparison with control zebrafish larvae. Although further research is needed, our in vivo work suggests a role for zfhx4 in facial skeleton patterning, palatal development and behavior.
Collapse
Affiliation(s)
- Pérez Baca María Del Rocío
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - María Palomares Bralo
- CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA- European Reference Network, Spain
| | - Michiel Vanhooydonck
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lisa Hamerlinck
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Eva D'haene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sebastian Leimbacher
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Eva Z Jacobs
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Laurenz De Cock
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Erika D'haenens
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Annelies Dheedene
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Zoë Malfait
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lies Vantomme
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Ananilia Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Fernando Santos-Simarro
- Unit of Molecular Diagnostics and Clinical Genetics, Hospital Universitari Son Espases, Health Research Institute of the Balearic Islands (IdiSBa), Palma, Spain
| | - Roser Lleuger-Pujol
- Hereditary Cancer Program, Catalan Institute of Oncology, Doctor Josep Trueta University Hospital; Precision Oncology Group (OncoGIR-Pro), Institut d'Investigació Biomèdica de Girona (IDIGBI), Girona, Spain
| | - Sixto García-Miñaúr
- CIBERER-ISCIII and INGEMM, Institute of Medical and Molecular Genetics, Hospital Universitario La Paz, Madrid, Spain
- ITHACA- European Reference Network, Spain
| | | | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Gaia Gestri
- University College London, London, England, Great Britain
| | - Nicola Ragge
- Birmingham Women's and Children's NHS Foundation Trust, Clinical Genetics Unit, Birmingham Womens Hospital, Lavender House, Mindelsohn Way, Edgbaston, Birmingham B15 2TG
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Elke Bogaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delfien Syx
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bert Callewaert
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sarah Vergult
- Center for Medical Genetics Ghent, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| |
Collapse
|
2
|
Rots D, Bouman A, Yamada A, Levy M, Dingemans AJM, de Vries BBA, Ruiterkamp-Versteeg M, de Leeuw N, Ockeloen CW, Pfundt R, de Boer E, Kummeling J, van Bon B, van Bokhoven H, Kasri NN, Venselaar H, Alders M, Kerkhof J, McConkey H, Kuechler A, Elffers B, van Beeck Calkoen R, Hofman S, Smith A, Valenzuela MI, Srivastava S, Frazier Z, Maystadt I, Piscopo C, Merla G, Balasubramanian M, Santen GWE, Metcalfe K, Park SM, Pasquier L, Banka S, Donnai D, Weisberg D, Strobl-Wildemann G, Wagemans A, Vreeburg M, Baralle D, Foulds N, Scurr I, Brunetti-Pierri N, van Hagen JM, Bijlsma EK, Hakonen AH, Courage C, Genevieve D, Pinson L, Forzano F, Deshpande C, Kluskens ML, Welling L, Plomp AS, Vanhoutte EK, Kalsner L, Hol JA, Putoux A, Lazier J, Vasudevan P, Ames E, O'Shea J, Lederer D, Fleischer J, O'Connor M, Pauly M, Vasileiou G, Reis A, Kiraly-Borri C, Bouman A, Barnett C, Nezarati M, Borch L, Beunders G, Özcan K, Miot S, Volker-Touw CML, van Gassen KLI, Cappuccio G, Janssens K, Mor N, Shomer I, Dominissini D, Tedder ML, Muir AM, Sadikovic B, Brunner HG, Vissers LELM, Shinkai Y, Kleefstra T. Comprehensive EHMT1 variants analysis broadens genotype-phenotype associations and molecular mechanisms in Kleefstra syndrome. Am J Hum Genet 2024; 111:1605-1625. [PMID: 39013458 PMCID: PMC11339614 DOI: 10.1016/j.ajhg.2024.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/18/2024] Open
Abstract
The shift to a genotype-first approach in genetic diagnostics has revolutionized our understanding of neurodevelopmental disorders, expanding both their molecular and phenotypic spectra. Kleefstra syndrome (KLEFS1) is caused by EHMT1 haploinsufficiency and exhibits broad clinical manifestations. EHMT1 encodes euchromatic histone methyltransferase-1-a pivotal component of the epigenetic machinery. We have recruited 209 individuals with a rare EHMT1 variant and performed comprehensive molecular in silico and in vitro testing alongside DNA methylation (DNAm) signature analysis for the identified variants. We (re)classified the variants as likely pathogenic/pathogenic (molecularly confirming Kleefstra syndrome) in 191 individuals. We provide an updated and broader clinical and molecular spectrum of Kleefstra syndrome, including individuals with normal intelligence and familial occurrence. Analysis of the EHMT1 variants reveals a broad range of molecular effects and their associated phenotypes, including distinct genotype-phenotype associations. Notably, we showed that disruption of the "reader" function of the ankyrin repeat domain by a protein altering variant (PAV) results in a KLEFS1-specific DNAm signature and milder phenotype, while disruption of only "writer" methyltransferase activity of the SET domain does not result in KLEFS1 DNAm signature or typical KLEFS1 phenotype. Similarly, N-terminal truncating variants result in a mild phenotype without the DNAm signature. We demonstrate how comprehensive variant analysis can provide insights into pathogenesis of the disorder and DNAm signature. In summary, this study presents a comprehensive overview of KLEFS1 and EHMT1, revealing its broader spectrum and deepening our understanding of its molecular mechanisms, thereby informing accurate variant interpretation, counseling, and clinical management.
Collapse
Affiliation(s)
- Dmitrijs Rots
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Genetics Laboratory, Children's Clinical University Hospital, Riga, Latvia
| | - Arianne Bouman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ayumi Yamada
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
| | - Michael Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | | | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Nicole de Leeuw
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Elke de Boer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Joost Kummeling
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bregje van Bon
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Nael Nadif Kasri
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Hanka Venselaar
- Department of Medical BioSciences, Radboudumc, Nijmegen, the Netherlands
| | - Marielle Alders
- Department of Human Genetics, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction and Development research institute, Amsterdam, the Netherlands
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Alma Kuechler
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Bart Elffers
- Cordaan, Amsterdam, the Netherlands; Department of Medical Care for Patients with Intellectual Disability, AMSTA, Amsterdam, the Netherlands
| | | | | | - Audrey Smith
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Maria Irene Valenzuela
- Department of Clinical and Molecular Genetics and Rare Disease Unit Hospital Vall d'Hebron, Barcelona, Spain; Medicine Genetics Group, Vall Hebron Research Institute, Barcelona, Spain
| | | | - Zoe Frazier
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Isabelle Maystadt
- Institut de Pathologie et de Génétique Centre de Génétique Humaineavenue G. Lemaître, 256041 Gosselies, Belgium
| | - Carmelo Piscopo
- Medical and Laboratory Unit, Antonio cardarelli Hospital, via A.Cardarelli 9, 80131 Naples, Italy
| | - Giuseppe Merla
- Department of Molecular Medicine and Medical Biotechnology, University of Naples, Naples, Italy; Laboratory of Regulatory and Functional Genomics, fondazione IRCCS casa sollievo della sofferenza, san giovanni rotondo, Foggia, Italy
| | - Meena Balasubramanian
- Division of Clinical Medicine, University of Sheffield, Sheffield, UK; Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, United Kingdom
| | - Gijs W E Santen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Soo-Mi Park
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Laurent Pasquier
- Reference Center for Rare Diseases, Hôpital Sud - CHU Rennes, Rennes, France
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Dian Donnai
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Daniel Weisberg
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | | | - Annemieke Wagemans
- Maasveld, Koraal, Maastricht, the Netherlands; Department of Family Medicine, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, the Netherlands
| | - Maaike Vreeburg
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, Southampton, Hampshire, UK
| | - Nicola Foulds
- Wessex Regional Genetics Services, UHS NHS Foundation Trust, Southampton, United Kingdom
| | - Ingrid Scurr
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy; Telethon Institute of Genetics and Medicine, Pozzuoli, Italy; Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Johanna M van Hagen
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Human Genetics, Amsterdam, the Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetica, Leiden University Medical Center, Leiden, the Netherlands
| | - Anna H Hakonen
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Carolina Courage
- Department of Clinical Genetics, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - David Genevieve
- Université Montpellier, Unité INSERM U1183, Montpellier, France; Centre de reference Anomalies du développement, ERN ITHACA, Service de génétique Clinique, CHU Montpellier, Montpellier, France
| | - Lucile Pinson
- Centre de reference Anomalies du développement, ERN ITHACA, Service de génétique Clinique, CHU Montpellier, Montpellier, France
| | - Francesca Forzano
- Clinical Genetics Department 7th Floor Borough WingGuy's Hospital, Guy's & St Thomas' NHS Foundation TrustGreat Maze Pond, London, UK
| | - Charu Deshpande
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | | | | | - Astrid S Plomp
- Department of Human Genetics, Amsterdam UMC location University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction and Development research institute, Amsterdam, the Netherlands
| | - Els K Vanhoutte
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Louisa Kalsner
- Department of Pediatrics, Division of Neurology, Connecticut Children's, University of Connecticut, Farmington, CT, USA
| | - Janna A Hol
- Clinical Genetics Department, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Audrey Putoux
- Hospices Civils de Lyon, Service de Génétique - Centre de Référence Anomalies du Développement, Bron, France; Centre de Recherche en Neurosciences de Lyon, Équipe GENDEV, INSERM U1028 CNRS UMR5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Johanna Lazier
- Regional Genetics Program, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Pradeep Vasudevan
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Elizabeth Ames
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, C.S. Mott Children's Hospital, Michigan Medicine, Ann Arbor, MI, USA
| | - Jessica O'Shea
- Division of Pediatric Genetics, Metabolism, and Genomic Medicine, C.S. Mott Children's Hospital, Michigan Medicine, Ann Arbor, MI, USA
| | - Damien Lederer
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Julie Fleischer
- Southern Illinois University School of Medicine, Department of Pediatrics, Springfield, IL, USA
| | - Mary O'Connor
- Southern Illinois University School of Medicine, Department of Pediatrics, Springfield, IL, USA
| | - Melissa Pauly
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Georgia Vasileiou
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Centre for Rare Diseases Erlangen (ZSEER), Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Centre for Rare Diseases Erlangen (ZSEER), Erlangen, Germany
| | - Catherine Kiraly-Borri
- Genetic Health Western Australia, Department of Health King Edward Memorial Hospital, Subiaco, WA 6008, Australia
| | - Arjan Bouman
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands
| | - Chris Barnett
- Paediatric and Reproductive Genetics Unit 8th Floor, Clarence Rieger Building Women's and Children's Hospital, 72 King William Road North, Adelaide, SA 5006, Australia
| | - Marjan Nezarati
- Genetics, North York General Hospital, Toronto, ON, Canada; University of Toronto, Toronto, ON, Canada
| | - Lauren Borch
- Department of Medical Genetics, North York General Hospital, University of Toronto, Toronto, ON, Canada
| | - Gea Beunders
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Kübra Özcan
- Neurodevelopmental Treatment Association Çocuk Fizyoterapistleri Derneği Bobath Terapistleri Derneği, Ankara, Turkey
| | - Stéphanie Miot
- Geriatrics department, Montpellier University Hospital, MUSE University, Montpellier, France; INSERM U1298, INM, Montpellier, France
| | | | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gerarda Cappuccio
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Via Pansini 5, Naples, Italy; TIGEM (Telethon Institute of Genetics and Medicine), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy
| | - Katrien Janssens
- Department of Medical Genetics, Antwerp University Hospital/University of Antwerp, Edegem, Wilrijk, Belgium
| | - Nofar Mor
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Inna Shomer
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Dan Dominissini
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv, Israel
| | | | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Research Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan.
| | - Tjitske Kleefstra
- Department of Clinical Genetics, Erasmus MC, Rotterdam, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Center of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, the Netherlands.
| |
Collapse
|
3
|
Ilaria S, Tamara D, Antonella DJ, Elena M. Role of mitochondria-endoplasmic reticulum contacts in neurodegenerative, neurodevelopmental and neuropsychiatric conditions. Eur J Neurosci 2024. [PMID: 39099373 DOI: 10.1111/ejn.16485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 04/15/2024] [Accepted: 07/15/2024] [Indexed: 08/06/2024]
Abstract
Mitochondria-endoplasmic reticulum contacts (MERCs) mediate a close and continuous communication between both organelles that is essential for the transfer of calcium and lipids to mitochondria, necessary for cellular signalling and metabolic pathways. Their structural and molecular characterisation has shown the involvement of many proteins that bridge the membranes of the two organelles and maintain the structural stability and function of these contacts. The crosstalk between the two organelles is fundamental for proper neuronal function and is now recognised as a component of many neurological disorders. In fact, an increasing proportion of MERC proteins take part in the molecular and cellular basis of pathologies affecting the nervous system. Here we review the alterations in MERCs that have been reported for these pathologies, from neurodevelopmental and neuropsychiatric disorders to neurodegenerative diseases. Although mitochondrial abnormalities in these debilitating conditions have been extensively attributed to the high energy demand of neurons, a distinct role for MERCs is emerging as a new field of research. Understanding the molecular details of such alterations may open the way to new paths of therapeutic intervention.
Collapse
Affiliation(s)
- Serangeli Ilaria
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Diamanti Tamara
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - De Jaco Antonella
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Miranda Elena
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| |
Collapse
|
4
|
Roychaudhury A, Lee YR, Choi TI, Thomas MG, Khan TN, Yousaf H, Skinner C, Maconachie G, Crosier M, Horak H, Constantinescu CS, Kim TY, Lee KH, Kyung JJ, Wang T, Ku B, Chodirker BN, Hammer MF, Gottlob I, Norton WHJ, Gerlai R, Kim HG, Graziano C, Pippucci T, Iovino E, Montanari F, Severi G, Toro C, Boerkoel CF, Cha HS, Choi CY, Kim S, Yoon JH, Gilmore K, Vora NL, Davis EE, Chudley AE, Schwartz CE, Kim CH. SRPK3 Is Essential for Cognitive and Ocular Development in Humans and Zebrafish, Explaining X-Linked Intellectual Disability. Ann Neurol 2024. [PMID: 39073169 DOI: 10.1002/ana.27037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
OBJECTIVE Intellectual disability is often the outcome of neurodevelopmental disorders and is characterized by significant impairments in intellectual and adaptive functioning. X-linked intellectual disability (XLID) is a subset of these disorders caused by genetic defects on the X chromosome, affecting about 2 out of 1,000 males. In syndromic form, it leads to a broad range of cognitive, behavioral, ocular, and physical disabilities. METHODS Employing exome or genome sequencing, here we identified 4 missense variants (c.475C > G; p.H159D, c.1373C > A; p.T458N, and c.1585G > A; p.E529K, c.953C > T; p.S318L) and a putative truncating variant (c.1413_1414del; p.Y471*) in the SRPK3 gene in 9 XLID patients from 5 unrelated families. To validate SRPK3 as a novel XLID gene, we established a knockout (KO) model of the SRPK3 orthologue in zebrafish. RESULTS The 8 patients ascertained postnatally shared common clinical features including intellectual disability, agenesis of the corpus callosum, abnormal eye movement, and ataxia. A ninth case, ascertained prenatally, had a complex structural brain phenotype. Together, these data indicate a pathological role of SRPK3 in neurodevelopmental disorders. In post-fertilization day 5 larvae (free swimming stage), KO zebrafish exhibited severe deficits in eye movement and swim bladder inflation, mimicking uncontrolled ocular movement and physical clumsiness observed in human patients. In adult KO zebrafish, cerebellar agenesis and behavioral abnormalities were observed, recapitulating human phenotypes of cerebellar atrophy and intellectual disability. INTERPRETATION Overall, these results suggest a crucial role of SRPK3 in the pathogenesis of syndromic X-linked intellectual disability and provide new insights into brain development, cognitive and ocular dysfunction in both humans and zebrafish. ANN NEUROL 2024.
Collapse
Affiliation(s)
| | - Yu-Ri Lee
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Mervyn G Thomas
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behavior, University of Leicester, Leicester, UK
| | - Tahir N Khan
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Hammad Yousaf
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | - Gail Maconachie
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behavior, University of Leicester, Leicester, UK
- Division of Ophthalmology and Orthoptics, Health Science School, University of Sheffield, Sheffield, UK
| | - Moira Crosier
- Human Developmental Biology Resource, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Holli Horak
- Department of Neurology, University of Arizona, Tucson, AZ, USA
| | - Cris S Constantinescu
- Academic Unit of Mental Health and Clinical Neuroscience, University of Nottingham, Nottingham, UK
- Cooper Neurological Institute and Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Tae-Yoon Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Kang-Han Lee
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Jae-Jun Kyung
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Tao Wang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Bernard N Chodirker
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | | | - Irene Gottlob
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behavior, University of Leicester, Leicester, UK
- Cooper Neurological Institute and Cooper Medical School of Rowan University, Camden, NJ, USA
| | - William H J Norton
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Robert Gerlai
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Emanuela Iovino
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Giulia Severi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Hyo Sun Cha
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Cheol Yong Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Sungjin Kim
- Department of Microbiology & Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Je-Hyun Yoon
- Department of Oncology Science, University of Oklahoma, Oklahoma City, OK, USA
| | - Kelly Gilmore
- Division of Maternal Fetal Medicine, Department of Ob/Gyn, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Neeta L Vora
- Division of Maternal Fetal Medicine, Department of Ob/Gyn, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica E Davis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Albert E Chudley
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Charles E Schwartz
- Greenwood Genetic Center, Greenwood, SC, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| |
Collapse
|
5
|
Hauptman AJ, Salpekar JA, Cohen JS, Asato MR. Navigating Neurogenetics for Child and Adolescent Psychiatry Practice. J Am Acad Child Adolesc Psychiatry 2024; 63:666-669. [PMID: 38325519 DOI: 10.1016/j.jaac.2023.09.555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/29/2023] [Accepted: 01/29/2024] [Indexed: 02/09/2024]
Abstract
Neurodevelopmental disorders (NDDs) are a group of conditions characterized by impairments of brain processes that impact cognition, communication, motor abilities, and/or behavior during development. These conditions typically have significant effects across the life span and impact personal, social, academic, or occupational functioning. The US Centers for Disease Control and report that 1 in 6 children has a developmental disability, making it highly likely for child and adolescent psychiatrists to encounter children with NDDs in daily practice.1 While the etiologies of NDDs are broad, genetic syndromes are a common cause of NDDs. The diagnostic yield of thorough genetic testing for NDDs as a group is about 40% based on meta-analysis, including 30% to 50% yield in patients with global developmental delay (GDD) or intellectual disability (ID) and 15% to 20% yield in patients with in autism spectrum disorder.1-3 The findings are extremely heterogeneous, including chromosomal copy number variants (CNVs) and more than 2,000 known monogenic disorders associated with NDDs.3 Diagnostic yields will increase over time with advances in technology and disease gene discovery.3.
Collapse
Affiliation(s)
- Aaron J Hauptman
- Kennedy Krieger Institute, Baltimore, Maryland, and Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Jay A Salpekar
- Kennedy Krieger Institute, Baltimore, Maryland, and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julie S Cohen
- Kennedy Krieger Institute, Baltimore, Maryland, and Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Miya R Asato
- Kennedy Krieger Institute, Baltimore, Maryland, and Johns Hopkins University School of Medicine, Baltimore, Maryland
| |
Collapse
|
6
|
Dillen L, Fatima N, Hommersom MP, Çepni E, Fatima F, van Beusekom E, Albert S, van Hagen JM, de Vries BBA, Khan AA, de Brouwer APM, van Bokhoven H. Generation of induced pluripotent stem cell lines from two unrelated patients affected by intellectual disability carrying homozygous variants in SGIP1. Stem Cell Res 2024; 77:103442. [PMID: 38739972 DOI: 10.1016/j.scr.2024.103442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024] Open
Abstract
Intellectual disability (ID) is a diverse neurodevelopmental condition and almost half of the cases have a genetic etiology. SGIP1 acts as an endocytic protein that influences the signaling of receptors in neuronal systems related to energy homeostasis through its interaction with endophilins. This study focuses on the generation and characterization of induced pluripotent stem cells (iPSC) from two unrelated patients due to a frameshift variant (c.764dupA, NM_032291.4) and a splice donor site variant (c.74 + 1G > A, NM_032291.4) in the SGIP1 gene.
Collapse
Affiliation(s)
- Lieke Dillen
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Neelam Fatima
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Marina P Hommersom
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
| | - Ece Çepni
- Institute of Health Sciences, Koç University, 34010 Istanbul, Turkey
| | - Fareeha Fatima
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Ellen van Beusekom
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Silvia Albert
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Asma Ali Khan
- Center of Excellence in Molecular Biology, University of Punjab, Lahore, Pakistan
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6500 HB Nijmegen, Netherlands.
| |
Collapse
|
7
|
Trevisan V, Meroni A, Leoni C, Sirchia F, Politano D, Fiandrino G, Giorgio V, Rigante D, Limongelli D, Perri L, Sforza E, Leonardi F, Viscogliosi G, Contaldo I, Orteschi D, Proietti L, Zampino G, Onesimo R. Trisomy 22 Mosaicism from Prenatal to Postnatal Findings: A Case Series and Systematic Review of the Literature. Genes (Basel) 2024; 15:346. [PMID: 38540405 PMCID: PMC10970670 DOI: 10.3390/genes15030346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Among aneuploidies compatible with life, trisomy 22 mosaicism is extremely rare, and only about 25 postnatal and 18 prenatal cases have been described in the literature so far. The condition is mainly characterized by facial and body asymmetry, cardiac heart defects, facial dysmorphisms, growth failure, delayed puberty, and variable degrees of neurodevelopmental delay. PROBLEM The scattered information regarding the condition and the dearth of data on its natural history and developmental outcomes restrict genetic counseling, particularly in prenatal settings. Moreover, a prompt diagnosis is frequently delayed by the negative selection of trisomic cells in blood, with mosaicism percentage varying among tissues, which often entails the need for further testing. Purpose/topic: The aim of our work is to provide assistance in prenatal and postnatal genetic counseling by systematically delineating the current knowledge of the condition. This entails defining the prenatal and postnatal characteristics of the condition and presenting novel data from three cases, both prenatally and postnatally. Additionally, we report the developmental outcomes observed in two new patients.
Collapse
Affiliation(s)
- Valentina Trevisan
- Centre for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (C.L.); (V.G.); (D.L.); (L.P.); (G.V.); (G.Z.); (R.O.)
- Genomic Medicine, Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, 00168 Rome, Italy; (F.L.); (D.O.)
| | - Anna Meroni
- Human Genetics, Molecular Medicine Department, University of Pavia and IRCCS Fondazione Policlinico San Matteo, 27100 Pavia, Italy; (A.M.); (F.S.)
| | - Chiara Leoni
- Centre for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (C.L.); (V.G.); (D.L.); (L.P.); (G.V.); (G.Z.); (R.O.)
| | - Fabio Sirchia
- Human Genetics, Molecular Medicine Department, University of Pavia and IRCCS Fondazione Policlinico San Matteo, 27100 Pavia, Italy; (A.M.); (F.S.)
| | - Davide Politano
- Department of Brain and Behavioral Sciences, University of Pavia, IRCCS Mondino, 27100 Pavia, Italy;
| | - Giacomo Fiandrino
- Department of Molecular Medicine, Anatomic Pathology Unit, University of Pavia and Fondazione IRCCS San Matteo Hospital, 27100 Pavia, Italy;
| | - Valentina Giorgio
- Centre for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (C.L.); (V.G.); (D.L.); (L.P.); (G.V.); (G.Z.); (R.O.)
| | - Donato Rigante
- Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, 00168 Rome, Italy;
- Child Neurology and Psychiatry Unit, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.S.); (I.C.)
| | - Domenico Limongelli
- Centre for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (C.L.); (V.G.); (D.L.); (L.P.); (G.V.); (G.Z.); (R.O.)
| | - Lucrezia Perri
- Centre for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (C.L.); (V.G.); (D.L.); (L.P.); (G.V.); (G.Z.); (R.O.)
| | - Elisabetta Sforza
- Child Neurology and Psychiatry Unit, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.S.); (I.C.)
| | - Francesca Leonardi
- Genomic Medicine, Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, 00168 Rome, Italy; (F.L.); (D.O.)
| | - Germana Viscogliosi
- Centre for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (C.L.); (V.G.); (D.L.); (L.P.); (G.V.); (G.Z.); (R.O.)
| | - Ilaria Contaldo
- Child Neurology and Psychiatry Unit, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (E.S.); (I.C.)
| | - Daniela Orteschi
- Genomic Medicine, Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, 00168 Rome, Italy; (F.L.); (D.O.)
- Genetic Unit, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy
| | - Luca Proietti
- Department of Orthopaedics and Traumatology, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy;
| | - Giuseppe Zampino
- Centre for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (C.L.); (V.G.); (D.L.); (L.P.); (G.V.); (G.Z.); (R.O.)
- Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, 00168 Rome, Italy;
| | - Roberta Onesimo
- Centre for Rare Diseases and Birth Defects, Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (C.L.); (V.G.); (D.L.); (L.P.); (G.V.); (G.Z.); (R.O.)
| |
Collapse
|
8
|
Schobers G, Derks R, den Ouden A, Swinkels H, van Reeuwijk J, Bosgoed E, Lugtenberg D, Sun SM, Corominas Galbany J, Weiss M, Blok MJ, Olde Keizer RACM, Hofste T, Hellebrekers D, de Leeuw N, Stegmann A, Kamsteeg EJ, Paulussen ADC, Ligtenberg MJL, Bradley XZ, Peden J, Gutierrez A, Pullen A, Payne T, Gilissen C, van den Wijngaard A, Brunner HG, Nelen M, Yntema HG, Vissers LELM. Genome sequencing as a generic diagnostic strategy for rare disease. Genome Med 2024; 16:32. [PMID: 38355605 PMCID: PMC10868087 DOI: 10.1186/s13073-024-01301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/02/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND To diagnose the full spectrum of hereditary and congenital diseases, genetic laboratories use many different workflows, ranging from karyotyping to exome sequencing. A single generic high-throughput workflow would greatly increase efficiency. We assessed whether genome sequencing (GS) can replace these existing workflows aimed at germline genetic diagnosis for rare disease. METHODS We performed short-read GS (NovaSeq™6000; 150 bp paired-end reads, 37 × mean coverage) on 1000 cases with 1271 known clinically relevant variants, identified across different workflows, representative of our tertiary diagnostic centers. Variants were categorized into small variants (single nucleotide variants and indels < 50 bp), large variants (copy number variants and short tandem repeats) and other variants (structural variants and aneuploidies). Variant calling format files were queried per variant, from which workflow-specific true positive rates (TPRs) for detection were determined. A TPR of ≥ 98% was considered the threshold for transition to GS. A GS-first scenario was generated for our laboratory, using diagnostic efficacy and predicted false negative as primary outcome measures. As input, we modeled the diagnostic path for all 24,570 individuals referred in 2022, combining the clinical referral, the transition of the underlying workflow(s) to GS, and the variant type(s) to be detected. RESULTS Overall, 95% (1206/1271) of variants were detected. Detection rates differed per variant category: small variants in 96% (826/860), large variants in 93% (341/366), and other variants in 87% (39/45). TPRs varied between workflows (79-100%), with 7/10 being replaceable by GS. Models for our laboratory indicate that a GS-first strategy would be feasible for 84.9% of clinical referrals (750/883), translating to 71% of all individuals (17,444/24,570) receiving GS as their primary test. An estimated false negative rate of 0.3% could be expected. CONCLUSIONS GS can capture clinically relevant germline variants in a 'GS-first strategy' for the majority of clinical indications in a genetics diagnostic lab.
Collapse
Affiliation(s)
- Gaby Schobers
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Amber den Ouden
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Hilde Swinkels
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Jeroen van Reeuwijk
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Ermanno Bosgoed
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | | | - Su Ming Sun
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Jordi Corominas Galbany
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Marjan Weiss
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Marinus J Blok
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Richelle A C M Olde Keizer
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Debby Hellebrekers
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Alexander Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | | | | | | | | | | | - Christian Gilissen
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | | | - Han G Brunner
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | - Marcel Nelen
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Helger G Yntema
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands.
- Research Institute for Medical Innovation, Radboudumc, Nijmegen, Netherlands.
| |
Collapse
|
9
|
Calame DG, Emrick LT. Functional genomics and small molecules in mitochondrial neurodevelopmental disorders. Neurotherapeutics 2024; 21:e00316. [PMID: 38244259 PMCID: PMC10903096 DOI: 10.1016/j.neurot.2024.e00316] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/16/2023] [Accepted: 01/02/2024] [Indexed: 01/22/2024] Open
Abstract
Mitochondria are critical for brain development and homeostasis. Therefore, pathogenic variation in the mitochondrial or nuclear genome which disrupts mitochondrial function frequently results in developmental disorders and neurodegeneration at the organismal level. Large-scale application of genome-wide technologies to individuals with mitochondrial diseases has dramatically accelerated identification of mitochondrial disease-gene associations in humans. Multi-omic and high-throughput studies involving transcriptomics, proteomics, metabolomics, and saturation genome editing are providing deeper insights into the functional consequence of mitochondrial genomic variation. Integration of deep phenotypic and genomic data through allelic series continues to uncover novel mitochondrial functions and permit mitochondrial gene function dissection on an unprecedented scale. Finally, mitochondrial disease-gene associations illuminate disease mechanisms and thereby direct therapeutic strategies involving small molecules and RNA-DNA therapeutics. This review summarizes progress in functional genomics and small molecule therapeutics in mitochondrial neurodevelopmental disorders.
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.
| | - Lisa T Emrick
- 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
| |
Collapse
|
10
|
Dumitru C. Exploring the transformative power of dance: A scoping review of dance interventions for adults with intellectual disabilities. JOURNAL OF INTELLECTUAL DISABILITIES : JOID 2023:17446295231218781. [PMID: 38059909 DOI: 10.1177/17446295231218781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The aim of this scoping literature review (SCR) was to analyze the impact of dance on adults with intellectual disabilities, specifically examining its influence on their mobility, interpersonal relationships, well-being, and overall quality of life. A total of 15 papers were reviewed in order to explore the effects of dance on the well-being and quality of life of adults with intellectual disabilities. The findings indicated significant improvements in body awareness, increased engagement in physical activity, and enhanced mental health. This SCR demonstrates that dance is an effective means of facilitating social interaction among adults with intellectual disabilities, both with their therapists and family members. Additionally, the review uncovered valuable data on dance therapy programs designed for adults with intellectual disabilities, highlighting their potential to promote physical activity and reduce stress levels.
Collapse
Affiliation(s)
- Cristina Dumitru
- Department of Educational Sciences, The National University of Science and Technology POLITEHNICA Bucharest, Pitești University Centre, Romania
| |
Collapse
|
11
|
Bassett AS, Reuter MS, Malecki S, Silversides C, Oechslin E. Clinically Relevant Genetic Considerations for Patients With Tetralogy of Fallot. CJC PEDIATRIC AND CONGENITAL HEART DISEASE 2023; 2:426-439. [PMID: 38161665 PMCID: PMC10755827 DOI: 10.1016/j.cjcpc.2023.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/05/2023] [Indexed: 01/03/2024]
Abstract
Genetic changes affect embryogenesis, cardiac and extracardiac phenotype, development, later onset conditions, and both short- and long-term outcomes and comorbidities in the increasing population of individuals with tetralogy of Fallot (TOF). In this review, we focus on current knowledge about clinically relevant genetics for patients with TOF across the lifespan. The latest findings for TOF genetics that are pertinent to day-to-day practice and lifelong management are highlighted: morbidity/mortality, cardiac/extracardiac features, including neurodevelopmental expression, and recent changes to prenatal screening and diagnostics. Genome-wide microarray is the first-line clinical genetic test for TOF across the lifespan, detecting relevant structural changes including the most common for TOF, the 22q11.2 microdeletion. Accumulating evidence illustrates opportunities for advances in understanding and care that may arise from genetic diagnosis at any age. We also glimpse into the near future when the multigenic nature of TOF will be more fully revealed, further enhancing possibilities for preventive care. Precision medicine is nigh.
Collapse
Affiliation(s)
- Anne S. Bassett
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
- Toronto Adult Congenital Heart Disease Program, Division of Cardiology, Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, and Campbell Family Mental Health Research Institute, Toronto, Ontario, Canada
| | - Miriam S. Reuter
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Sarah Malecki
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Candice Silversides
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Toronto Adult Congenital Heart Disease Program, Division of Cardiology, Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Erwin Oechslin
- The Dalglish Family 22q Clinic, University Health Network, Toronto, Ontario, Canada
- Toronto Adult Congenital Heart Disease Program, Division of Cardiology, Peter Munk Cardiac Centre, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
12
|
Gupta V, Ben-Mahmoud A, Ku B, Velayutham D, Jan Z, Yousef Aden A, Kubbar A, Alshaban F, Stanton LW, Jithesh PV, Layman LC, Kim HG. Identification of two novel autism genes, TRPC4 and SCFD2, in Qatar simplex families through exome sequencing. Front Psychiatry 2023; 14:1251884. [PMID: 38025430 PMCID: PMC10644705 DOI: 10.3389/fpsyt.2023.1251884] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
This study investigated the genetic underpinnings of autism spectrum disorder (ASD) in a Middle Eastern cohort in Qatar using exome sequencing. The study identified six candidate autism genes in independent simplex families, including both four known and two novel autosomal dominant and autosomal recessive genes associated with ASD. The variants consisted primarily of de novo and homozygous missense and splice variants. Multiple individuals displayed more than one candidate variant, suggesting the potential involvement of digenic or oligogenic models. These variants were absent in the Genome Aggregation Database (gnomAD) and exhibited extremely low frequencies in the local control population dataset. Two novel autism genes, TRPC4 and SCFD2, were discovered in two Qatari autism individuals. Furthermore, the D651A substitution in CLCN3 and the splice acceptor variant in DHX30 were identified as likely deleterious mutations. Protein modeling was utilized to evaluate the potential impact of three missense variants in DEAF1, CLCN3, and SCFD2 on their respective structures and functions, which strongly supported the pathogenic natures of these variants. The presence of multiple de novo mutations across trios underscored the significant contribution of de novo mutations to the genetic etiology of ASD. Functional assays and further investigations are necessary to confirm the pathogenicity of the identified genes and determine their significance in ASD. Overall, this study sheds light on the genetic factors underlying ASD in Qatar and highlights the importance of considering diverse populations in ASD research.
Collapse
Affiliation(s)
- Vijay Gupta
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Afif Ben-Mahmoud
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Dinesh Velayutham
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Zainab Jan
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Abdi Yousef Aden
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Ahmad Kubbar
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Fouad Alshaban
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Lawrence W. Stanton
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Puthen Veettil Jithesh
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Hyung-Goo Kim
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| |
Collapse
|