Mutations in EBF3 Disturb Transcriptional Profiles and Cause Intellectual Disability, Ataxia, and Facial Dysmorphism

  • Am J Hum Genet. 2017 Jan 5;100(1):117-127. doi: 10.1016/j.ajhg.2016.11.012.
Frederike Leonie Harms  1 ,  Katta M Girisha  2 ,  Andrew A Hardigan  3 ,  Fanny Kortüm  1 ,  Anju Shukla  2 ,  Malik Alawi  4 ,  Ashwin Dalal  5 ,  Lauren Brady  6 ,  Mark Tarnopolsky  6 ,  Lynne M Bird  7 ,  Sophia Ceulemans  8 ,  Martina Bebin  9 ,  Kevin M Bowling  10 ,  Susan M Hiatt  10 ,  Edward J Lose  11 ,  Michelle Primiano  12 ,  Wendy K Chung  12 ,  Jane Juusola  13 ,  Zeynep C Akdemir  14 ,  Matthew Bainbridge  15 ,  Wu-Lin Charng  14 ,  Margaret Drummond-Borg  16 ,  Mohammad K Eldomery  14 ,  Ayman W El-Hattab  17 ,  Mohammed A M Saleh  18 ,  Stéphane Bézieau  19 ,  Benjamin Cogné  19 ,  Bertrand Isidor  20 ,  Sébastien Küry  19 ,  James R Lupski  14 ,  Richard M Myers  10 ,  Gregory M Cooper  21 ,  Kerstin Kutsche  22
Affiliations
  • 1. Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
  • 2. Department of Medical Genetics, Kasturba Medical College, Manipal University, 576104 Manipal, India.
  • 3. HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
  • 4. Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Center for Bioinformatics, University of Hamburg, 20246 Hamburg, Germany; Virus Genomics, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, 20246 Hamburg, Germany.
  • 5. Diagnostics Division, Centre for DNA Fingerprinting and Diagnostics, 500001 Hyderabad, Telangana, India.
  • 6. Department of Pediatrics, McMaster University Medical Center, Hamilton, ON L8N 3Z5, Canada.
  • 7. Department of Pediatrics, University of California, San Diego, San Diego, CA 92123, USA; Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA.
  • 8. Division of Genetics/Dysmorphology, Rady Children's Hospital San Diego, San Diego, CA 92123, USA.
  • 9. Department of Neurology, University of Alabama at Birmingham, Birmingham, AL35294, USA.
  • 10. HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA.
  • 11. Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
  • 12. Department of Pediatrics and Medicine, Columbia University, New York, NY 10032, USA.
  • 13. GeneDx, Gaithersburg, MD 20877, USA.
  • 14. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
  • 15. Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
  • 16. Cook Children's Genetic Clinic, Fort Worth, TX 76102, USA.
  • 17. Division of Clinical Genetics and Metabolic Disorders, Department of Pediatrics, Tawam Hospital, 15258 Al-Ain, United Arab Emirates.
  • 18. Section of Medical Genetics, Children's Hospital, King Fahad Medical City, 11564 Riyadh, Saudi Arabia.
  • 19. Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France.
  • 20. Service de Génétique Médicale, Centre Hospitalier Universitaire Nantes, 44093 Nantes Cedex 1, France; INSERM UMR-S 957, 44035 Nantes, France.
  • 21. HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA. Electronic address: [email protected].
  • 22. Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany. Electronic address: [email protected].
PMID: 28017373 DOI: 10.1016/j.ajhg.2016.11.012
Abstract

From a GeneMatcher-enabled international collaboration, we identified ten individuals affected by intellectual disability, speech delay, ataxia, and facial dysmorphism and carrying a deleterious EBF3 variant detected by whole-exome Sequencing. One 9-bp duplication and one splice-site, five missense, and two nonsense variants in EBF3 were found; the mutations occurred de novo in eight individuals, and the missense variant c.625C>T (p.Arg209Trp) was inherited by two affected siblings from their healthy mother, who is mosaic. EBF3 belongs to the early B cell factor family (also known as Olf, COE, or O/E) and is a transcription factor involved in neuronal differentiation and maturation. Structural assessment predicted that the five amino acid substitutions have damaging effects on DNA binding of EBF3. Transient expression of EBF3 mutant proteins in HEK293T cells revealed mislocalization of all but one mutant in the cytoplasm, as well as nuclear localization. By transactivation assays, all EBF3 mutants showed significantly reduced or no ability to activate transcription of the reporter gene CDKN1A, and in situ subcellular fractionation experiments demonstrated that EBF3 mutant proteins were less tightly associated with chromatin. Finally, in RNA-seq and ChIP-seq experiments, EBF3 acted as a transcriptional regulator, and mutant EBF3 had reduced genome-wide DNA binding and gene-regulatory activity. Our findings demonstrate that variants disrupting EBF3-mediated transcriptional regulation cause intellectual disability and developmental delay and are present in ∼0.1% of individuals with unexplained neurodevelopmental disorders.

Keywords
EBF3; de novo mutation; developmental delay; gene regulation; intellectual disability; transcription factor.