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Human Genetics

, Volume 137, Issue 6–7, pp 459–470 | Cite as

De novo variants in GREB1L are associated with non-syndromic inner ear malformations and deafness

  • Isabelle Schrauwen
  • Elina Kari
  • Jacob Mattox
  • Lorida Llaci
  • Joanna Smeeton
  • Marcus Naymik
  • David W. Raible
  • James A. Knowles
  • J. Gage Crump
  • Matthew J. Huentelman
  • Rick A. Friedman
Original Investigation

Abstract

Congenital inner ear malformations affecting both the osseous and membranous labyrinth can have a devastating impact on hearing and language development. With the exception of an enlarged vestibular aqueduct, non-syndromic inner ear malformations are rare, and their underlying molecular biology has thus far remained understudied. To identify molecular factors that might be important in the developing inner ear, we adopted a family-based trio exome sequencing approach in young unrelated subjects with severe inner ear malformations. We identified two previously unreported de novo loss-of-function variants in GREB1L [c.4368G>T;p.(Glu1410fs) and c.982C>T;p.(Arg328*)] in two affected subjects with absent cochleae and eighth cranial nerve malformations. The cochlear aplasia in these affected subjects suggests that a developmental arrest or problem at a very early stage of inner ear development exists, e.g., during the otic pit formation. Craniofacial Greb1l RNA expression peaks in mice during this time frame (E8.5). It also peaks in the developing inner ear during E13–E16, after which it decreases in adulthood. The crucial function of Greb1l in craniofacial development is also evidenced in knockout mice, which develop severe craniofacial abnormalities. In addition, we show that Greb1l−/− zebrafish exhibit a loss of abnormal sensory epithelia innervation. An important role for Greb1l in sensory epithelia innervation development is supported by the eighth cranial nerve deficiencies seen in both affected subjects. In conclusion, we demonstrate that GREB1L is a key player in early inner ear and eighth cranial nerve development. Abnormalities in cochleovestibular anatomy can provide challenges for cochlear implantation. Combining a molecular diagnosis with imaging techniques might aid the development of individually tailored therapeutic interventions in the future.

Notes

Acknowledgements

The authors thank the families for participating in this study. This study was supported by private donations to TGen’s Center for Rare Childhood Disorders (https://www.tgen.org/giving/tgen-foundation/), the American Hearing Research Foundation to I.S. (http://american-hearing.org/), National Institutes of Health R01 010856 (https://www.nih.gov/) and the Mills Auditory Foundation (http://millsauditoryfoundation.org/) to R.A.F. We would like to acknowledge Brunskill et al., Lu et al., Liu et al., and Scheffer et al. for the creation and public deposition of their RNA expression data that was used in this study.

Compliance with ethical standards

Ethical approval

Institutional review board (IRB) approval for human research was obtained, and the principles outlined in the Declaration of Helsinki were followed.

Informed consent

Informed consent was obtained from the participants involved (University of Southern California (USC) IRB #HS-14-00513-CR002 and Western (IRB) #20120512). The Institutional Animal Care and Use Committee of the USC approved the animal experiments performed in this study (no. 10885).

Conflict of interest

The authors declare that they have no conflict of interest.

Web resources

Bravo TOPMed variant browser, https://bravo.sph.umich.edu/. Burrows-Wheeler Aligner, http://bio-bwa.sourceforge.net/. CDC, hearing loss in children, http://cdc.gov/ncbddd/hearingloss/data.html/. Clinvar, https://www.ncbi.nlm.nih.gov/clinvar/. Combined Annotation Dependent Depletion (CADD), http://cadd.gs.washington.edu/. dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP/. dbSNP, https://www.ncbi.nlm.nih.gov/projects/SNP/. Database of Genomic Variants (DGV), http://dgv.tcag.ca/dgv/app/home/. DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources (DECIPHER), https://decipher.sanger.ac.uk/. Exome Aggregation Consortium (ExAC), http://exac.broadinstitute.org/. Genome Aggregation Database (gnomAD), http://gnomad.broadinstitute.org/. Genome Analysis Toolkit (GATK), https://software.broadinstitute.org/gatk/. Genome Browser, https://genome.ucsc.edu/. Online Mendelian Inheritance of Man (OMIM), https://www.omim.org/. Picard, http://broadinstitute.github.io/picard/.

Supplementary material

439_2018_1898_MOESM1_ESM.docx (15 kb)
Genetic variations have been deposited in ClinVar Accession numbers #SCV000611707 and #SCV000611708). (DOCX 14 KB)
439_2018_1898_MOESM2_ESM.docx (15 kb)
Supplementary material 2 (DOCX 14 KB)
439_2018_1898_MOESM3_ESM.xlsx (65 kb)
Supplementary material 3 (XLSX 64 KB)
439_2018_1898_MOESM4_ESM.docx (18.8 mb)
Supplementary material 4 (DOCX 19207 KB)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Isabelle Schrauwen
    • 1
    • 2
  • Elina Kari
    • 3
  • Jacob Mattox
    • 4
  • Lorida Llaci
    • 2
  • Joanna Smeeton
    • 5
  • Marcus Naymik
    • 2
  • David W. Raible
    • 6
  • James A. Knowles
    • 7
  • J. Gage Crump
    • 5
  • Matthew J. Huentelman
    • 2
  • Rick A. Friedman
    • 3
  1. 1.Molecular and Human Genetics Department, Center for Statistical GeneticsBaylor College of MedicineHoustonUSA
  2. 2.Neurogenomics Division and Center for Rare Childhood DisordersTranslational Genomics Research InstitutePhoenixUSA
  3. 3.Division of Otolaryngology, Head and Neck Surgery, Department of SurgeryUniversity of California, San DiegoLa JollaUSA
  4. 4.Tina and Rick Caruso Department of Otolaryngology-Head and Neck SurgeryKeck University of Southern California School of MedicineLos AngelesUSA
  5. 5.Department of Stem Cell Biology and Regenerative MedicineUniversity of Southern California Keck School of MedicineLos AngelesUSA
  6. 6.Department of Biological StructureUniversity of WashingtonSeattleUSA
  7. 7.Department of Cell Biology-MSC 5SUNY Downstate Medical CenterBrooklynUSA

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