De novo variants in GREB1L are associated with non-syndromic inner ear malformations and deafness
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.
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
Institutional review board (IRB) approval for human research was obtained, and the principles outlined in the Declaration of Helsinki were followed.
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.
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/.
- Aldrich J, Keats JJ, Liang WS et al (2016) Abstract 45: detection of focal somatic copy number variants in whole genome, whole exome, and targeted next-generation sequencing data of tumor/normal pairs. Clin Cancer Res 22:45–45. https://doi.org/10.1158/1557-3265.PMSCLINGEN15-45 CrossRefGoogle Scholar
- Kari E, Go JL, Loggins J et al (2018) Abnormal cochleovestibular nerves and pediatric hearing outcomes: patients with “absent cochlear nerves” can derive benefit from cochlear implantation. Otol Neurotol (in press) Google Scholar
- Marques AH, O’Connor TG, Roth C et al (2013) The influence of maternal prenatal and early childhood nutrition and maternal prenatal stress on offspring immune system development and neurodevelopmental disorders. Front Neurosci 7:120. https://doi.org/10.3389/fnins.2013.00120 CrossRefPubMedPubMedCentralGoogle Scholar
- Pryor SP (2005) SLC26A4/PDS genotype–phenotype correlation in hearing loss with enlargement of the vestibular aqueduct (EVA): evidence that Pendred syndrome and non-syndromic EVA are distinct clinical and genetic entities. J Med Genet 42:159–165. https://doi.org/10.1136/jmg.2004.024208 CrossRefPubMedPubMedCentralGoogle Scholar
- Westerfield M (1993) The zebrafish book: a guide for the laboratory use of zebrafish, 2nd edn. University of Oregon Press, EugeneGoogle Scholar