Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2020 Aug 3;130(8):4213-4217.
doi: 10.1172/JCI136951.

Long-range cis-regulatory elements controlling GDF6 expression are essential for ear development

Guney Bademci  1 , Clemer Abad  1 , Filiz B Cengiz  1 , Serhat Seyhan  1 , Armagan Incesulu  2 , Shengru Guo  1 , Suat Fitoz  3 , Emine Ikbal Atli  4 , Nicholas C Gosstola  1 , Selma Demir  4 , Brett M Colbert  1   5 , Gozde Cosar Seyhan  6 , Claire J Sineni  1 , Duygu Duman  7 , Hakan Gurkan  4 , Cynthia C Morton  8   9   10   11   12 , Derek M Dykxhoorn  1   13 , Katherina Walz  1   13 , Mustafa Tekin  1   13   14
Affiliations

Long-range cis-regulatory elements controlling GDF6 expression are essential for ear development

Guney Bademci et al. J Clin Invest. .

Abstract

Molecular mechanisms governing the development of the mammalian cochlea, the hearing organ, remain largely unknown. Through genome sequencing in 3 subjects from 2 families with nonsyndromic cochlear aplasia, we identified homozygous 221-kb and 338-kb deletions in a noncoding region on chromosome 8 with an approximately 200-kb overlapping section. Genomic location of the overlapping deleted region started from approximately 350 kb downstream of GDF6, which codes for growth and differentiation factor 6. Otic lineage cells differentiated from induced pluripotent stem cells derived from an affected individual showed reduced expression of GDF6 compared with control cells. Knockout of Gdf6 in a mouse model resulted in cochlear aplasia, closely resembling the human phenotype. We conclude that GDF6 plays a necessary role in early cochlear development controlled by cis-regulatory elements located within an approximately 500-kb region of the genome in humans and that its disruption leads to deafness due to cochlear aplasia.

Keywords: Genetic diseases; Genetics; Organogenesis; Otology.

PubMed Disclaimer

Conflict of interest statement

Conflict of interest: The authors have declared that no conflict of interest exists.

Figures

Figure 1
Figure 1. Clinical features and variant information.
(A and B) Pedigrees of the studied families with segregation of detected deletions. –/–, homozygous deletion; +/–, heterozygous deletion; +/+, homozygous WT; M: 1-kb ladder; amplicons of deletion-specific primers are 425 bp and 269 bp in families 1 and 2, respectively; amplicons of WT-specific primers are 307 bp and 592 bp in families 1 and 2, respectively. (C) Heavily T2-weighted MRI of temporal bone, axial maximum intensity projection, and volume-rendered images when the proband of family 1 was 9 years old, showing complete absence of the cochlea. Vestibule and semicircular canals (blue arrows) are of normal shape and caliper. Control: MRI of a normal 9-year-old male reveals normal cochleas (red arrows) and semicircular canals.
Figure 2
Figure 2. Deleted genomic region, mRNA expression, and mouse studies.
(A) TAD on chromosome 8 including detected deletions (3D Genome Browser; http://promoter.bx.psu.edu/hi-c/chic.php). Boundaries of the TAD are shown with a blue bar under a triangle marked with dotted lines. The overlapping deletion is 207,127 bp shown with vertical dotted lines. This region contains multiple highly activated transcription sites, as demonstrated by the presence of the active enhancer mark H3K27Ac and DNAse I–hypersensitive sites (DHSs); the deleted region also includes multiple highly conserved DNA sequences, as shown by PhyloP (phylogenetic P value) scores. ENCODE, Encyclopedia of DNA Elements. (B) GDF6 mRNA levels during differentiation from iPSCs. Data are represented as mean ± SEM (n = 4 cases; n = 4 controls). *For day 11, mRNA levels and AUC between patient-derived and control cells were significantly different (P = 0.029). Mann-Whitney U test with independent variables was used for comparisons. FPKM, fragments per kilobase of transcript per million mapped reads. (C–E) Cochlear aplasia in Gdf6-mutant mice. (C) Paint fill of P0 mouse inner ear for WT and KO mice. The red arrow indicates normal cochlear morphology, and blue arrows show semicircular canals. (D and E) Bright-field photographs of the whole dissected inner ear on P0 from different angles. Note that the Gdf6 mutant lacks the entire cochlea. Scale bars: 500 μm.
See this image and copyright information in PMC

References

    1. Wu DK, Kelley MW. Molecular mechanisms of inner ear development. Cold Spring Harb Perspect Biol. 2012;4(8):a008409. - PMC - PubMed
    1. Diaz-Horta O, et al. ROR1 is essential for proper innervation of auditory hair cells and hearing in humans and mice. Proc Natl Acad Sci U S A. 2016;113(21):5993–5998. doi: 10.1073/pnas.1522512113. - DOI - PMC - PubMed
    1. Whitfield TT. Development of the inner ear. Curr Opin Genet Dev. 2015;32:112–118. doi: 10.1016/j.gde.2015.02.006. - DOI - PubMed
    1. Morton CC, Nance WE. Newborn hearing screening — a silent revolution. N Engl J Med. 2006;354(20):2151–2164. doi: 10.1056/NEJMra050700. - DOI - PubMed
    1. Mafong DD, Shin EJ, Lalwani AK. Use of laboratory evaluation and radiologic imaging in the diagnostic evaluation of children with sensorineural hearing loss. Laryngoscope. 2002;112(1):1–7. doi: 10.1097/00005537-200201000-00001. - DOI - PubMed

Publication types

Substances