EPS8L2 is a new causal gene for childhood onset autosomal recessive progressive hearing loss
© Dahmani et al. 2015
Received: 28 April 2015
Accepted: 3 August 2015
Published: 19 August 2015
More than 70 % of the cases of congenital deafness are of genetic origin, of which approximately 80 % are non-syndromic and show autosomal recessive transmission (DFNB forms). To date, 60 DFNB genes have been identified, most of which cause congenital, severe to profound deafness, whereas a few cause delayed progressive deafness in childhood. We report the study of two Algerian siblings born to consanguineous parents, and affected by progressive hearing loss.
After exclusion of GJB2 (the gene most frequently involved in non-syndromic deafness in Mediterranean countries), we performed whole-exome sequencing in one sibling.
A frame-shift variant (c.1014delC; p.Ser339Alafs*15) was identified in EPS8L2, encoding Epidermal growth factor receptor Pathway Substrate 8 L2, a protein of hair cells’ stereocilia previously implicated in progressive deafness in the mouse. This variant predicts a truncated, inactive protein, or no protein at all owing to nonsense-mediated mRNA decay. It was detected at the homozygous state in the two clinically affected siblings, and at the heterozygous state in the unaffected parents and one unaffected sibling, whereas it was never found in a control population of 150 Algerians with normal hearing or in the Exome Variant Server database.
Whole-exome sequencing allowed us to identify a new gene responsible for childhood progressive hearing loss transmitted on the autosomal recessive mode.
Deafness is the most common sensory deficit in humans, with an incidence of 1 in 700 live births. It is estimated that about two thirds of prelingual severe to profound isolated (non-syndromic) deafness cases have a genetic cause in developed countries , and autosomal recessive inheritance (DFNB) accounts for 80 % of the genetic cases . Cases with autosomal recessive non-syndromic hearing loss (ARNSHL) are more prevalent in populations where consanguineous marriages are common, including Maghrebi populations. To date, 60 DFNB genes have been identified (http://hereditaryhearingloss.org/). Recessive deafness is usually prelingual, severe or profound, and fully penetrant, but some DFNB genes cause progressive hearing loss with delayed onset in childhood [3, 4].
In Algeria, mutations in GJB2, encoding connexin 26 (Gap Junction Protein Beta 2), account for no less than 35 % of the cases [5–7]. Mutations in other DFNB genes have also been identified, which illustrates the ARNSHL genetic heterogeneity in this population . However, the genetic bases of progressive deafness beginning in childhood have not been characterized yet. Here, we report the identification, by whole-exome sequencing (WES), of a new causal gene for recessively inherited progressive deafness in an Algerian family.
Patients and methods
The two affected siblings were recruited in deafness schools of Blida and Baraki in Algiers (Algeria), and clinically examined in the otorhinolaryngology department at Bab El Oued hospital in Algiers. Medical history and physical examination of the patients did not reveal any non-genetic cause for the deafness and confirmed its non-syndromic nature. Hearing thresholds were determined by pure tone audiometry between 125 Hz and 8000 Hz, using air-conduction and bone conduction of sound.
The study was approved by the local Ethics Committee and the Committee for the Protection of Individuals in Biochemical Research as required by French legislation. A written consent for genetic testing was obtained from every family member. DNA was extracted from peripheral blood lymphocytes using the Promega Wizard Genomic DNA Purification Kit (Promega, Madison, MI, USA, Cat. # A1120). Whole-exome sequencing and bioinformatic analysis were carried out as previously described . To validate the mutation in EPS8L2, sequencing of exon 12 was performed by the Sanger technique with the following primers: EPS8L2-12 F 5′-GTCTGTGCTGAGGGGAGG-3′ and EPS8L2-12R 5′-CTCTCCAGAACTGGCCCAC-3′ (http://bioinfo.ut.ee/primer3-0.4.0/primer3/).
Results and discussion
Analysis of Indel and SNP files showing the variants found in the homozygous state in patient IV.2
Type of variant
c.643G > A; p.Asp215Asn
c.1848A > G; p.Lys616Lys
c.2138C > T; p.Ala713Val
c.631C > G; p.Leu211Val
c.481G > A; p.Asp161Asn
EPS8L2 has 24 exons and codes for a 715 amino acid protein (Fig. 1d), which is a member of the actin-binding protein EPS8 (epidermal growth factor receptor pathway substrate 8) family. This family includes four members, EPS8 and the three EPS8-like proteins (EPS8L1, EPS8L2, and EPS8L3), with partially overlapping functions . In the mouse ear, EPS8L2 was detected at the stereocilia tips of both cochlear and vestibular hair cells. Eps8L2 knockout mice undergo progressive hearing loss, as the result of the progressive disorganization of the hair bundles of both inner and outer hair cells. Scanning electron microscopy analysis of the hair bundles in the cochlea of these mice showed that stereocilia of the tall row are shorter and fewer than those of wild-type mice, whereas both the middle and small stereocilia rows seem to be preserved and unaffected . By contrast, mutations in the EPS8 gene cause profound congenital deafness in mice and humans [34, 35]. In the mouse cochlea, Eps8 is essential for the initial elongation of stereocilia [34, 36], whereas Eps8L2 is required for their maintenance in mature hair cells .
Deafness is a highly heterogeneous disorder, and many causative genes still remain to be identified. Here, despite several limitations (e.g. only a single family possibly analysed, uneven exon coverage at certain loci by WES), we were able to identify a new pathogenic variant responsible for ARNSHL in two Algerian siblings, by combining the powers of WES and genetics. This report is the first to incriminate EPS8L2, a gene formerly known to cause deafness in rodents, as a causal gene for progressive hearing loss in humans.
We thank all the family members for their participation in the study. This work was supported by grants from the Algerian government, the BNP Paribas Foundation, the French LABEX LIFESENSES grant [reference ANR-10-LABX-65], and the Pasteur-Weizmann program.
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