Research Article: OTOF mutation analysis with massively parallel DNA sequencing in 2,265 Japanese sensorineural hearing loss patients

Date Published: May 16, 2019

Publisher: Public Library of Science

Author(s): Yoh-ichiro Iwasa, Shin-ya Nishio, Akiko Sugaya, Yuko Kataoka, Yukihiko Kanda, Mirei Taniguchi, Kyoko Nagai, Yasushi Naito, Tetsuo Ikezono, Rie Horie, Yuika Sakurai, Rina Matsuoka, Hidehiko Takeda, Satoko Abe, Chiharu Kihara, Takashi Ishino, Shin-ya Morita, Satoshi Iwasaki, Masahiro Takahashi, Tsukasa Ito, Yasuhiro Arai, Shin-ichi Usami, Tao Cai.

http://doi.org/10.1371/journal.pone.0215932

Abstract

The OTOF gene (Locus: DFNB9), encoding otoferlin, is reported to be one of the major causes of non-syndromic recessive sensorineural hearing loss, and is also reported to be the most common cause of non-syndromic recessive auditory neuropathy spectrum disorder (ANSD). In the present study, we performed OTOF mutation analysis using massively parallel DNA sequencing (MPS). The purpose of this study was to reveal the frequency and precise genetic and clinical background of OTOF-related hearing loss in a large hearing loss population. A total of 2,265 Japanese sensorineural hearing loss (SNHL) patients compatible with autosomal recessive inheritance (including sporadic cases) from 53 otorhinolaryngology departments nationwide participated in this study. The mutation analysis of 68 genes, including the OTOF gene, reported to cause non-syndromic hearing loss was performed using MPS. Thirty-nine out of the 2,265 patients (1.72%) carried homozygous or compound heterozygous mutations in the OTOF gene. It is assumed that the frequency of hearing loss associated with OTOF mutations is about 1.72% of autosomal recessive or sporadic SNHL cases. Hearing level information was available for 32 of 39 patients with biallelic OTOF mutations; 24 of them (75.0%) showed profound hearing loss, 7 (21.9%) showed severe hearing loss and 1 (3.1%) showed mild hearing loss. The hearing level of patients with biallelic OTOF mutations in this study was mostly severe to profound, which is consistent with the results of past reports. Eleven of the 39 patients with biallelic OTOF mutations had been diagnosed with ANSD. The genetic diagnosis of OTOF mutations has significant benefits in terms of clinical decision-making. Patients with OTOF mutations would be good candidates for cochlear implantation; therefore, the detection of OTOF mutations is quite beneficial for patients, especially for those with ANSD.

Partial Text

Hearing loss is one of the most frequent congenital sensory disorders, with one out of every 500 newborns having bilateral hearing loss[1]. It is reported that 50–60% of these cases show a genetic etiology, with 80% of them demonstrating autosomal recessive hearing loss[2]. The OTOF gene (Locus: DFNB9), encoding otoferlin, is reported to be one of the frequent causes of non-syndromic recessive sensorineural hearing loss. To date, more than 160 mutations in OTOF have been reported, and most of the patients with OTOF mutations have stable, prelingual and severe to profound hearing loss. OTOF is also known to be the most common cause of non-syndromic recessive auditory neuropathy spectrum disorder (ANSD)[3–5]. ANSD is a unique form of hearing loss characterized by the absence of or severe abnormalities in auditory brainstem response (ABR) and the presence of otoacoustic emissions (OAE). OTOF is mainly expressed in cochlear inner hair cells, and is necessary for synaptic exocytosis at the ribbon synapse[6]. While the function of the inner hair cells is impaired, that of the outer hair cells is preserved for the first one or two years; therefore, hearing loss due to OTOF gene mutation can also present as ANSD.

Hearing level of the participating 2,265 patients was diagnosed as follows: mild hearing loss, 215 patients; moderate hearing loss, 679 patients; severe hearing loss, 524 patients; profound hearing loss, 599 patients; and unknown, 248 patients. The mutations found in this study were categorized into pathogenic, likely pathogenic, benign, likely benign and variant of uncertain significance according to the ACMG (American College of Medical Genetics) standards and guidelines[16]. The mutations judged to be pathogenic variants and likely pathogenic variants are presented in Table 1. Ten mutations including 6 previously reported variants and 4 novel variants (p.R425X, p.Y474X, p.W717X, p.L1003fs, p.Y1064X, p.Q1072X, p.I1449fs, p.R1856Q, p.R1172Q, c.4960+2T>C) were categorized as pathogenic variants. Five mutations (p.P489S, p.H513R, p.R1583H, p.R1792C, p.R1792H) were categorized as likely pathogenic variants. The 5 likely pathogenic variants were thought to be likely pathogenic because 1) they were found with previously reported pathogenic variants in trans (in different alleles of the gene): PM3 (p.R1856Q or p.R1172Q), 2) they were not found in the control: PM2, 3) the prediction programs scores support their pathogenicity: PP3 and 4) co-segregation with family members with disease: PP1. The mutations judged to be likely benign and variants of uncertain significance are presented in S2 Table. Ten mutations (p.G36A, p.G123S, p.I622V, p.E643K, p.R652Q, p.R654Q, p.R818W, p.V1012A, p.R1249W, c.4023+1G>A) were categorized as likely benign variants because 1) the allele frequency was greater than expected for the disorder (p.R818W): BS1, 2) the prediction programs scores did not support their pathogenicity (p.G36A, p.G123S, p.I622V, p.E643K, p.R652Q, p.R654Q, p.R1249W): BP4, 3) the variant was found in a case with an alternate molecular basis for disease (p.R652Q is found with homozygote CDH23 mutations; p.V1012A is found with compound heterozygote GJB2 mutations; c.4023+1G>A is found with compound heterozygote SLC26A4 mutations or mitochondrial 3243A>G mutations): BP5 and 4) a reputable source (deafness variation database[17]) reports these mutations as benign or likely benign variants (p.G36A, p.G123S, p.I622V, p.E643K, p.R652Q, p.R654Q, p.R818W, p.V1012A, p.R1249W, c.4023+1G>A): BP6.

In this study, 39 (1.72%) of 2,265 SNHL patients compatible with autosomal recessive (including sporadic cases) inheritance carried homozygous or compound heterozygous mutations in the OTOF gene. Two patients with heterozygous mutations (p.Y474X and p.R1172Q) showed an ANSD phenotype, and it is strongly suspected that they had OTOF related deafness. Possible explanations for these heterozygous cases are 1) the co-existence of copy number variations, 2) the existence of a second mutation in the exonic region that could not be covered in this study or in regulatory region of OTOF, which was not explored, 3) the contribution to hearing loss of an additional modulatory gene, and 4) the existence of a mutation in another gene (DIAPH3, AIFM1, ATP1A3 and mitochondrial 12SrRNA) which causes non-syndromic ANSD not examined in this study [18], so that the patients were just coincidental carriers of the OTOF mutations.

 

Source:

http://doi.org/10.1371/journal.pone.0215932

 

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