SLC26A4 pathogenic variants as a third cause of hearing loss: Role of three exons in DFNB4 deafness in Iran

Elham Davoudi-Dehaghani; Nejat Mahdieh; Atefeh Shirkavand; Hamideh Bagherian; Samira DabbaghBagheri; Sirous Zeinali

doi:10.4103/indianjotol.INDIANJOTOL_36_19

ORIGINAL ARTICLE

Year : 2019 | Volume : 25 | Issue : 3 | Page : 146-150

SLC26A4 pathogenic variants as a third cause of hearing loss: Role of three exons in DFNB4 deafness in Iran

Elham Davoudi-Dehaghani¹, Nejat Mahdieh², Atefeh Shirkavand³, Hamideh Bagherian⁴, Samira DabbaghBagheri⁴, Sirous Zeinali⁵
¹ Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
² Rajaie Cardiovascular Medical and Research Center, Genetic Research Laboratory, Iran University of Medical Sciences, Tehran, Iran
³ Division of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
⁴ Kawsar Human Genetics Research Center, Tehran, Iran
⁵ Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran; Kawsar Human Genetics Research Center, Tehran, Iran

Date of Submission	23-Mar-2019
Date of Acceptance	24-Jun-2019
Date of Web Publication	18-Oct-2019

Correspondence Address:
Prof. Sirous Zeinali
Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur St., Tehran; Kawsar Human Genetics Research Center, Medical Genetics Laboratory, No. 41, Majlesi St., ValiAsr St., Tehran
Iran

Source of Support: None, Conflict of Interest: None

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DOI: 10.4103/indianjotol.INDIANJOTOL_36_19

Abstract

Context: Pathogenic variants in SLC26A4 gene are the third-most frequent cause of autosomal recessive hearing loss in different populations. Aims: This article reports results of homozygosity mapping and SLC26A4 variant analysis in Iran. Settings and Design: A case series study was performed on forty GJB2-negative Iranian deaf families. Subjects and Methods: Homozygosity mapping, using microsatellite markers flanking the SLC26A4 gene, was performed on GJB2-negative Iranian deaf families. The SLC26A4 variant analysis was done by Sanger sequencing. A literature review was performed to identify all reported SLC26A4 pathogenic variants in Iran. Results: In one of the families, the hearing loss showed co-segregation with the DFNB4 STR markers. A previously reported SLC26A4 pathogenic variant was identified in homozygous state in all the affected members of this family. The literature review showed that variant screening of only three SLC26A4 exons and their boundary regions can detect variants responsible for deafness in about half of all DFNB4 Iranian deaf cases. Conclusions: The results of this study emphasize the important role of SLC26A4 pathogenic variants in the development of deafness in Iran. More information on the frequency of pathogenic variants can help in choosing faster and cost-effective methods for genetic testing.

Keywords: Deafness, DFNB4, hearing loss, Iran, SLC26A4 gene, variant

How to cite this article:
Davoudi-Dehaghani E, Mahdieh N, Shirkavand A, Bagherian H, DabbaghBagheri S, Zeinali S. SLC26A4 pathogenic variants as a third cause of hearing loss: Role of three exons in DFNB4 deafness in Iran. Indian J Otol 2019;25:146-50

How to cite this URL:
Davoudi-Dehaghani E, Mahdieh N, Shirkavand A, Bagherian H, DabbaghBagheri S, Zeinali S. SLC26A4 pathogenic variants as a third cause of hearing loss: Role of three exons in DFNB4 deafness in Iran. Indian J Otol [serial online] 2019 [cited 2023 Mar 21];25:146-50. Available from: https://www.indianjotol.org/text.asp?2019/25/3/146/269553

Introduction

Hearing loss is a common health problem that can be caused by changes in genes, environmental factors, or a combination of them.^{[1],[2],[3],[4],[5]} Previous studies on GJB2-negative cases have shown that pathogenic variants in the SLC26A4 gene are the second cause of autosomal recessive hearing loss after STRC pathogenic variants.^[2],[5] Various changes in the SLC26A4 gene can cause syndromic or nonsyndromic hearing loss.^{[6],[7],[8],[9],[10]}

Iran is a country in the Middle East with a high prevalence of consanguineous marriages. The prevalence of deafness in this country has been reported to be about 1 in 213 newborns.^{[11],[12],[13],[14]} So far, several studies have been performed on the genetic causes of deafness in Iran, but it seems that there is still a long way ahead of achieving a clear genetic structure in this population.^[15],[16]

This article presents the results of homozygosity mapping and SLC26A4 pathogenic variant study in Iran. The spectrum of reported pathogenic variants in the SLC26A4 in Iran is also represented here.

Subjects and Methods

Subjects

A total of forty GJB2-negative Iranian deaf families with at least two affected members were selected for homozygosity mapping. All the affected members were the result of consanguineous marriage, suggesting an autosomal recessive inheritance pattern. A bilateral severe-to-profound sensorineural nonsyndromic hearing loss was determined by pure-tone audiometry in all the affected members. A questionnaire and an informed consent form were completed and signed by adult participants or parents of the investigated children.

Methods

Genomic DNA was extracted from the peripheral blood of all members of the investigated families using salting-out method.^[17] STR marker flanking DFNB4 locus was used for homozygosity mapping in the forty families [Table 1]. For variant screening, all the SLC26A4 exons and exon–intron boundaries were analyzed using Sanger sequencing. Sequences of primers are not shown but are available upon request.

Table 1: The heterozygosity and position of selected markers for the DFNB4 locus

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Results

The hearing loss showed co-segregation with the DFNB4 STR markers in one family (Irn-Deaf-18002) [Figure 1]. A variant, NM_000441: c.1226G>A (p. Arg409His), was identified by Sanger sequencing in the homozygous state in the affected members of this family. Parents and other members of this family were then screened for this variant. This variant was identified in a heterozygous state in parents of the deaf children but was not identified in a homozygous state in healthy members of this family.

Figure 1: The pedigree of the Irn-Deaf-18002 family. Affected members are shown in black

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A review of studies on SLC26A4 pathogenic variants in Iran showed that a total of 41 different SLC26A4 pathogenic variants have been reported in 76 Iranian families with DFNB4 deafness. A list of these variants and their frequencies are shown in [Table 2]. This study showed that c.1334T>G (p. Leu445Trp), c.1001G>T (p. Gly334Val), c.1198delT (p. Cys400Valfs), and c.1226G>A (p. Arg409His) are the most common pathogenic variants in the SLC26A4 gene in Iran [Figure 2]a. About half (51.13%) of the DFNB4 deafness-causing variants are located in exons 8, 10, and 11 and their boundary regions [Figure 2]b.

Table 2: The spectrum of the SLC26A4 pathogenic variants identified in Iran

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Figure 2: Pie charts representing the scattering of pathogenic variants in SLC26A4 in Iran. (a) Percentage of the most common DFNB4 deafness-causing variants in Iran. (b) Percentage of the reported pathogenic variants in different exons of the SLC26A4

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Discussion

The cause of hearing loss in family Irn-Deaf-18002 was detected by homozygosity mapping and Sanger sequencing of the SLC26A4 gene. So far, several linkage studies have been performed to identify the genetic causes of hearing loss in Iran.^{[15],[18],[19],[20],[21]} Kahrizi et al. in 2009 reported biallelic SLC26A4 pathogenic variants in 8 of 80 (10%) GJB2-negative Iranian deaf families using homozygosity mapping and Sanger sequencing.^[18] In another study in Iran (Yazdanpanahi et al., 2015), a total of 121 GJB2-negative deaf cases have been analyzed by linkage study and/or Sanger sequencing of the SLC26A4 gene, which resulted in the identification of DFNB4 deafness in about 9% of the investigated cases.^[21] In a recent report, a linkage to the DFNB4 locus has been shown in two out of forty (5%) Iranian pedigrees with nonsyndromic GJB2-negative hearing loss.^[22] Homozygosity mapping followed by Sanger sequencing of the candidate gene in linked families makes it possible to examine a number of deaf families at a lower cost than exon-by-exon Sanger sequencing of the investigated gene.

In two recent studies (Sloan-Heggen et al., 2015, and Cengiz et al., 2017) on 302 and 61 GJB2-negative Iranian deaf families by using the targeted genomic enrichment and massively parallel sequencing, respectively, the SLC26A4-related deafness has been identified in about 12%–15% of the investigated families.^[23],[24] A higher rate of DFNB4 deafness detected in Next-generation sequencing (NGS)-based studies can be explained by the ability of this method to identify compound heterozygous cases.

Both syndromic and nonsyndromic forms of hearing loss have been included in the mentioned studies above except the one by Azadegan-Dehkordi et al.^{[18],[21],[22],[23],[24]} In our study, suspected cases of syndromic forms have not been included, which can describe a lower detection rate in our study compared to the studies that have examined the both forms of this disease. It seems that studies with larger sample sizes can determine the contribution of SLC26A4 pathogenic variants in deafness in Iran.

The variant c.1226G>A (p. Arg409His) identified in the homozygous state in the family Irn-Deaf-18002 has been previously reported in different studies in Iran and other countries.^{[18],[23],[24],[25],[26],[27]}

Our review study showed a genetic heterogeneity among DFNB4 cases in Iran. Although the variants are scattered throughout the SLC26A4 gene, about half (51.13%) of them are located in exons 8, 10, and 11 and their boundary regions.^{[15],[18],[19],[21],[22],[23],[28]} This can be considered in a step-wise, targeted screening of the SLC26A4 gene in cases suspected to have the SLC26A4-related deafness.

In a recent comprehensive study of 1119 deaf people using NGS technology from different populations (Sloan-Heggen et al., 2016), a total of sixty cases with SLC26A4-related deafness have been identified. The spectrum of variants identified in this study differs from that found in the Iranian population [Table 2]. Of the three common mutations in Iran, only one of them has been reported in the Sloan-Heggen et al.'s study. It seems that the spectrum of variants and their frequency are specific to each population.^[2]

Conclusion

This article presents a new case of DFNB4 deafness as well as reviews the literature on SLC26A4 variant study in Iran. More studies are needed to assess the role of SLC26A4 variants in hearing loss in this country. It is clear that more information about variants and their frequencies in a population can help develop a better strategy for the SLC26A4 gene screening in cases suspected to have DFNB4 deafness.

Financial support and sponsorship

Nil.

Conflicts of interest

There are no conflicts of interest.

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