The role and spectrum of SLC26A4 mutations in Iranian patients with autosomal recessive hereditary deafness

Insight into the Natural History of Pathogenic Variant c.919-2A>G in the SLC26A4 Gene Involved in Hearing Loss: The Evidence for Its Common Origin in Southern Siberia (Russia)

Pathogenic variants in the SLC26A4 gene leading to nonsyndromic recessive deafness (DFNB4), or Pendred syndrome, are some of the most common causes of hearing loss worldwide. Earlier, we found a high proportion of SLC26A4-related hearing loss with prevailing pathogenic variant c.919-2A>G (69.3% among all mutated SLC26A4 alleles that have been identified) in Tuvinian patients belonging to the indigenous Turkic-speaking Siberian people living in the Tyva Republic (Southern Siberia, Russia), which implies a founder effect in the accumulation of c.919-2A>G in Tuvinians. To evaluate a possible common origin of c.919-2A>G, we genotyped polymorphic STR and SNP markers, intragenic and flanking SLC26A4, in patients homozygous for c.919-2A>G and in healthy controls. The common STR and SNP haplotypes carrying c.919-2A>G were revealed, which convincingly indicates the origin of c.919-2A>G from a single ancestor, supporting a crucial role of the founder effect in the c.919-2A>G prevalence in Tuvinians. Comparison analysis with previously published data revealed the identity of the small SNP haplotype (~4.5 kb) in Tuvinian and Han Chinese carriers of c.919-2A>G, which suggests their common origin from founder chromosomes. We assume that c.919-2A>G could have originated in the geographically close territories of China or Tuva and subsequently spread to other regions of Asia. In addition, the time intervals of the c.919-2A>G occurrence in Tuvinians were roughly estimated.

SLC26A4 Phenotypic Variability Influences Intra- and Inter-Familial Diagnosis and Management

SLC26A4 is one of the most common genes causing autosomal recessive non-syndromic sensorineural hearing loss (SNHL). It has been reported to cause Pendred Syndrome (PDS) and DFNB4 which is deafness with enlarged vestibular aqueduct (EVA). However, mutated SLC26A4 is not conclusive for having either DFNB4 or PDS. Three unrelated Jordanian families consisting of eight affected individuals with congenital bilateral hearing loss (HL) participated in this study. Whole-exome and Sanger sequencing were performed to investigate the underlying molecular etiology of HL. Further clinical investigations, including laboratory blood workup for the thyroid gland, CT scan for the temporal bone, and thyroid ultrasound were performed. Three disease-causing variants were identified in SLC26A4 in the three families, two of which were novel. Two families had a novel pathogenic homozygous splice-site accepter variant (c.165-1G>C), while the third family had compound heterozygous pathogenic variants (c.1446G>A; p.Trp482* and c.304G>A; p.Gly102Arg). Our approach helped in redirecting the diagnosis of several affected members of three different families from non-syndromic HL to syndromic HL. Two of the affected individuals had typical PDS, one had DFNB4, while the rest had atypical PDS. Our work emphasized the intra- and inter-familial variability of SLC26A4-related phenotypes. In addition, we highlighted the variable phenotypic impact of SLC26A4 on tailoring a personalized healthcare management.

Molecular diagnosis of SLC26A4-related hereditary hearing loss in a group of patients from two provinces of Iran

The SLC26A4 gene has been described as the second gene involved in most cases of autosomal recessive non-syndromic hearing loss (ARNSHL), after GJB2. Over 500 different SLC26A4 mutations have been reported, with each ethnic population having its own distinctive mutations. Here, we aimed to determine the frequency and mutation profile of the SLC26A4 gene from two different provinces (center and west) of Iran. This study included 50 nuclear families with two or more siblings segregating presumed ARNSHL. All affected tested negative for mutations in GJB2 at the DFNB1 locus and were therefore screened for autozygosity by descent using short tandem repeat polymorphisms (STRPs) of DFNB4. Sanger sequencing was performed to screen the 20 exons of the SLC26A4 gene for the families linked to this locus. In silico analyses were also performed using available software tools. Four out of 25 (16%) and 3 of 25 (12%) studied families of Isfahan and Hamedan provinces, respectively. were linked to DFNB4. Sanger sequencing led to the identification of six different mutations, one of which (c.919-2A>G) was recurrent and accounted for 31% of all mutant alleles. One out of 7 (14.3%) families with mutations were confirmed to be Pendred syndrome (PS). The SLC26A4 mutations have a high carrying rate in ARNSHL Iranian patients. The identification of a disease causing mutation can be used to establish a genotypic diagnosis and provide important information to the patients and their families.

Improving the Management of Patients with Hearing Loss by the Implementation of an NGS Panel in Clinical Practice

A cohort of 128 patients from 118 families diagnosed with non-syndromic or syndromic hearing loss (HL) underwent an exhaustive clinical evaluation. Molecular analysis was performed using targeted next-generation sequencing (NGS) with a custom panel that included 59 genes associated with non-syndromic HL or syndromic HL. Variants were prioritized according to the minimum allele frequency and classified according to the American College of Medical Genetics and Genomics guidelines. Variant(s) responsible for the disease were detected in a 40% of families including autosomal recessive (AR), autosomal dominant (AD) and X-linked patterns of inheritance. We identified pathogenic or likely pathogenic variants in 26 different genes, 15 with AR inheritance pattern, 9 with AD and 2 that are X-linked. Fourteen of the found variants are novel. This study highlights the clinical utility of targeted NGS for sensorineural hearing loss. The optimal panel for HL must be designed according to the spectrum of the most represented genes in a given population and the laboratory capabilities considering the pressure on healthcare.

Investigation of DFNB4 SLC26A4 mutation in patients with enlarged vestibular aquaduct

OBJECTIVES

Mutations of the SLC26A4 gene causing enlarged vestibular aqueduct (EVA) syndrome have not yet been fully elucidated. The study aimed to investigate SLC26A4 mutations in patients with EVA syndrome in the Turkish population. Identifying these mutations may play an essential role in determining the prognosis, follow-up, and management options of these patients.

METHODS

Whole exome sequencing and/or Sanger sequencing of SLC26A4 in 22 patients with sensorineural hearing loss associated with isolated EVA without inner ear anomalies, and 22 controls were performed.

RESULTS

Twenty-two patients and 22 control subjects were included in the study. The onset of hearing loss was pre-lingual in 15 patients, and post-lingual in 7. The mean (standard deviation) vestibular aqueduct width of the patients was 3.23 mm (1.28). Twenty SLC26A4 variants, 15 of them unique, were identified in 22 patients. Among them, seven variants were heterozygous, and 13 were homozygous. The variants p.E37X (c.109G > T), p.Y27H (c.79T > C), p.C706Y (c.2117G > A) have not been previously reported.

CONCLUSION

The detection of rare and previously unreported mutations in our study showed that studies with a larger number of patients with EVA might reveal more role of the SLC26A4 gene. Besides, to understand the etiopathogenesis of the disease, other related genes also should be investigated.

Next generation sequencing and genetics of hereditary hearing loss in the iranian population: New insights from a systematic review

BACKGROUND

Hereditary hearing loss (HL) as a common disorder is genetically heterogeneous, which poses a challenge for clinical and molecular diagnosis. Next-generation sequencing (NGS) technologies have proven to be the best solution for mutational screening, even though it is not always conclusive. Here, we have reviewed the results of previously published data on HL mutations identified with NGS, as well as the efficiency of this technology in detecting HL in Iran.

METHODS

A systematic literature review of the PubMed, Google Scholar, Web of Science, and Science Direct databases were conducted for articles published before May 2019. The primary data of these studies, including the number of samples, mutation frequency and so on were extracted.

RESULTS

Seventy-five articles were reviewed, and 10 met our inclusion criteria. Totally 432 unrelated families were included and analyzed for the type and prevalence of the gene mutations and pathogenic variants were discovered in 34 non-syndromic HL (NSHL) genes. Altogether 237 different genetic mutations were detected. However, p. Gln1576Stop in PCDH15 was the most common mutation accounting for 1% of the populations studied. NGS platforms have yielded only a 47.1% molecular diagnosis rate for NSHL etiologies in the Iranian population, which is significantly lower than that identified in the other part of the Middle East.

CONCLUSION

The results showed that NGS platforms can greatly assist and enhance HL diagnosis and improve molecular diagnostic outcome. However, researchers were unable to provide 53% of their Iranian cohort with a molecular diagnosis for their HL. It seems that many rare genes are responsible for the majority of HL in the Iranian cohort. Future explorative investigations utilizing NGS technologies, such as WES, into the Iranian population are warranted.

Global genetic insight contributed by consanguineous Pakistani families segregating hearing loss

Consanguineous Pakistani pedigrees segregating deafness have contributed decisively to the discovery of 31 of the 68 genes associated with nonsyndromic autosomal recessive hearing loss (HL) worldwide. In this study, we utilized genome-wide genotyping, Sanger and exome sequencing to identify 163 DNA variants in 41 previously reported HL genes segregating in 321 Pakistani families. Of these, 70 (42.9%) variants identified in 29 genes are novel. As expected from genetic studies of disorders segregating in consanguineous families, the majority of affected individuals (94.4%) are homozygous for HL-associated variants, with the other variants being compound heterozygotes. The five most common HL genes in the Pakistani population are SLC26A4, MYO7A, GJB2, CIB2 and HGF, respectively. Our study provides a profile of the genetic etiology of HL in Pakistani families, which will allow for the development of more efficient genetic diagnostic tools, aid in accurate genetic counseling, and guide application of future gene-based therapies. These findings are also valuable in interpreting pathogenicity of variants that are potentially associated with HL in individuals of all ancestries. The Pakistani population, and its infrastructure for studying human genetics, will continue to be valuable to gene discovery for HL and other inherited disorders.

An update of common autosomal recessive non-syndromic hearing loss genes in Iranian population

Autosomal-recessive genes are responsible for about 80% of the hereditary non-syndromic hearing loss (NSHL) cases. In Iran, due to consanguineous marriages, NSHL is the second most frequent disability after intellectual disability, occurring one in 16 individuals. Enormous heterogeneity in the genetic pathology of hearing loss causes a major challenge in identification of responsible genes. In Iran, GJB2 is responsible for the most cases of pre-lingual and non-syndromic hearing loss (with frequency of 16.7%) which followed by other genes with lower frequency. Although several studies have indicated that a large proportion of both syndromic and non-syndromic hearing loss in Iranian populations are caused by defects in just a few genes, new detection strategies such as NGS (Next-generation sequencing) have increased the spectrum of responsible mutations. However, by applying this technique in Iran patients screening, the role of lots of novel related genes have been reported. In this review, we aim to describe function of these genes and their contribution to non-syndromic genetic hearing loss in Iranian population and we classify the genes by their functions.

Heterogeneity of Hereditary Hearing Loss in Iran: a Comprehensive Review

A significant contribution to the causes of hereditary hearing impairment comes from genetic factors. More than 120 genes and 160 loci have been identified to be involved in hearing impairment. Given that consanguine populations are more vulnerable to most inherited diseases, such as hereditary hearing loss (HHL), the genetic picture of HHL among the Iranian population, which consists of at least eight ethnic subgroups with a high rate of intermarriage, is expected to be highly heterogeneous. Using an electronic literature review through various databases such as PubMed, MEDLINE, and Scopus, we review the current picture of HHL in Iran. In this review, we present more than 39 deafness genes reported to cause non-syndromic HHL in Iran, of which the most prevalent causative genes include GJB2, SLC26A4, MYO15A, and MYO7A. In addition, we highlight some of the more common genetic causes of syndromic HHL in Iran. These results are of importance for further investigation and elucidation of the molecular basis of HHL in Iran and also for developing a national diagnostic tool tailored to the Iranian context enabling early and efficient diagnosis of hereditary hearing impairment.

Genetic Effects on Sensorineural Hearing Loss and Evidence-based Treatment for Sensorineural Hearing Loss

In this article, the mechanism of inheritance behind inherited hearing loss and genetic susceptibility in noise-induced hearing loss are reviewed. Conventional treatments for sensorineural hearing loss (SNHL), i.e. hearing aid and cochlear implant, are effective for some cases, but not without limitations. For example, they provide little benefit for patients of profound SNHL or neural hearing loss, especially when the hearing loss is in poor dynamic range and with low frequency resolution. We emphasize the most recent evidence-based treatment in this field, which includes gene therapy and allotransplantation of stem cells. Their promising results have shown that they might be options of treatment for profound SNHL and neural hearing loss. Although some treatments are still at the experimental stage, it is helpful to be aware of the novel therapies and endeavour to explore the feasibility of their clinical application.