Clinical characteristics and genotype-phenotype correlation of hearing loss patients with SLC26A4 mutations

Exonic Deletions and Deep Intronic Variants of the SLC26A4 Gene Contribute to the Genetic Diagnosis of Unsolved Patients With Enlarged Vestibular Aqueduct

Enlarged vestibular aqueduct (EVA) is a frequently occurring inner ear malformation that associates with sensorineural hearing loss (SNHL), with SLC26A4 being the responsible gene. Based on multiplex PCR enrichment and sequencing of the exonic and flanking regions of the SLC26A4 gene, we developed a panel specifically for EVA and found that up to 95% of EVA patients in our Chinese cohorts carried biallelic SLC26A4 pathogenic variants (M2). In this study, we tried to investigate the genetic etiology of 13 previously undiagnosed EVA patients with monoallelic (M1) or none (M0) SLC26A4 variant using a stepwise approach, including copy number variation (CNV) analysis of multiplex PCR enrichment and next-generation sequencing data, single-molecule real-time (SMRT) sequencing of the whole SLC26A4 gene, whole exome sequencing (WES), and whole genome sequencing (WGS). CNV analysis revealed deletions in Exons 1-3, Exons 5-6, and Exons 9-10 of the SLC26A4 gene in seven patients, and SMRT sequencing identified the same heterozygous deep intronic variant (NM_000441.2:c.304+941C>T) in two patients, resulting in a final diagnosis in 9/13 patients. Notably, the variants of Exons 9-10 deletion and c.304+941C>T have not been reported previously. We further showed that the variant c.304+941C>T led to the exonization of partial AluSz6 element (126 bp) where the variant is located through sequencing of the mRNA extracted from the blood of a heterozygous variant carrier. In conclusion, our stepwise approach improved the diagnosis rate of EVA, expanded the mutational spectrum of the SLC26A4 gene, and highlighted the contribution of exonic deletions and deep intronic variants to EVA.

Review and research gap identification in genetics causes of syndromic and nonsyndromic hearing loss in Saudi Arabia

Congenital hearing loss is one of the most common sensory disabilities worldwide. The genetic causes of hearing loss account for 50% of hearing loss. Genetic causes of hearing loss can be classified as nonsyndromic hearing loss (NSHL) or syndromic hearing loss (SHL). NSHL is defined as a partial or complete hearing loss without additional phenotypes; however, SHL, known as hearing loss, is associated with other phenotypes. Both types follow a simple Mendelian inheritance fashion. Several studies have been conducted to uncover the genetic factors contributing to NSHL and SHL in Saudi patients. However, these studies have encountered certain limitations. This review assesses and discusses the genetic factors underpinning NSHL and SHL globally, with a specific emphasis on the Saudi Arabian context. It also explores the prevalence of the most observed genetic causes of NSHL and SHL in Saudi Arabia. It also sheds light on areas where further research is needed to fully understand the genetic foundations of hearing loss in the Saudi population. This review identifies several gaps in research in NSHL and SHL and provides insights into potential research to be conducted.

Comprehensive Genetic Evaluation in Patients with Special Reference to Late-Onset Sensorineural Hearing Loss

Hearing loss (HL) is a common and multi-complex etiological deficit that can occur at any age and can be caused by genetic variants, aging, toxic drugs, noise, injury, viral infection, and other factors. Recently, a high incidence of genetic etiologies in congenital HL has been reported, and the usefulness of genetic testing has been widely accepted in congenital-onset or early-onset HL. In contrast, there have been few comprehensive reports on the relationship between late-onset HL and genetic causes. In this study, we performed next-generation sequencing analysis for 91 HL patients mainly consisting of late-onset HL patients. As a result, we identified 23 possibly disease-causing variants from 29 probands, affording a diagnostic rate for this study of 31.9%. The highest diagnostic rate was observed in the congenital/early-onset group (42.9%), followed by the juvenile/young adult-onset group (31.7%), and the middle-aged/aged-onset group (21.4%). The diagnostic ratio decreased with age; however, genetic etiologies were involved to a considerable degree even in late-onset HL. In particular, the responsible gene variants were found in 19 (55.9%) of 34 patients with a familial history and progressive HL. Therefore, this phenotype is considered to be a good candidate for genetic evaluation based on this diagnostic panel.

Characterization of Vestibular Phenotypes in Patients with Genetic Hearing Loss

Background: The vestibular phenotypes of patients with genetic hearing loss are poorly understood. Methods: we performed genetic testing including exome sequencing and vestibular function tests to investigate vestibular phenotypes and functions in patients with genetic hearing loss. Results: Among 627 patients, 143 (22.8%) had vestibular symptoms. Genetic variations were confirmed in 45 (31.5%) of the 143 patients. Nineteen deafness genes were linked with vestibular symptoms; the most frequent genes in autosomal dominant and recessive individuals were COCH and SLC26A4, respectively. Vestibular symptoms were mostly of the vertigo type, recurrent, and persisted for hours in the genetically confirmed and unconfirmed groups. Decreased vestibular function in the caloric test, video head impulse test, cervical vestibular-evoked myogenic potential, and ocular vestibular-evoked myogenic potential was observed in 42.0%, 16.3%, 57.8%, and 85.0% of the patients, respectively. The caloric test revealed a significantly higher incidence of abnormal results in autosomal recessive individuals than in autosomal dominant individuals (p = 0.011). The genes, including SLC26A4, COCH, KCNQ4, MYH9, NLRP3, EYA4, MYO7A, MYO15A, and MYH9, were heterogeneously associated with abnormalities in the vestibular function test. Conclusions: In conclusion, diverse vestibular symptoms are commonly concomitant with genetic hearing loss and are easily overlooked.

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.

Pendred Syndrome, or Not Pendred Syndrome? That Is the Question

Pendred syndrome (PDS) is the most common form of syndromic Hearing Loss (HL), characterized by sensorineural HL, inner ear malformations, and goiter, with or without hypothyroidism. SLC26A4 is the major gene involved, even though ~50% of the patients carry only one pathogenic mutation. This study aims to define the molecular diagnosis for a cohort of 24 suspected-PDS patients characterized by a deep radiological and audiological evaluation. Whole-Exome Sequencing (WES), the analysis of twelve variants upstream of SLC26A4, constituting the "CEVA haplotype" and Multiplex Ligation Probe Amplification (MLPA) searching for deletions/duplications in SLC26A4 gene have been carried out. In five patients (20.8%) homozygous/compound heterozygous SLC26A4 mutations, or pathogenic mutation in trans with the CEVA haplotype have been identified, while five subjects (20.8%) resulted heterozygous for a single variant. In silico protein modeling supported the pathogenicity of the detected variants, suggesting an effect on the protein stabilization/function. Interestingly, we identified a genotype-phenotype correlation among those patients carrying SLC26A4 mutations, whose audiograms presented a characteristic slope at the medium and high frequencies, providing new insights into PDS. Finally, an interesting homozygous variant in MYO5C has been identified in one patient negative to SLC26A4 gene, suggesting the identification of a new HL candidate gene.

The genetic etiology of hearing loss in Japan revealed by the social health insurance-based genetic testing of 10K patients

Etiological studies have shown genetic disorders to be a major cause of sensorineural hearing loss, but there are a limited number of comprehensive etiological reports based on genetic analysis. In the present study, the same platform using a diagnostic DNA panel carrying 63 deafness genes and the same filtering algorithm were applied to 10,047 samples obtained from social health insurance-based genetic testing of hearing loss. The most remarkable result obtained in this comprehensive study was that the data first clarified the genetic epidemiology from congenital/early-onset deafness to late-onset hearing loss. The overall diagnostic rate was 38.8%, with the rate differing for each age group; 48.6% for the congenital/early-onset group (~5y.o.), 33.5% for the juvenile/young adult-onset group, and 18.0% for the 40+ y.o. group. Interestingly, each group showed a different kind of causative gene. With regard to the mutational spectra, there are certain recurrent variants that may be due to founder effects or hot spots. A series of haplotype studies have shown many recurrent variants are due to founder effects, which is compatible with human migration. It should be noted that, regardless of differences in the mutational spectrum, the clinical characteristics caused by particular genes can be considered universal. This comprehensive review clarified the detailed clinical characteristics (onset age, severity, progressiveness, etc.) of hearing loss caused by each gene, and will provide useful information for future clinical application, including genetic counseling and selection of appropriate interventions.

Exploring the missing heritability in subjects with hearing loss, enlarged vestibular aqueducts, and a single or no pathogenic SLC26A4 variant

Pathogenic variants in SLC26A4 have been associated with autosomal recessive hearing loss (arHL) and a unilateral or bilateral enlarged vestibular aqueduct (EVA). SLC26A4 is the second most frequently mutated gene in arHL. Despite the strong genotype–phenotype correlation, a significant part of cases remains genetically unresolved. In this study, we investigated a cohort of 28 Dutch index cases diagnosed with HL in combination with an EVA but without (M0) or with a single (M1) pathogenic variant in SLC26A4. To explore the missing heritability, we first determined the presence of the previously described EVA-associated haplotype (Caucasian EVA (CEVA)), characterized by 12 single nucleotide variants located upstream of SLC26A4. We found this haplotype and a delimited V1-CEVA haplotype to be significantly enriched in our M1 patient cohort (10/16 cases). The CEVA haplotype was also present in two M0 cases (2/12). Short- and long-read whole genome sequencing and optical genome mapping could not prioritize any of the variants present within the CEVA haplotype as the likely pathogenic defect. Short-read whole-genome sequencing of the six M1 cases without this haplotype and the two M0/CEVA cases only revealed previously overlooked or misinterpreted splice-altering SLC26A4 variants in two cases, who are now genetically explained. No deep-intronic or structural variants were identified in any of the M1 subjects. With this study, we have provided important insights that will pave the way for elucidating the missing heritability in M0 and M1 SLC26A4 cases. For pinpointing the pathogenic effect of the CEVA haplotype, additional analyses are required addressing defect(s) at the RNA, protein, or epigenetic level.

Selected Otologic Disorders Causing Dizziness

PURPOSE OF REVIEW

This article details updated clinical presentations and current treatment paradigms of the common otologic disorders that may present to the neurologist for vertigo, including Ménière disease, superior semicircular canal dehiscence syndrome, perilymphatic fistula, barotrauma, cholesteatoma, Ramsay Hunt syndrome, enlarged vestibular aqueduct syndrome, and autoimmune inner ear disease including Cogan syndrome.

RECENT FINDINGS

The recent data on modern imaging techniques with three-dimensional delayed IV contrast in Ménière disease, findings on the clinical and testing parameters to diagnose semicircular canal dehiscence and barotrauma, and clinical findings in Ramsay Hunt syndrome, cholesteatoma, and enlarged vestibular aqueduct syndrome are discussed in the article. The most recent findings on the treatment and evaluation of autoimmune inner ear disease and Cogan syndrome are also covered.

SUMMARY

This article discusses the common clinical otologic entities in patients who may present to the neurologist for vertigo, and it can be used as a guide in the diagnosis of these conditions with the use of auditory, vestibular, and imaging results.

Toward the Pathogenicity of the SLC26A4 p.C565Y Variant Using a Genetically Driven Mouse Model

Recessive variants of the SLC26A4 gene are globally a common cause of hearing impairment. In the past, cell lines and transgenic mice were widely used to investigate the pathogenicity associated with SLC26A4 variants. However, discrepancies in pathogenicity between humans and cell lines or transgenic mice were documented for some SLC26A4 variants. For instance, the p.C565Y variant, which was reported to be pathogenic in humans, did not exhibit functional pathogenic consequences in cell lines. To address the pathogenicity of p.C565Y, we used a genotype-based approach in which we generated knock-in mice that were heterozygous (Slc26a4+/C565Y), homozygous (Slc26a4C565Y/C565Y), and compound heterozygous (Slc26a4919-2A>G/C565Y) for this variant. Subsequent phenotypic characterization revealed that mice with these genotypes demonstrated normal auditory and vestibular functions, and normal inner-ear morphology and pendrin expression. These findings indicate that the p.C565Y variant is nonpathogenic for mice, and that a single p.C565Y allele is sufficient to maintain normal inner-ear physiology in mice. Our results highlight the differences in pathogenicity associated with certain SLC26A4 variants between transgenic mice and humans, which should be considered when interpreting the results of animal studies for SLC26A4-related deafness.

Interpreting pendred syndrome as a foetal hydrops: Clinical and animal model evidence

BACKGROUND

Menière disease (MD) and SLC26A4 related deafness (Pendred syndrome (PS) or DFNB4) are two different inner ear disorders which present with fluctuating and progressive hearing loss, which could be a direct consequence of endolymphatic hydrops.

OBJECTIVE

To present similarities between both pathologies and explore how the concept of hydrops may be applied to PS/DFNB4.

METHODS

Review of the literature on MD, PS/DFNB4 and mouse model of PS/DFNB4.

RESULTS

MD and PS/DFNB4 share a number of similarities such as fluctuating and progressive hearing loss, acute episodes with vertigo and tinnitus, MRI and histological evidence of endolymphatic hydrops (although with different underlying mechanisms). MD is usually diagnosed during the fourth decade of life whereas PS/DFNB4 is congenital. The PS/DFNB4 mouse models have shown that biallelic slc26a4 mutations lead to Na+ and water retention in the endolymph during the perinatal period, which in turn induces degeneration of the stria vascularis and hearing loss. Crossing clinical/imagery characteristics and animal models, evidence seems to support the hypothesis of PS being a foetal hydrops.

CONCLUSIONS

When understanding PS/DFNB4 as a developmental hydrops, treatments used in MD could be repositioned to PS.

Pendred syndrome with hyperthyroidism

Objectives: Pendred syndrome is an autosomal recessive disorder characterized by the combination of sensorineural deafness and goiter and is caused by biallelic mutations in the SLC26A4/PDS gene. Thyroid function is generally reported as euthyroid or hypothyroid in this condition. We present a case of Pendred syndrome with hyperthyroidism.

Patient: An 83-year-old woman with congenital deaf–mutism presented with complaints of nausea. She developed a large goiter and had hearing impairment. Her hearing level was 105 dB in both ears. She presented with hyperthyroidism and was treated with thiamazole.

Results: She had a homozygous mutation in c.1579A>C:p.T527P of the SLC26A4 gene, confirming a diagnosis of Pendred syndrome.

Conclusion: Pendred syndrome may develop into hyperthyroidism if the size of the goiter increases. Moreover, a homozygous mutation in c.1579A>C:p.T527P of the SLC26A4 gene, which was previously reported to be associated with nonsyndromic hearing loss with enlarged vestibular aqueduct, may also cause Pendred syndrome.

Detailed MR imaging assessment of endolymphatic hydrops in patients with SLC26A4 mutations

OBJECTIVE

Mutations in SLC26A4 represent the second most common mutations in deafness patients. The majority of patients with SLC26A4 mutations have a large vestibular aqueduct (LVA). Recently, some reports showed the presence of endolymphatic hydrops (ELH) in patients with LVA on the basis of high-resolution enhanced 3T-MRI. However, detailed evaluation has not been performed. We provide the first report on ELH in LVA patients with biallelic SLC26A4 mutations. In this study, we focused on 1) the findings of ELH in LVA patients with biallelic SLC26A4 mutations, and 2) the findings of the endolymphatic duct (ED) and endolymphatic sac (ES) by using two different gadodimide (Gd) enhancement methods.

SUBJECTS AND METHODS

Five patients with SLC26A4 mutations underwent enhanced 3T-MRI using the intratympanic (IT) or intravenous (IV) injection of Gd for the diagnosis ELH.

RESULTS

All of the patients had ELH in at least one ear. ELH was identified in the vestibule (8/10 ears) as well as in the cochlea (7/10 ears). With regard to the ED and ES, all ears for which MRI was performed with an IT injection of Gd had black areas in the ES or VA or both; however, all of the ears receiving an IV injection had no black areas and were well enhanced.

CONCLUSIONS

A majority of the patients had severe ELH in the cochleo-vestibular endolymph, with two different patterns observed in the MRI findings of the ED and ES.

The Natural History of Hearing Loss in Pendred Syndrome and Non-Syndromic Enlarged Vestibular Aqueduct

INTRODUCTION

The aim was to investigate the progress of hearing loss over time in a cohort of pendred syndrome and non-syndromic enlarged vestibular aqueduct (PS/NSEVA) with one or two confirmed pathogenic variations in SLC26A4.

STUDY DESIGN

Retrospective cohort study.

SUBJECTS AND METHODS

At our tertiary referral center, a retrospective search of all patients with enlarged vestibular aqueduct, hearing loss and SLC26A4 mutations yielded 103 individuals by March 2017, 96 of whom had records of hearing levels; both an early audiometry and the latest between 3 and 668 months follow-up. Pure-tone average (PTA; average of thresholds at 0.5, 1, 2 and 4 kHz) was calculated for both ears at time 1 and time 2. Neonatal screening results were retrieved.

RESULTS

Eighty-seven (87) individuals had biallelic (M2) and 16 had monoallelic alterations (M1) in their SLC26A4. On average, the PTA progressed to 80 dB HL by the age of 6 years for the entire cohort, and 3.2 years for the biallelic (M2) affected individuals. 25% of the cohort was screened in the neonatal screening program; of these 42% had "passed" at least monaurally. Audiometric profiles related to age show faster deterioration in high frequencies than in low frequencies.

CONCLUSION

In patients with PS/NSEVA and SLC26A4 mutations, the average hearing loss progresses to 80 dB HL by the age of 6 years. For biallelic (M2) affected individuals it was 3.2 years. Although hearing levels reached severe to profound during childhood, almost 1/2 had passed neonatal hearing screening, at least monaurally, emphasizing the need for close follow-up.

Association of SLC26A4 mutations, morphology, and hearing in pendred syndrome and NSEVA

OBJECTIVE

To investigate the relations of monoallelic (M1), biallelic (M2), or the absence of mutations (M0) in SLC26A4 to inner ear morphology and hearing levels in individuals with Pendred syndrome (PS) or nonsyndromic enlarged vestibular aqueduct (NSEVA) associated with hearing loss.

METHODS

In a cohort of 139 PS/NSEVA individuals, 115 persons from 95 unrelated families had full genetic sequencing of SLC26A4, and 113 had retrievable images for re-assessment of inner ear morphology. The association between the number of mutant alleles in SLC26A4, inner ear morphology (including endolymphatic sac size and protein content on magnetic resonance imaging), and hearing level (pure tone average) was explored.

RESULTS

Biallelic SLC26A4 mutations (M2) occurred in three-quarters of the cohort and was invariably associated with poor hearing; in 87%, it was associated with incomplete partition type II of the cochlea as well as enlarged endolymphatic sac and vestibular aqueduct. M1 or M0 individuals exhibited a greater variability in inner ear morphology. Endolymphatic sac size and presence of "high-protein" sac contents were significantly higher in M2 individuals compared to M1 and M0 individuals.

CONCLUSION

The number of SLC26A4 mutations is associated with severity and variability of inner ear morphology and hearing level in individuals with PS or NSEVA. M2 individuals have poorer hearing and present largely incomplete partition type II of the cochleas with enlarged endolymphatic sacs, whereas individuals with M1 and no detectable SLC26A4 mutations have less severe hearing loss and more diverse inner ear morphology.

LEVEL OF EVIDENCE

4. Laryngoscope, 129:2574-2579, 2019.

Intronic variants of SLC26A4 gene enhance splicing efficiency in hybrid minigene assay

The SLC26A4 genomic sequence screening in autoimmune thyroid diseases (AITD) revealed different variants types with possible pathogenic effects. Although intronic variants may have more detrimental effects than those coding, they are poorly explored. Thus, in a first assessment, our bioinformatics analysis of intronic variants predicted a pathogenic effect of c.1002-9A>C, c.1545-5T>G and c.1544+9C>T variants. Validating these variants pathogenicity may provide new clues on the AITD physiopathology. Variants were explored in a general population by PCR-RFLP. These variants effects on the mRNA processing was assessed using functional splicing assay based in DNA hybrid minigene in HeLa cell lines. The constructs splicing efficiency was investigated by real time PCR. Our results revealed that c.1002-9A>C is a rare allele (minor frequency allele (MFA)=0.007) whereas c.1545-5T>G and c.1544+9C>T are low frequency variants. The RT-PCR analysis showed that these variants did not affect the mRNA processing. However, quantifying the transcripts generated from minigene constructs proved an mRNA splicing enhancement. Our study suggests a pathogenic effect of three intronic variants on the mRNA splicing efficiency using a DNA Hybrid minigene. By quantifying these transcripts, we unveil the limit of standard RT-PCR in analyzing a splicing minigene assay.

A novel missense mutation in the SLC26A4 gene causes nonsyndromic hearing loss and enlarged vestibular aqueduct

OBJECTIVES

We aimed to investigate the genetic causes of hearing loss in a Chinese proband with nonsyndromic hearing loss and enlarged vestibular aqueduct syndrome.

METHODS

We conducted clinical and genetic evaluations in a deaf proband and his normal-hearing parents. Multiplex PCR technology combined with Ion Torrent™ next-generation sequencing technology was used to detect the pathogenic mutations. As a control, a group of 1500 previously studied healthy newborns from the same ethnic background were subjected to deafness gene screening using the same method as in our previous study.

RESULTS

The proband harbored two mutations in the SLC26A4 gene in the form of compound heterozygosity. He was found to be heterozygous for a novel mutation named c.1742 G > T (p.Arg581Met) in exon 13 and for the known mutation c.589 G > A (p.Gly197Arg). These variants were carried in the heterozygous state by the parents and therefore co-segregated with the genetic disease. The c.1742 G > T (p.Arg581Met) mutation was absent in 1500 healthy newborns. Protein alignment indicated high evolutionary conservation of the p.R581 residue, and this mutation was predicted by PolyPhen-2 and other online tools to be damaging.

CONCLUSION

This study demonstrates that the novel mutation c.1742 G > T (p.Arg581Met) in compound heterozygosity with c.589 G > A in the SLC26A4 gene is the main cause of deafness in a family clinically diagnosed with enlarged vestibular aqueduct (EVA). Our study will provide a basic foundation for further investigations to elucidate the SLC26A4-related mechanisms of hearing loss.

Mapping pathogenic mutations suggests an innovative structural model for the pendrin (SLC26A4) transmembrane domain

Human pendrin (SLC26A4) is an anion transporter mostly expressed in the inner ear, thyroid and kidney. SLC26A4 gene mutations are associated with a broad phenotypic spectrum, including Pendred Syndrome and non-syndromic hearing loss with enlarged vestibular aqueduct (ns-EVA). No experimental structure of pendrin is currently available, making phenotype-genotype correlations difficult as predictions of transmembrane (TM) segments vary in number. Here, we propose a novel three-dimensional (3D) pendrin transmembrane domain model based on the SLC26Dg transporter. The resulting 14 TM topology was found to include two non-canonical transmembrane segments crucial for pendrin activity. Mutation mapping of 147 clinically validated pathological mutations shows that most affect two previously undescribed TM regions.

A Novel Frameshift Mutation of SLC26A4 in a Korean Family With Nonsyndromic Hearing Loss and Enlarged Vestibular Aqueduct

Objectives

We aimed to identify the causative mutation for siblings in a Korean family with nonsyndromic hearing loss (HL) and enlarged vestibular aqueduct (EVA). The siblings were a 19-year-old female with bilateral profound HL and an 11-year-old male with bilateral moderately severe HL.

Methods

We extracted genomic DNA from blood samples of the siblings with HL, their parents, and 100 controls. We performed mutation analysis for SLC26A4 using direct sequencing.

Results

The two siblings were compound heterozygotes with the novel mutation p.I713LfsX8 and the previously described mutation p.H723R. Their parents had heterozygous mono-allelic mutations. Father had p.I713LfsX8 mutation as heterozygous, and mother had p.H723R mutation as heterozygous. However, novel mutation p.I713LfsX8 was not detected in 100 unrelated controls.

Conclusion

Both mutations identified in this study were located in the sulfate transporter and anti-sigma factor antagonist domain, the core region for membrane targeting of SulP/SLC26 anion transporters, which strongly suggests that failure in membrane trafficking by SLC26A4 is a direct cause of HL in this family. Our study could therefore provide a foundation for further investigations elucidating the SLC26A4-related mechanisms of HL.

An effective screening strategy for deafness in combination with a next-generation sequencing platform: a consecutive analysis

The diagnosis of the genetic etiology of deafness contributes to the clinical management of patients. We performed the following four genetic tests in three stages for 52 consecutive deafness subjects in one facility. We used the Invader assay for 46 mutations in 13 genes and Sanger sequencing for the GJB2 gene or SLC26A4 gene in the first-stage test, the TaqMan genotyping assay in the second-stage test and targeted exon sequencing using massively parallel DNA sequencing in the third-stage test. Overall, we identified the genetic cause in 40% (21/52) of patients. The diagnostic rates of autosomal dominant, autosomal recessive and sporadic cases were 50%, 60% and 34%, respectively. When the sporadic cases with congenital and severe hearing loss were selected, the diagnostic rate rose to 48%. The combination approach using these genetic tests appears to be useful as a diagnostic tool for deafness patients. We recommended that genetic testing for the screening of common mutations in deafness genes using the Invader assay or TaqMan genotyping assay be performed as the initial evaluation. For the remaining undiagnosed cases, targeted exon sequencing using massively parallel DNA sequencing is clinically and economically beneficial.

Gene expression profiles of the cochlea and vestibular endorgans: localization and function of genes causing deafness

OBJECTIVES

We sought to elucidate the gene expression profiles of the causative genes as well as the localization of the encoded proteins involved in hereditary hearing loss.

METHODS

Relevant articles (as of September 2014) were searched in PubMed databases, and the gene symbols of the genes reported to be associated with deafness were located on the Hereditary Hearing Loss Homepage using localization, expression, and distribution as keywords.

RESULTS

Our review of the literature allowed us to systematize the gene expression profiles for genetic deafness in the inner ear, clarifying the unique functions and specific expression patterns of these genes in the cochlea and vestibular endorgans.

CONCLUSIONS

The coordinated actions of various encoded molecules are essential for the normal development and maintenance of auditory and vestibular function.

Molecular etiology of non-dominant, non-syndromic, mild-to-moderate childhood hearing impairment in Chinese Hans

Childhood hearing impairment (HI) is genetically heterogeneous. Compared with the severe-to-profound HI, the molecular etiology of mild-to-moderate HI in children has been less well characterized, especially for those not inherited in the dominant mode. In this study, we recruited 114 probands with non-dominant, non-syndromic, mild-to-moderate childhood HI. Sequencing of GJB2, SLC26A4, and MTRNR1 identified causative mutations in 30.7% (35/114), 4.4% (5/114), and 4.4% (5/114) of subjects, respectively. A majority (62.9%) of bi-allelic GJB2 mutations have non-truncating mutations in at least one allele. In 10 multiplex probands with no GJB2, SLC26A4, and MTRNR1 mutations identified, targeted next-generation sequencing (NGS) of 79 known deafness genes did not identify any additional causes. Our data showed that the molecular etiology of mild-to-moderate childhood HI is considerably different from what reported for severe-to-profound HI and far from complete for those inherited in non-dominant modes.

Mutation spectrum and genotype-phenotype correlation of hearing loss patients caused by SLC26A4 mutations in the Japanese: a large cohort study

Mutations in SLC26A4 cause a broad phenotypic spectrum, from typical Pendred syndrome to nonsyndromic hearing loss associated with enlarged vestibular aqueduct. Identification of these mutations is important for accurate diagnosis, proper medical management and appropriate genetic counseling and requires updated information regarding spectrum, clinical characteristics and genotype-phenotype correlations, based on a large cohort. In 100 patients with bilateral enlarged vestibular aqueduct among 1511 Japanese hearing loss probands registered in our gene bank, goiter data were available for 79, of whom 15 had Pendred syndrome and 64 had nonsyndromic hearing loss. We clarified the mutation spectrum for the SLC26A4 mutations and also summarized hearing levels, progression, fluctuation and existence of genotype-phenotype correlation. SLC26A4 mutations were identified in 82 of the 100 patients (82.0%). Of the Pendred syndrome patients, 93% (14/15) were carriers, as were 77% (49/64) of the nonsyndromic hearing loss patients. Clinical characteristics of patients with SLC26A4 mutations were congenital, fluctuating and progressive hearing loss usually associated with vertigo and/or goiter. We found no genotype-phenotype correlations, indicating that, unlike in the case of GJB2 mutations, the phenotype cannot be predicted from the genotype. Our mutation analysis confirmed the importance of mutations in the SLC26A4 gene among hearing loss patients with enlarged vestibular aqueduct and revealed the mutation spectrum, essential information when performing genetic testing.

Mouse models for pendrin-associated loss of cochlear and vestibular function

The human gene SLC26A4 and the mouse ortholog Slc26a4 code for the protein pendrin, which is an anion exchanger expressed in apical membranes of selected epithelia. In the inner ear, pendrin is expressed in the cochlea, the vestibular labyrinth and the endolymphatic sac. Loss-of-function and hypo-functional mutations cause an enlargement of the vestibular aqueduct (EVA) and sensorineural hearing loss. The relatively high prevalence of SLC26A4 mutations provides a strong imperative to develop rational interventions that delay, ameliorate or prevent pendrin-associated loss of cochlear and vestibular function. This review summarizes recent studies in mouse models that have been developed to delineate the role of pendrin in the physiology of hearing and balance and that have brought forward the concept that a temporally and spatially limited therapy may be sufficient to secure a life-time of normal hearing in children bearing mutations of SLC26A4.

Intrafamilial phenotypic variability in families with biallelic SLC26A4 mutations

OBJECTIVES/HYPOTHESIS

Enlarged vestibular aqueduct (EVA) and hearing loss are known to be caused by SLC26A4 mutations, but large phenotypic variability exists among patients with biallelic SLC26A4 mutations. Intrafamilial phenotypic variability was analyzed in multiplex EVA families carrying biallelic SLC26A4 mutations to identify the contribution of SLC26A4 mutations and other genetic or environmental factors influencing the clinical manifestations.

STUDY DESIGN

Retrospective case series.

METHODS

Eleven multiplex Korean families with EVA and hearing loss that carry biallelic mutations of the SLC26A4 gene were included. Genetic analysis for SLC26A4 and other genes including FOXI1, FOXI1-DBD, and KCNJ10 was performed. The auditory and other phenotypes were compared among siblings with the same SLC26A4 mutations.

RESULTS

The difference in the auditory phenotypes was identified between siblings in approximately half of the EVA families. Families with SLC26A4 mutations other than H723R homozygous mutations demonstrated more phenotypic variability, especially in those carrying IVS7-2A>G splice site mutation. Cochlear malformation was a consistent finding among siblings with the same SLC26A4 mutations. No mutation was identified in the FOXI1, FOXI1-DBD, and KCNJ10 genes in the tested families.

CONCLUSIONS

The possibility of variability concerning auditory phenotype should be considered even within family members carrying the same SLC26A4 mutations when providing genetic counseling to multiplex EVA families. Mutations in the currently known genes associated with EVA other than SLC26A4 were not found to be responsible for the intrafamilial phenotypic variability. Modifier genes or environmental factors other than the currently known genes seem to play a role in the phenotypic expressions of EVA patients.

High prevalence of inner-ear and/or internal auditory canal malformations in children with unilateral sensorineural hearing loss

OBJECTIVE

Radiological and genetic examination has recently advanced for diagnosis of congenital hearing loss. The aim of this study was to elucidate the prevalence of inner-ear and/or internal auditory canal malformations in children with unilateral sensorineural hearing loss (USNHL) for better management of hearing loss and genetic and lifestyle counseling.

METHODS

We conducted a retrospective study of charts and temporal bone computed tomography (CT) findings of 69 consecutive patients 0-15 years old with USNHL. In two cases, genetic examination was conducted.

RESULTS

Of these patients, 66.7% had inner-ear and/or internal auditory canal malformations. The prevalence of malformations in infants (age <1 year) was 84.6%, which was significantly higher than that in children 1-15 years old (55.8%; p<0.01). Almost half of the patients (32; 46.4%) had cochlear nerve canal stenosis; 13 of them had cochlear nerve canal stenosis alone, and in 19 it accompanied other malformations. Internal auditory canal malformations were observed in 22 subjects (31.8%), 14 (20.3%) had cochlear malformations, and 5 (7.2%) had vestibular/semicircular canal malformations. These anomalies were seen only in the affected ear, except in two of five patients with vestibular and/or semicircular canal malformations. Two patients (2.9%) had bilateral enlarged vestibular aqueducts. Mutations were found in SLC26A4 in one of the two patients with bilateral large vestibular aqueducts. The prevalence of a narrow internal auditory canal was significantly higher in subjects with cochlear nerve canal stenosis (50.0%) than in subjects with normal cochlear nerve canals (11.1%; p<0.01). There were no correlations between the type and number of malformations and hearing level.

CONCLUSIONS

The prevalence of inner-ear and/or internal auditory canal malformations detected by high-resolution temporal bone CT in children with USNHL was very high. Radiological and genetic examination provided important information to consider the pathogenesis and management of hearing loss. Temporal bone CT should be recommended to children with USNHL early in life. SLC26A4 mutation also should be examined in cases with bilateral enlarged vestibular aqueduct.

Identification of two heterozygous deafness mutations in SLC26A4 (PDS) in a Chinese family with two siblings

OBJECTIVE

To detect genetic cause of two Chinese siblings (patient 1 and 2) with Pendred syndrome.

DESIGN

Patients and their parents underwent clinical and genetic evaluations. To identify genetic mutations, sequencing of SLC26A4 was carried out.

STUDY SAMPLE

Two siblings and their parents.

RESULTS

Clinical evaluations showed that patient 1 suffered from bilateral postlingual progressive sensorineural hearing loss with enlarged vestibular aqueduct and slight diffuse multinodular goiter with euthyroid, and patient 2 suffered from bilateral prelingual progressive sensorineural hearing loss with enlarged vestibular aqueduct and no goiter with euthyroid. Furthermore, the sequence analysis of SLC26A4 indicated that either of the two siblings presented a compound heterozygote for the c.919A>G mutation in the splice site of intron 7 and for the c.1548insC mutation in exon 14. Their mother was a heterozygous carrier of the splice site mutation in intron 7, and their father was a heterozygous carrier of the insertion mutation in exon 14.

CONCLUSIONS

Mutation analysis identified a compound heterozygous mutation (c.919A>G/c.1548insC) in SLC26A4 in two Chinese siblings with Pendred syndrome. Also, c.1548insC was first reported in the Chinese population. Although the two siblings from the same family carried the same genotype, they presented different phenotypes.

Mutational analysis of the SLC26A4 gene in Chinese sporadic nonsyndromic hearing-impaired children

OBJECTIVE

To investigate the mutations of SLC26A4 gene and the relevant phenotype in Chinese sporadic nonsyndromic hearing-impaired children.

METHODS

195 Chinese sporadic nonsyndromic hearing-impaired children were subjected to microarray-based mutation detection for 9 hot spot mutations in four of the most common deafness-related genes (GJB2, SLC26A4, GJB3, and 12s rRNA). Subsequently, twenty-one patients with one SLC26A4 mutation detected by microarray were subjected to sequencing analysis of the whole SLC26A4 coding region and the splice sites in order to identify the second mutant allele. The inner ear malformation and hearing loss level were compared among different genotypes.

RESULTS

The incidence of genetic mutations was found to be 43.59% (85/195) in this patient group using CapitalBio Deafness Gene Mutation Detection Array Kit. A total of 34 children (17.44%) were found carrying the mutant SLC26A4 sequences. Thirteen (6.67%) children carried two mutant alleles of SLC26A4 and 21 (10.77%) children carried one mutant allele of SLC26A4. After the application of subsequent sequencing analysis, 13 mutational variants including 4 novel variants, two missense (p.D661G, p.N457D), one splice site mutation (IVS15+1G>A) and one frameshift mutation (624_632del9insACTTGGC), were identified in SLC26A4 gene in 15 of the 21 previously monoallelic patients. No second mutation was identified in the remaining 6 children. Biallelic mutations of SLC26A4 were identified in 20 of 21 children with enlarged vestibular aqueduct.

CONCLUSIONS

Our results demonstrated that genetic factors were important causes for sporadic nonsyndromic hearing loss in Chinese pediatric cases. Mutation of SLC26A4 is one of the major genetic causes in nonsyndromic hearing loss with inner ear malformation. IVS7-2A>G, 2168A>G and 1229C>T were the most frequent mutations identified in our studies. The combination of microarray testing and sequencing analysis is a useful and high-throughput method for the diagnosis of genetic hearing loss.

Simultaneous screening of multiple mutations by invader assay improves molecular diagnosis of hereditary hearing loss: a multicenter study

Although etiological studies have shown genetic disorders to be a common cause of congenital/early-onset sensorineural hearing loss, there have been no detailed multicenter studies based on genetic testing. In the present report, 264 Japanese patients with bilateral sensorineural hearing loss from 33 ENT departments nationwide participated. For these patients, we first applied the Invader assay for screening 47 known mutations of 13 known deafness genes, followed by direct sequencing as necessary. A total of 78 (29.5%) subjects had at least one deafness gene mutation. Mutations were more frequently found in the patients with congenital or early-onset hearing loss, i.e., in those with an awareness age of 0-6 years, mutations were significantly higher (41.8%) than in patients with an older age of awareness (16.0%). Among the 13 genes, mutations in GJB2 and SLC26A4 were mainly found in congenital or early-onset patients, in contrast with mitochondrial mutations (12S rRNA m.1555A>G, tRNA(Leu(UUR)) m.3243A>G), which were predominantly found in older-onset patients. The present method of simultaneous screening of multiple deafness mutations by Invader assay followed by direct sequencing will enable us to detect deafness mutations in an efficient and practical manner for clinical use.

The role of pendrin in the development of the murine inner ear

Enlargement of the vestibular aqueduct (EVA) is a common inner ear malformation found in children with sensorineural hearing loss that is frequently associated with loss-of-function or hypo-function mutations of SLC26A4. SLC26A4 codes for pendrin, which is a protein that is expressed in apical membranes of selected epithelia and functions as an anion exchanger. The comparatively high prevalence of EVA provides a strong imperative to develop rational interventions that delay, ameliorate or prevent hearing loss associated with this phenotype. The development of rational interventions requires a fundamental understanding of the role that pendrin plays in the normal development of hearing, as well as a detailed understanding of the pathobiologic mechanisms that, in the absence of fully functional pendrin, lead to an unstable hearing phenotype, with fluctuating or progressive loss of hearing. This review summarizes studies in mouse models that have focused on delineating the role of pendrin in the physiology of the inner ear and the pathobiology that leads to hearing loss.

Integration of human and mouse genetics reveals pendrin function in hearing and deafness

Genomic technology has completely changed the way in which we are able to diagnose human genetic mutations. Genomic techniques such as the polymerase chain reaction, linkage analysis, Sanger sequencing, and most recently, massively parallel sequencing, have allowed researchers and clinicians to identify mutations for patients with Pendred syndrome and DFNB4 non-syndromic hearing loss. While thus far most of the mutations have been in the SLC26A4 gene coding for the pendrin protein, other genetic mutations may contribute to these phenotypes as well. Furthermore, mouse models for deafness have been invaluable to help determine the mechanisms for SLC26A4-associated deafness. Further work in these areas of research will help define genotype-phenotype correlations and develop methods for therapy in the future.

Different cortical metabolic activation by visual stimuli possibly due to different time courses of hearing loss in patients with GJB2 and SLC26A4 mutations

Conclusion.

We have demonstrated differences in cortical activation with language-related visual stimuli in patients who were profoundly deafened due to genetic mutations in GJB2 and SLC26A4. The differences in cortical processing patterns between these two cases may have been influenced by the differing clinical courses and pathogenesis of hearing loss due to genetic mutations. Our results suggest the importance of hearing during early childhood for the development of a normal cortical language network.

Objectives.

To investigate the cortical activation with language-related visual stimuli in patients who were profoundly deafened due to genetic mutations in GJB2 and SLC26A4.

Methods:

The cortical activity of two adult patients with known genetic mutations (GJB2, SLC26A4) was evaluated with fluorodeoxyglucose-positron emission tomography (FDG-PET) with a visual language task and compared with that of normal-hearing controls.

Results:

A patient with a GJB2 mutation showed activation in the right auditory association area [BA21, BA22], and the left auditory association area [BA42] even with visual language task; in contrast, a patient with an SLC26A4 mutation showed no significant activation in the corresponding area.

Establishment of a knock-in mouse model with the SLC26A4 c.919-2A>G mutation and characterization of its pathology

Recessive mutations in the SLC26A4 gene are a common cause of hereditary hearing impairment worldwide. Previous studies have demonstrated that different SLC26A4 mutations may have different pathogenetic mechanisms. In the present study, we established a knock-in mouse model (i.e., Slc26a4^{tm1Dontuh/tm1Dontuh} mice) homozygous for the c.919-2A>G mutation, which is a common mutation in East Asians. Mice were then subjected to audiologic assessment, a battery of vestibular evaluations, and inner ear morphological studies. All Slc26a4^{tm1Dontuh/tm1Dontuh} mice revealed profound hearing loss, whereas 46% mice demonstrated pronounced head tilting and circling behaviors. There was a significant difference in the vestibular performance between wild-type and Slc26a4^{tm1Dontuh/tm1Dontuh} mice, especially those exhibiting circling behavior. Inner ear morphological examination of Slc26a4^{tm1Dontuh/tm1Dontuh} mice revealed an enlarged endolymphatic duct, vestibular aqueduct and sac, atrophy of stria vascularis, deformity of otoconia in the vestibular organs, consistent degeneration of cochlear hair cells, and variable degeneration of vestibular hair cells. Audiologic and inner ear morphological features of Slc26a4^{tm1Dontuh/tm1Dontuh} mice were reminiscent of those observed in humans. These features were also similar to those previously reported in both knock-out Slc26a4^−/− mice and Slc26a4^loop/loop mice with the Slc26a4 p.S408F mutation, albeit the severity of vestibular hair cell degeneration appeared different among the three mouse strains.

Failure of fluid absorption in the endolymphatic sac initiates cochlear enlargement that leads to deafness in mice lacking pendrin expression

Mutations of SLC26A4 are among the most prevalent causes of hereditary deafness. Deafness in the corresponding mouse model, Slc26a4^−/−, results from an abnormally enlarged cochlear lumen. The goal of this study was to determine whether the cochlear enlargement originates with defective cochlear fluid transport or with a malfunction of fluid transport in the connected compartments, which are the vestibular labyrinth and the endolymphatic sac. Embryonic inner ears from Slc26a4^+/− and Slc26a4^−/− mice were examined by confocal microscopy ex vivo or after 2 days of organ culture. Culture allowed observations of intact, ligated or partially resected inner ears. Cochlear lumen formation was found to begin at the base of the cochlea between embryonic day (E) 13.5 and 14.5. Enlargement was immediately evident in Slc26a4^−/− compared to Slc26a4^+/− mice. In Slc26a4^+/− and Slc26a4^−/− mice, separation of the cochlea from the vestibular labyrinth by ligation at E14.5 resulted in a reduced cochlear lumen. Resection of the endolymphatic sacs at E14.5 led to an enlarged cochlear lumen in Slc26a4^+/− mice but caused no further enlargement of the already enlarged cochlear lumen in Slc26a4^−/− mice. Ligation or resection performed later, at E17.5, did not alter the cochlea lumen. In conclusion, the data suggest that cochlear lumen formation is initiated by fluid secretion in the vestibular labyrinth and temporarily controlled by fluid absorption in the endolymphatic sac. Failure of fluid absorption in the endolymphatic sac due to lack of Slc26a4 expression appears to initiate cochlear enlargement in mice, and possibly humans, lacking functional Slc26a4 expression.

Efficient molecular genetic diagnosis of enlarged vestibular aqueducts in East Asians

CONTEXT

Enlargement of the vestibular aqueduct (EVA) is a commonly detected inner ear anomaly related to hearing loss and often associated with mutations of SLC26A4 encoding pendrin, a transmembrane exchanger of Cl(-), I(-), and HCO(3)(-). Here we describe the phenotypes of 27 Korean EVA subjects and their SLC26A4 genotypes determined by bidirectional nucleotide sequencing.

RESULTS

The detected variants include two novel missense substitutions (p.V138L and p.P542R). We characterized the ability of p.V138L and p.P542R pendrin products to traffic to the plasma membrane in COS-7 cells and to transport Cl(-), I(-), and HCO(3)(-) in Xenopus oocytes. The results indicate that p.P542R is a benign polymorphic variant, whereas p.V138L is a pathogenic mutation. Since this and other studies of East Asian EVA cohorts show that the majority of SLC26A4 mutations affect either or both of two amplicons (exons 7-8 and 19), we developed a hierarchical protocol that integrates direct sequencing with denaturing high-performance liquid chromatography analyses for detection of SLC26A4 mutations in these populations. We validated the cost efficiency of the integrated protocol by a simulated screen of published East Asian EVA cohorts with known SLC26A4 genotypes.

CONCLUSIONS

Our study further defines the spectrum of SLC26A4 mutations among East Asians and demonstrates a rapid and efficient protocol for their detection.

The responsible genes in Japanese deafness patients and clinical application using Invader assay

Discovery of deafness genes has progressed but clinical application lags because of the genetic heterogeneity. To establish clinical application strategy, we reviewed the frequency and spectrum of mutations found in Japanese hearing loss patients and compared them to those in populations of European ancestry. Screening revealed that in Japanese, mutations in GJB2, SLC26A4, and CDH23, and the mitochondrial 12S rRNA are the major causes of hearing loss. Also, mutations in KCNQ4, TECTA, COCH, WFS1, CRYM, COL9A3, and KIAA1199 were found in independent autosomal dominant families. Interestingly, spectrums of GJB2, SLC26A4, and CDH23 mutations in Japanese were quite different from those in Europeans. Simultaneous screening of multiple deafness mutations based on the mutation spectrum of a corresponding population using an Invader panel revealed that approximately 30% of subjects could be diagnosed. This assay will enable us to detect deafness mutations in an efficient and practical manner in the clinical platform. We conclude that specific racial populations may have unique deafness gene epidemiologies; therefore, ethnic background should be considered when genetic testing is performed. Simultaneous examination of multiple mutations based on a population's spectrum may be appropriate and effective for detecting deafness genes, facilitating precise clinical diagnosis, appropriate counseling, and proper management.