Different Rates of the SLC26A4-Related Hearing Loss in Two Indigenous Peoples of Southern Siberia (Russia)

Hereditary hearing loss (HL) is known to be highly locus/allelic heterogeneous, and the prevalence of different HL forms significantly varies among populations worldwide. Investigation of region-specific landscapes of hereditary HL is important for local healthcare and medical genetic services. Mutations in the SLC26A4 gene leading to nonsyndromic recessive deafness (DFNB4) and Pendred syndrome are common genetic causes of hereditary HL, at least in some Asian populations. We present for the first time the results of a thorough analysis of the SLC26A4 gene by Sanger sequencing in the large cohorts of patients with HL of unknown etiology belonging to two neighboring indigenous Turkic-speaking Siberian peoples (Tuvinians and Altaians). A definite genetic diagnosis based on the presence of biallelic SLC26A4 mutations was established for 28.2% (62/220) of all enrolled Tuvinian patients vs. 4.3% (4/93) of Altaian patients. The rate of the SLC26A4-related HL in Tuvinian patients appeared to be one of the highest among populations worldwide. The SLC26A4 mutational spectrum was characterized by the presence of Asian-specific mutations c.919-2A>G and c.2027T>A (p.Leu676Gln), predominantly found in Tuvinian patients, and c.2168A>G (p.His723Arg), which was only detected in Altaian patients. In addition, a novel pathogenic variant c.1545T>G (p.Phe515Leu) was found with high frequency in Tuvinian patients. Overall, based on the findings of this study and our previous research, we were able to uncover the genetic causes of HL in 50.5% of Tuvinian patients and 34.5% of Altaian patients.

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.

Mutation analysis of the SLC26A4 gene in patients in Yakutia with inner ear abnormalities: IP-I, IP-II (Mondini) and/or EVA

Мутации гена SLC26A4 могут приводить как к формированию аутосомно-рецессивной тугоухости 4 типа (DFNB4, OMIM #600791), так и к синдрому Пендреда (PDS, OMIM #274600), при котором нейросенсорная потеря слуха сочетается с дисфункцией щитовидной железы, клинически проявляющейся во второй декаде жизни. Обе формы могут сопровождаться специфическими аномалиями внутреннего уха: IP-I, IP-II (Mondini) и/или EVA. В Якутии аудиологическими, рентгенологическими и молекулярно-генетическими методами обследовано 165 пациентов с врожденным нарушением слуха. При компьютерной томографии пирамиды височных костей у 9 из 165 (5,5%) пациентов были обнаружены аномалии IP-I, IP-II (Mondini) и/или EVA. Методом прямого секвенирования по Сэнгеру у этих 9 пациентов было проведено определение нуклеотидной последовательности гена SLC26A4 (21 экзон). В гене SLC26A4 обнаружено 5 ранее известных вариантов, среди которых 4 варианта относились к миссенс-заменам: c.85G>C p.(Glu29Gln), c.441G>A p.(Met147Ile), c.757A>G p.(Ile253Val), c.2027T>A p.(Leu676Gln) и один вариант затрагивал донорный сайт сплайсинга - c.2089+1G>A (IVS18+1G>A). У 4-х из 9 пациентов патогенные варианты гена SLC26A4 обнаружены в гомозиготном или компаунд-гетерозиготном состоянии. Доля биаллельных мутаций гена SLС26A4 у пациентов с IP-I, IP-II (Mondini) и/или EVA составила 44,4%. Пациенты с биаллельными мутациями гена SLC26A4 имели тяжелые врожденные нарушения слуха (двусторонняя нейросенсорная тугоухость от III степени до глухоты), при этом доминирующим типом аномалий были IP-II (Mondini)+EVA (62,5%), аномалии IP-I не были выявлены ни у одного пациента. По совокупности полученных клинических и молекулярно-генетических данных у трех пациентов форма заболевания классифицирована как аутосомно-рецессивная тугоухость 4 типа (DFNB4), а у одной пациентки с двусторонней аномалией EVA, нейросенсорной тугоухостью III степени и узловым зобом (оперирован) подтвержден синдром Пендреда. Mutations in the SLC26A4 gene can lead to both the formation of autosomal recessive deafness type 4 (DFNB4, OMIM#600791), and to Pendred’s syndrome (PDS, OMIM#274600), in which sensorineural hearing loss is combined with thyroid dysfunction, with both forms can be accompanied by specific anomalies of the inner ear: IP-I, IP-II (Mondini) and/or EVA. Using audiological, radiological and molecular genetics methods, 165 patients with congenital hearing impairment in Yakutia were examined. Computed tomography revealed IP-I, IP-II (Mondini) and/or EVA abnormalities in 9 of 165 (5,5%) patients. Then, using direct Sanger sequencing in these 9 patients, the nucleotide sequence of the coding regions of the SLC26A4 gene (21 exons) was determined. In total, 5 previously known variants were found in the SLC26A4 gene, among which 4 variants were missense substitutions: c.85G>C p.(Glu29Gln), c.441G>A p.(Met147Ile), c.757A>G p.(Ile253Val), c.2027T>A p.(Leu676Gln) and one variant affected the splice donor site - c.2089+1G>A (IVS18+1G>A). In 4 out of 9 patients, pathogenic variants of the SLC26A4 gene were found in a homozygous or compound heterozygous state. The total contribution of biallelic mutations in the SLC26A4 gene among patients with inner ear anomalies was 44,4%. Patients with biallelic SLC26A4-mutations had several to profound bilateral sensorineural hearing loss. In patients with biallelic SLC26A4-mutations, the dominant type of anomaly was IP-II (Mondini)+EVA (62,5%), IP-I anomalies were not detected in any patient. In three patients we were able to confirm the diagnosis of DFNB4, and in one patient, due to the sum of phenotypic features (operated on for nodular goiter, autosomal recessive deafness with EVA), Pendred’s syndrome was diagnosed.

Neonatal Dyshormonogenetic Goiter with Hypothyroidism Associated with Novel Mutations in Thyroglobulin and SLC26A4 Gene

Congenital goiter is an uncommon cause of neck swelling and it can be associated with hypothyroidism. We discuss a case of primary hypothyroidism with goiter presenting at birth. Ultrasound showed the enlargement of the gland and thyroid function tests detected marked hypothyroidism. Genetic analysis via next generation sequencing (NGS) was performed finding two mutations associated with thyroid dyshormonogenesis: c.7813 C > T, homozygous in the exon 45 of the thyroglobulin gene (TG) and c.1682 G > A heterozygous in exon 15 of the SLC26A4 gene (pendrin). Sanger sequencing of parents’ DNA samples revealed that the first mutation (c.7813 C > T) was inherited from both of them, while the second one (c.1682 G > A) was inherited from the mother. Hormone replacement therapy was started, following which a gradual decrease in the size of the goiter was seen with the normalization of hormonal levels. Normal infant growth status and neurological development were recorded during follow-up. Neonatal dyshormonogenetic goiter with hypothyroidism may represent an unusual cause of neonatal neck mass. Early identification and hormone replacement therapy are crucial for a better neurodevelopmental outcome. Genetic analysis is mandatory in order to reach a specific diagnosis and to elucidate new patterns of thyroid disorder.

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.

Analysis of the mutational spectrum of the SLC26A4 gene and its contribution to the etiology of inherited hearing loss in the indigenous population of Southern Siberia

Мутации в гене SLC26A4 являются частой причиной потери слуха во многих регионах мира. В работе приводятся результаты молекулярно-генетического анализа (с использованием секвенирования по Сэнгеру) последовательности гена SLC26A4, впервые проведенного в выборке пациентов с потерей слуха неустановленной этиологии (n=232) из Республик Тыва и Алтай. Установлены контрастные различия патогенетического вклада мутаций в гене SLC26A4 в этиологию нарушения слуха у коренных жителей этих географически близких регионов: 28,2% - для тувинцев и 4,3% - для алтайцев. Выявлены как уже известные, так и новые патогенные варианты, а также широкий спектр полиморфных вариантов гена SLC26A4. Mutations in the SLC26A4 gene are a common cause of hearing loss in many regions of the world. This paper presents the results of molecular genetic analysis (by Sanger sequencing) of the SLC26A4 sequence, first performed in the sample of patients with hearing loss of unknown etiology (n=232) from the Tyva Republic and the Altai Republic. Contrast differences of the pathogenic contribution of SLC26A4 mutations to the etiology of hearing impairment were revealed in the indigenous peoples of these geographically close regions: 28.2% for Tuvinians and 4.3% for Altaians. Both known and novel pathogenic variants as well as a wide range of polymorphic variants were found in the SLC26A4 gene sequence.

Mutation analysis of the SLC26A4 gene in patients in Yakutia with inner ear abnormalities: IP-I, IP-II (Mondini) and / or EVA

В работе представлены результаты обследований 165 пациентов с врожденными нарушениями слуха из Якутии, проведенных с использованием аудиологических, рентгенологических и молекулярно-генетических методов с целью изучения аутосомно-рецессивной формы глухоты, связанной с аномалиями внутреннего уха (IP-I, IP-II и/или EVA) и мутациями гена SLC26A4 (DFNB4, MIM 600791). We presents the results of audiological, radiological and molecular genetic studies of 165 patients with congenital hearing impairment in Yakutia to investigate of autosomal recessive form of deafness associated with anomalies of the inner ear (IP-I, IP-II and / or EVA) and mutations in the SLC26A4 gene (DFNB4, MIM 600791).