Origins and frequencies of SLC26A4 (PDS) mutations in east and south Asians: global implications for the epidemiology of deafness

Unraveling the Genetic Basis of Combined Deafness and Male Infertility Phenotypes through High-Throughput Sequencing in a Unique Cohort from South India

The co-occurrence of sensorineural hearing loss and male infertility has been reported in several instances, suggesting potential shared genetic underpinnings. One such example is the contiguous gene deletion of CATSPER2 and STRC genes, previously associated with deafness-infertility syndrome (DIS) in males. Fifteen males with both hearing loss and infertility from southern India after exclusion for the DIS contiguous gene deletion and the FOXI1 gene mutations are subjected to exome sequencing. This resolves the genetic etiology in four probands for both the phenotypes; In the remaining 11 probands, two each conclusively accounted for deafness and male infertility etiologies. Genetic heterogeneity is well reflected in both phenotypes. Four recessive (TRIOBP, SLC26A4, GJB2, COL4A3) and one dominant (SOX10) for the deafness; six recessive genes (LRGUK, DNAH9, ARMC4, DNAH2, RSPH6A, and ACE) for male infertility can be conclusively ascribed. LRGUK and RSPH6A genes are implicated earlier only in mice models, while the ARMC4 gene is implicated in chronic destructive airway diseases due to primary ciliary dyskinesia. This study would be the first to document the role of these genes in the male infertility phenotype in humans. The result suggests that deafness and infertility are independent events and do not segregate together among the probands.

The molecular principles underlying diverse functions of the SLC26 family of proteins

Mammalian SLC26 proteins are membrane-based anion transporters that belong to the large SLC26/SulP family, and many of their variants are associated with hereditary diseases. Recent structural studies revealed a strikingly similar homodimeric molecular architecture for several SLC26 members, implying a shared molecular principle. Now a new question emerges as to how these structurally similar proteins execute diverse physiological functions. In this study, we sought to identify the common versus distinct molecular mechanism among the SLC26 proteins using both naturally occurring and artificial missense changes introduced to SLC26A4, SLC26A5, and SLC26A9. We found: (i) the basic residue at the anion binding site is essential for both anion antiport of SLC26A4 and motor functions of SLC26A5, and its conversion to a nonpolar residue is crucial but not sufficient for the fast uncoupled anion transport in SLC26A9; (ii) the conserved polar residues in the N- and C-terminal cytosolic domains are likely involved in dynamic hydrogen-bonding networks and are essential for anion antiport of SLC26A4 but not for motor (SLC26A5) and uncoupled anion transport (SLC26A9) functions; (iii) the hydrophobic interaction between each protomer's last transmembrane helices, TM14, is not of functional significance in SLC26A9 but crucial for the functions of SLC26A4 and SLC26A5, likely contributing to optimally orient the axis of the relative movements of the core domain with respect to the gate domains within the cell membrane. These findings advance our understanding of the molecular mechanisms underlying the diverse physiological roles of the SLC26 family of proteins.

Autosomal recessive non-syndromic hearing loss genes in Pakistan during the previous three decades

Hearing loss is a clinically and genetically heterogeneous disorder, with over 148 genes and 170 loci associated with its pathogenesis. The spectrum and frequency of causal variants vary across different genetic ancestries and are more prevalent in populations that practice consanguineous marriages. Pakistan has a rich history of autosomal recessive gene discovery related to non-syndromic hearing loss. Since the first linkage analysis with a Pakistani family that led to the mapping of the DFNB1 locus on chromosome 13, 51 genes associated with this disorder have been identified in this population. Among these, 13 of the most prevalent genes, namely CDH23, CIB2, CLDN14, GJB2, HGF, MARVELD2, MYO7A, MYO15A, MSRB3, OTOF, SLC26A4, TMC1 and TMPRSS3, account for more than half of all cases of profound hearing loss, while the prevalence of other genes is less than 2% individually. In this review, we discuss the most common autosomal recessive non-syndromic hearing loss genes in Pakistani individuals as well as the genetic mapping and sequencing approaches used to discover them. Furthermore, we identified enriched gene ontology terms and common pathways involved in these 51 autosomal recessive non-syndromic hearing loss genes to gain a better understanding of the underlying mechanisms. Establishing a molecular understanding of the disorder may aid in reducing its future prevalence by enabling timely diagnostics and genetic counselling, leading to more effective clinical management and treatments of hearing loss.

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.

Functional Studies of Deafness-Associated Pendrin and Prestin Variants

Pendrin and prestin are evolutionary-conserved membrane proteins that are essential for normal hearing. Dysfunction of these proteins results in hearing loss in humans, and numerous deafness-associated pendrin and prestin variants have been identified in patients. However, the pathogenic impacts of many of these variants are ambiguous. Here, we report results from our ongoing efforts to experimentally characterize pendrin and prestin variants using in vitro functional assays. With previously established fluorometric anion transport assays, we determined that many of the pendrin variants identified on transmembrane (TM) 10, which contains the essential anion binding site, and on the neighboring TM9 within the core domain resulted in impaired anion transport activity. We also determined the range of functional impairment in three deafness-associated prestin variants by measuring nonlinear capacitance (NLC), a proxy for motor function. Using the results from our functional analyses, we also evaluated the performance of AlphaMissense (AM), a computational tool for predicting the pathogenicity of missense variants. AM prediction scores correlated well with our experimental results; however, some variants were misclassified, underscoring the necessity of experimentally assessing the effects of variants. Together, our experimental efforts provide invaluable information regarding the pathogenicity of deafness-associated pendrin and prestin variants.

Low frequency of SLC26A4 c.919-2A > G variant among patients with nonsyndromic hearing loss in Yunnan of Southwest China

BACKGROUND

Gene variants are responsible for more than half of hearing loss, particularly in nonsyndromic hearing loss (NSHL). The most common pathogenic variant in SLC26A4 gene found in East Asian populations is c.919-2A > G followed by c.2168A > G (p.H723R). This study was to evaluate their variant frequencies in patients with NSHL from special education schools in nine different areas of Southwest China's Yunnan.

METHODS

We performed molecular characterization by PCR-products directly Sanger sequencing of the SLC26A4 c.919-2AG and c.2168 A > G variants in 1167 patients with NSHL including 533 Han Chinese and 634 ethnic minorities.

RESULTS

The SLC26A4 c.919-2A > G variant was discovered in 8 patients with a homozygous state (0.69%) and twenty-five heterozygous (2.14%) in 1167 patients with NSHL. The total carrier rate of the c.919-2A > G variant was found in Han Chinese patients with 4.50% and ethnic minority patients with 1.42%. A significant difference existed between the two groups (P < 0.05). The c.919-2A > G allele variant frequency was ranged from 3.93% in Kunming to zero in Lincang and Nvjiang areas of Yunnan. We further detected the SLC26A4 c.2168 A > G variant in this cohort with one homozygotes (0.09%) and seven heterozygotes (0.60%), which was detected in Baoshan, Honghe, Licang and Pu`er areas. Between Han Chinese group (0.94%) and ethnic minority group (0.47%), there was no statistical significance (P > 0.05). Three Han Chinese patients (0.26%) carried compound heterozygosity for c.919-2A > G and c.2168 A > G.

CONCLUSION

These data suggest that the variants in both SLC26A4 c.919-2A > G and c.2168 A > G were relatively less frequencies in this cohort compared to the average levels in most regions of China, as well as significantly lower than that in Han-Chinese patients. These results broadened Chinese population genetic information resources and provided more detailed information for regional genetic counselling for Yunnan.

Spectrum of genetic variants in bilateral sensorineural hearing loss

Background: Hearing loss (HL) is an impairment of auditory function with identified genetic forms that can be syndromic (30%) or non-syndromic (70%). HL is genetically heterogeneous, with more than 1,000 variants across 150 causative genes identified to date. The genetic diagnostic rate varies significantly depending on the population being tested. Countries with a considerably high rate of consanguinity provide a unique resource for studying rare forms of recessive HL. In this study, we identified genetic variants associated with bilateral sensorineural HL (SNHL) using whole-exome sequencing (WES) in 11 families residing in the United Arab Emirates (UAE). Results: We established the molecular diagnosis in six probands, with six different pathogenic or likely pathogenic variants in the genes MYO15A, SLC26A4, and GJB2. One novel nonsense variant, MYO15A:p.Tyr1962Ter*, was identified in a homozygous state in one family, which has not been reported in any public database. SLC26A4 and GJB2 were found to be the most frequently associated genes in this study. In addition, six variants of uncertain significance (VUS) were detected in five probands in the genes CDH23, COL11A1, ADGRV1, NLRP3, and GDF6. In total, 12 variants were observed in eight genes. Among these variants, eight missense variants (66.7%), three nonsense variants (25.0%), and one frameshift (8.3%) were identified. The overall diagnostic rate of this study was 54.5%. Approximately 45.5% of the patients in this study came from consanguineous families. Conclusion: Understanding the genetic basis of HL provides insight for the clinical diagnosis of hearing impairment cases through the utilization of next-generation sequencing (NGS). Our findings contribute to the knowledge of the heterogeneous genetic profile of HL, especially in a population with a high rate of consanguineous marriage in the Arab population.

A novel intronic variant causing aberrant splicing identified in two deaf Chinese siblings with enlarged vestibular aqueducts

OBJECTIVE

We aimed to evaluate the genotype-phenotype relationship in two Chinese family members with enlarged vestibular aqueduct (EVA).

METHODS

We collected blood samples and clinical data from each pedigree family member. Genomic DNA was isolated from peripheral leukocytes using standard methods. Targeted next-generation sequencing and Sanger sequencing were performed to find the pathogenic mutation in this family. Minigene assays were used to verify whether the novel intronic mutation SLC26A4c.765+4A>G influenced mRNA splicing.

RESULTS

Hearing loss in the patients with EVA was diagnosed using auditory tests and imaging examinations. Two pathogenic mutations, c.765+4A>G and c.919-2A>G were detected in SLC26A4. In vitro minigene analysis confirmed that c.765+4A>G variant could cause aberrant splicing, resulting in skipping over exon 6.

CONCLUSIONS

The SLC26A4c.765+4A>G mutation is the causative variant in the Chinese family with EVA. Particular attention should be paid to intronic variants.

Whole Exome Sequencing of Non-Syndromic Hearing Loss Patients

Background

Hearing loss is the second most common disease after mental retardation in Iran. Autosomal recessive non-syndromic hearing loss (ARNSHL) is an extreme and highly heterogeneous disease, for which more than 70 genes have been identified. Considering the frequency of family marriage as well as the importance of ARNSHL in Iran, we evaluated the genetic factors involved in this type of deafness.

Methods

We performed the whole exome sequencing (WES) of eight Iranian subjects with severe nonsyndromic hearing loss selected from 110 well-characterized subjects with non-syndromic hearing loss from 2017-2019. The patients with mutated GJB2 and GJB6 genes were excluded from the study.

Results

The use of the whole exome sequencing method revealed 10 different mutations in 7 genes, including SLC26A4 (c.1234G>T), FGF3 (c.45DelC, c.466T>C), ADGRV1 (c.12528-2A>C, c.16226-16227insAGTC), OTOG (c.7454delG), OTOF (c.3570+2T>C), ESPN (c.992G>A), OTOA (c.2359G>T, c.2353A>C). Seven new variants were observed in seven families including SLC26A4 (c.1234G>T), FGF3 (c.45DelC), ADGRV1 (c.12528-2A>C), OTOG (c.7454delG), ADGRV1 (c.16226-16227insAGTC), OTOF (c.3570+2T>C).

Conclusion

The causal mutation of ARNSHL was found in all patients using the WES. Meta-analysis studies can help to identify common mutations causing deafness in any population to facilitate identification of carriers and subjects with deafness.

Functional studies of deafness-associated pendrin and prestin variants

Pendrin and prestin are evolutionary conserved membrane proteins that are essential for normal hearing. Pendrin is an anion transporter required for normal development and maintenance of ion homeostasis in the inner ear, while prestin is a voltage-dependent motor responsible for cochlear amplification essential for high sensitivity and frequency selectivity of mammalian hearing. Dysfunction of these proteins result in hearing loss in humans, and numerous deafness-associated pendrin and prestin variants have been identified in patients. However, the pathogenic impacts of many of these variants are ambiguous. Here we report results from our ongoing efforts in experimentally characterizing pendrin and prestin variants using in vitro functional assays, providing invaluable information regarding their pathogenicity.

The molecular principles underlying diverse functions of the SLC26 family of proteins

Mammalian SLC26 proteins are membrane-based anion transporters that belong to the large SLC26/SulP family, and many of their variants are associated with hereditary diseases. Recent structural studies revealed a strikingly similar homodimeric molecular architecture for several SLC26 members, implying a shared molecular principle. Now a new question emerges as to how these structurally similar proteins execute diverse physiological functions. In this study we sought to identify the common vs. distinct molecular mechanism among the SLC26 proteins using both naturally occurring and artificial missense changes introduced to SLC26A4, SLC26A5, and SLC26A9. We found: (i) the basic residue at the anion binding site is essential for both anion antiport of SLC26A4 and motor functions of SLC26A5, and its conversion to a nonpolar residue is crucial but not sufficient for the fast uncoupled anion transport in SLC26A9; (ii) the conserved polar residues in the N- and C-terminal cytosolic domains are likely involved in dynamic hydrogen-bonding networks and are essential for anion antiport of SLC26A4 but not for motor (SLC26A5) and uncoupled anion transport (SLC26A9) functions; (iii) the hydrophobic interaction between each protomer's last transmembrane helices, TM14, is not of functional significance in SLC26A9 but crucial for the functions of SLC26A4 and SLC26A5, likely contributing to optimally orient the axis of the relative movements of the core domain with respect to the gate domains within the cell membrane. These findings advance our understanding of the molecular mechanisms underlying the diverse physiological roles of the SLC26 family of proteins.

Novel small molecule-mediated restoration of the surface expression and anion exchange activity of mutated pendrin causing Pendred syndrome and DFNB4

Variants in SLC26A4 (pendrin) are the most common reasons for genetic hearing loss and vestibular dysfunction in East Asians. In patients with Pendred syndrome and DFNB4 (autosomal recessive type of genetic hearing loss 4), caused by variants in SLC26A4, the hearing function is residual at birth and deteriorates over several years, with no curative treatment for these disorders. In the present study, we revealed that a novel small molecule restores the expression and function of mutant pendrin. High-throughput screening of 54,000 small molecules was performed. We observed that pendrin corrector (PC2-1) increased the surface expression and anion exchange activity of p.H723R pendrin (H723R-PDS), the most prevalent genetic variant that causes Pendred syndrome and DFNB4. Furthermore, in endogenous H723R-PDS-expressing human nasal epithelial cells, PC2-1 significantly increased the surface expression of pendrin. PC2-1 exhibited high membrane permeability in vitro and high micromolar concentrations in the cochlear perilymph in vivo. In addition, neither inhibition of Kv11.1 activity in the human ether-a-go-go-related gene assay nor cell toxicity in the cell proliferation assay was observed at a high PC2-1 concentration (30 μM). These preclinical data support the hypothesis of the druggability of mutant pendrin using the novel corrector molecule PC2-1. In conclusion, PC2-1 may be a new therapeutic molecule for ameliorating hearing loss and treating vestibular disorders in patients with Pendred syndrome or DFNB4.

The applications of CRISPR/Cas-mediated genome editing in genetic hearing loss

Hearing loss (HL) can be caused by a number of different genetic factors. Non-syndromic HL refers that HL occurs as an isolated symptom in an individual, whereas syndromic HL refers that HL is associated with other symptoms or abnormalities. To date, more than 140 genes have been identified as being associated with non-syndromic HL, and approximately 400 genetic syndromes can include HL as one of the clinical symptoms. However, no gene therapeutic approaches are currently available to restore or improve hearing. Therefore, there is an urgent necessity to elucidate the possible pathogenesis of specific mutations in HL-associated genes and to investigate the promising therapeutic strategies for genetic HL. The development of the CRISPR/Cas system has revolutionized the field of genome engineering, which has become an efficacious and cost-effective tool to foster genetic HL research. Moreover, several in vivo studies have demonstrated the therapeutic efficacy of the CRISPR/Cas-mediated treatments for specific genetic HL. In this review, we briefly introduce the progress in CRISPR/Cas technique as well as the understanding of genetic HL, and then we detail the recent achievements of CRISPR/Cas technique in disease modeling and therapeutic strategies for genetic HL. Furthermore, we discuss the challenges for the application of CRISPR/Cas technique in future clinical treatments.

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.

Epidemiology, etiology, genetic variants in non- syndromic hearing loss in Iran: A systematic review and meta-analysis

OBJECTIVES

Hearing loss is one of the most common heterogeneous complicated disorders worldwide. We previously analyzed the results of published data on non-syndromic hearing loss in the Iranian population systematically. A broad range of genes is a challenge for molecular screening and clinical diagnosis in our populations on the ground of distinct genetics. The aim of this study was to analyze the role and frequency of the variants accountable for non-syndromic hearing loss (NSHL) in the Iranian population. These were identified with different methods including whole exome sequencing (WES), next-generation sequencing (NGS), targeted genomic enrichment and massively parallel sequencing (TGE + MPS), autozygosity mapping, STR markers, linkage analysis, and direct sequencing. This is the comprehensively study focusing on classifying 13 common NSHL genes according to their frequencies. Previous studies have not studied different regions and the Iranian population, and this is the definitive study on the topic.

METHODS

We searched Scopus, PubMed, Science Direct databases, and Google Scholar. After a systematic review of the evidence 95 studies were considered then 31 studies were eligible for meta-analysis. In total, 6995 families, 358 variants, and 117 novel variants were included. Statistical analyses were conducted using Stata SE version 11 software. The inverse variance method enjoyed combining data. Heterogeneity of the preliminary results was assessed using Q (Cochrane test), and I square index. Random effects or fixed models were applied to combine the results, relying on the degree of heterogeneity. Point and pooled prevalence of variants acting on different regions were illustrated by forest plots.

RESULTS

The total prevalence of at least one variant of GJB2 and SLC26A genes was estimated at 26% and 5%, respectively. Variant c.35delG accounted for 18% of the GJB2 variants while 1% of these variants were novel ones. The next most common variants in the GJB2 gene were c.109G>A at 3.5% and c.-23+1G>A at 2.3%. Moreover, the prevalence of GJB2 gene variants varied on average 0.002% from one region to another in Iran (p=0.849). Our meta-analysis also showed that the frequency of at least one variant of MYO15A varied between 1.2% and 12.5%. Corresponding prevalences for the other variants were as follows: ILDR1 (3.5%-3.7%), CDH23 (2%-10%), PJVK (1.4%-33%), TECTA (1.3%-6.7%), MYO6 (2%-4.8%), TMC1 (1.8%-2%), MYO7A (0.7%-5%), MARVELD2 (0.7-5%), OTOF (0.7%-4%), LRTOMT (0.7%-2.5%). Finally, we did not find any relationship between geographic area and the presence of these variants.

CONCLUSION

GJB2 gene variants were the most common cause of NSHL in Iran. Understanding the prevalence of NSHL gene frequency in Iran may be the foundation for future studies in an Iranian population which may lead to future NSHL therapy.

Global Distribution of Founder Variants Associated with Non-Syndromic Hearing Impairment

The genetic etiology of non-syndromic hearing impairment (NSHI) is highly heterogeneous with over 124 distinct genes identified. The wide spectrum of implicated genes has challenged the implementation of molecular diagnosis with equal clinical validity in all settings. Differential frequencies of allelic variants in the most common NSHI causal gene, gap junction beta 2 (GJB2), has been described as stemming from the segregation of a founder variant and/or spontaneous germline variant hot spots. We aimed to systematically review the global distribution and provenance of founder variants associated with NSHI. The study protocol was registered on PROSPERO, the International Prospective Register of Systematic Reviews, with the registration number "CRD42020198573". Data from 52 reports, involving 27,959 study participants from 24 countries, reporting 56 founder pathogenic or likely pathogenic (P/LP) variants in 14 genes (GJB2, GJB6, GSDME, TMC1, TMIE, TMPRSS3, KCNQ4, PJVK, OTOF, EYA4, MYO15A, PDZD7, CLDN14, and CDH23), were reviewed. Varied number short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) were used for haplotype analysis to identify the shared ancestral informative markers in a linkage disequilibrium and variants' origins, age estimates, and common ancestry computations in the reviewed reports. Asia recorded the highest number of NSHI founder variants (85.7%; 48/56), with variants in all 14 genes, followed by Europe (16.1%; 9/56). GJB2 had the highest number of ethnic-specific P/LP founder variants. This review reports on the global distribution of NSHI founder variants and relates their evolution to population migration history, bottleneck events, and demographic changes in populations linked with the early evolution of deleterious founder alleles. International migration and regional and cultural intermarriage, coupled to rapid population growth, may have contributed to re-shaping the genetic architecture and structural dynamics of populations segregating these pathogenic founder variants. We have highlighted and showed the paucity of data on hearing impairment (HI) variants in Africa, establishing unexplored opportunities in genetic traits.

The effect of SLC26A4 gene mutations on long-term rehabilitative outcomes in cochlear implant patients

BACKGROUND

SLC26A4 gene mutations related to hearing loss patients can obtain good hearing and speech rehabilitation effects after cochlear implantation (CI).

OBJECTIVE

To explore the long-term rehabilitative outcomes of CI in patients with different SLC26A4 mutation groups.

MATERIAL AND METHODS

Clinical data of 71 patients with SLC26A4 gene mutations who received CI in the Second Hospital of Lanzhou University from 2012 to 2015 were retrospectively reviewed. According to the genetic test results, use One-way ANOVA analysis to compare the differences in auditory results, categories of auditory performance (CAP) and speech intelligibility rating (SIR) index questionnaire scores and speech recognition rates among different groups in 4-5 years after CI.

RESULT

Compared with other genotypes of SLC26A4, the patients with homozygous mutation of c.919-2A > G in SLC26A4 had better hearing aid threshold at 500 Hz and better recognition rates of Yangyang words than other monoallelic mutation groups after CI (p < .05).

CONCLUSIONS AND SIGNIFICANCE

The most common hot spot mutation of SLC26A4 gene is c.919-2A > G. The patients with homozygous mutation of c.919-2A > G in SLC26A4 gene had partly better hearing and speech rehabilitation than other monoallelic mutation groups after CI.

The Genetic Background of Hearing Loss in Patients with EVA and Cochlear Malformation

The most frequently observed congenital inner ear malformation is enlarged vestibular aqueduct (EVA). It is often accompanied with incomplete partition type 2 (IP2) of the cochlea and a dilated vestibule, which together constitute Mondini malformation. Pathogenic SLC26A4 variants are considered the major cause of inner ear malformation but the genetics still needs clarification. The aim of this study was to identify the cause of EVA in patients with hearing loss (HL). Genomic DNA was isolated from HL patients with radiologically confirmed bilateral EVA (n = 23) and analyzed by next generation sequencing using a custom HL gene panel encompassing 237 HL-related genes or a clinical exome. The presence and segregation of selected variants and the CEVA haplotype (in the 5' region of SLC26A4) was verified by Sanger sequencing. Minigene assay was used to evaluate the impact of novel synonymous variant on splicing. Genetic testing identified the cause of EVA in 17/23 individuals (74%). Two pathogenic variants in the SLC26A4 gene were identified as the cause of EVA in 8 of them (35%), and a CEVA haplotype was regarded as the cause of EVA in 6 of 7 patients (86%) who carried only one SLC26A4 genetic variant. In two individuals with a phenotype matching branchio-oto-renal (BOR) spectrum disorder, cochlear hypoplasia resulted from EYA1 pathogenic variants. In one patient, a novel variant in CHD7 was detected. Our study shows that SLC26A4, together with the CEVA haplotype, accounts for more than half of EVA cases. Syndromic forms of HL should also be considered in patients with EVA. We conclude that to better understand inner ear development and the pathogenesis of its malformations, there is a need to look for pathogenic variants in noncoding regions of known HL genes or to link them with novel candidate HL genes.

The Frequency of Common Deafness-Associated Variants Among 3,555,336 Newborns in China and 141,456 Individuals Across Seven Populations Worldwide

OBJECTIVES

Genetic screening can benefit early detection and intervention for hearing loss. The frequency of common deafness-associated variants in general populations is highly important for genetic screening and genetic counseling tailored to different ethnic backgrounds. We aimed to analyze the frequency of common deafness-associated variants in a large population-based Chinese newborn cohort and to explore the population-specific features in diverse populations worldwide.

DESIGN

This population-based cohort study analyzed the frequency of common deafness-associated variants in 3,555,336 newborns in the Chinese Newborn Concurrent Hearing and Genetic Screening cohort. Participants were newborn infants born between January 2007 and September 2020. Limited genetic screening for 20 variants in 4 common deafness-associated genes and newborn hearing screening were offered concurrently to all newborns in the Chinese Newborn Concurrent Hearing and Genetic Screening cohort. Sequence information of 141,456 individuals was also analyzed from seven ethnic populations from the Genome Aggregation Database for 20 common deafness-related variants. Statistical analysis was performed using R.

RESULTS

A total of 3,555,326 Chinese neonates completed the Newborn Concurrent Hearing and Genetic Screening were included for analysis. We reported the distinct landscape of common deafness-associated variants in this large population-based cohort. We found that the carrier frequencies of GJB2 , SLC26A4 , GJB3 , and MT-RNR were 2.53%, 2.05%, 0.37%, and 0.25%, respectively. Furthermore, GJB2 c.235delC was the most common variant with an allele frequency of 0.99% in the Chinese newborn population. We also demonstrated nine East-Asia-enriched variants, one Ashkenazi Jewish-enriched variant, and one European/American-enriched variant for hearing loss.

CONCLUSIONS

We showed the distinct landscape of common deafness-associated variants in the Chinese newborn population and provided insights into population-specific features in diverse populations. These data can serve as a powerful resource for otolaryngologists and clinical geneticists to inform population-adjusted genetic screening programs for hearing loss.

Spectrum of Genes for Non-GJB2-Related Non-Syndromic Hearing Loss in the Russian Population Revealed by a Targeted Deafness Gene Panel

Hearing loss is one of the most genetically heterogeneous disorders known. Over 120 genes are reportedly associated with non-syndromic hearing loss (NSHL). To date, in Russia, there have been relatively few studies that apply massive parallel sequencing (MPS) methods to elucidate the genetic factors underlying non-GJB2-related hearing loss cases. The current study is intended to provide an understanding of the mutation spectrum in non-GJB2-related hearing loss in a cohort of Russian sensorineural NSHL patients and establish the best diagnostic algorithm. Genetic testing using an MPS panel, which included 33 NSHL and syndromic hearing loss (SHL) genes that might be misdiagnosed as NSHL genes, was completed on 226 sequentially accrued and unrelated patients. As a result, the molecular basis of deafness was found in 21% of the non-GJB2 NSHL cases. The total contribution pathogenic, and likely pathogenic, variants in the genes studied among all hereditary NSHL Russian patients was 12%. STRC pathogenic and likely pathogenic, variants accounted for 30% of diagnoses in GJB2-negative patients, providing the most common diagnosis. The majority of causative mutations in STRC involved large copy number variants (CNVs) (80%). Among the point mutations, the most common were c.11864G>A (p.Trp3955*) in the USH2A gene, c.2171_2174delTTTG (p.Val724Glyfs*6) in the STRC gene, and c.107A>C (p.His36Pro) and c.1001G>T (p.Gly334Val) in the SLC26A4 gene. Pathogenic variants in genes involved in SHL accounted for almost half of the cases with an established molecular genetic diagnosis, which were 10% of the total cohort of patients with non-GJB2-related hearing loss.

Analysis of SLC26A4, FOXI1, and KCNJ10 Gene Variants in Patients with Incomplete Partition of the Cochlea and Enlarged Vestibular Aqueduct (EVA) Anomalies

Pathogenic variants in the SLC26A4, FOXI1, and KCNJ10 genes are associated with hearing loss (HL) and specific inner ear abnormalities (DFNB4). In the present study, phenotype analyses, including clinical data collection, computed tomography (CT), and audiometric examination, were performed on deaf individuals from the Sakha Republic of Russia (Eastern Siberia). In cases with cochleovestibular malformations, molecular genetic analysis of the coding regions of the SLC26A4, FOXI1, and KCNJ10 genes associated with DFNB4 was completed. In six of the 165 patients (3.6%), CT scans revealed an incomplete partition of the cochlea (IP-1 and IP-2), in isolation or combined with an enlarged vestibular aqueduct (EVA) anomaly. Sequencing of the SLC26A4, FOXI1, and KCNJ10 genes was performed in these six patients. In the SLC26A4 gene, we identified four variants, namely c.85G>C p.(Glu29Gln), c.757A>G p.(Ile253Val), c.2027T>A p.(Leu676Gln), and c.2089+1G>A (IVS18+1G>A), which are known as pathogenic, as well as c.441G>A p.(Met147Ile), reported previously as a variant with uncertain significance. Using the AlphaFold algorithm, we found in silico evidence of the pathogenicity of this variant. We did not find any causative variants in the FOXI1 and KCNJ10 genes, nor did we find any evidence of digenic inheritance associated with double heterozygosity for these genes with monoallelic SLC26A4 variants. The contribution of biallelic SLC26A4 variants in patients with IP-1, IP-2, IP-2+EVA, and isolated EVA was 66.7% (DFNB4 in three patients, Pendred syndrome in one patient). Seventy-five percent of SLC26A4-biallelic patients had severe or profound HL. The morphology of the inner ear anomalies demonstrated that, among SLC26A4-biallelic patients, all types of incomplete partition of the cochlea are possible, from IP-1 and IP-2, to a normal cochlea. However, the dominant type of anomaly was IP-2+EVA (50.0%). This finding is very important for cochlear implantation, since the IP-2 anomaly does not have an increased risk of “gushers” and recurrent meningitis.

Selection of Diagnostically Significant Regions of the SLC26A4 Gene Involved in Hearing Loss

Screening pathogenic variants in the SLC26A4 gene is an important part of molecular genetic testing for hearing loss (HL) since they are one of the common causes of hereditary HL in many populations. However, a large size of the SLC26A4 gene (20 coding exons) predetermines the difficulties of its complete mutational analysis, especially in large samples of patients. In addition, the regional or ethno-specific prevalence of SLC26A4 pathogenic variants has not yet been fully elucidated, except variants c.919-2A>G and c.2168A>G (p.His723Arg), which have been proven to be most common in Asian populations. We explored the distribution of currently known pathogenic and likely pathogenic (PLP) variants across the SLC26A4 gene sequence presented in the Deafness Variation Database for the selection of potential diagnostically important parts of this gene. As a result of this bioinformatic analysis, we found that molecular testing ten SLC26A4 exons (4, 6, 10, 11, 13−17 and 19) with flanking intronic regions can provide a diagnostic rate of 61.9% for all PLP variants in the SLC26A4 gene. The primary sequencing of these SLC26A4 regions may be applied as an initial effective diagnostic testing in samples of patients of unknown ethnicity or as a subsequent step after the targeted testing of already-known ethno- or region-specific pathogenic SLC26A4 variants.

Mutation spectrum of non-syndromic hearing loss in the UAE, a retrospective cohort study and literature review

BACKGROUND

Hearing loss (HL) is a heterogeneous condition that causes partial or complete hearing impairment. Hundreds of variants in >60 genes have been reported to be associated with Hereditary HL (HHL), variants of the GJB2 gene are the most common cause of congenital SNHL, with >100 variants reported. The HHL prevalence is thought to be high in the Arab population; however, the genetic epidemiology of HHL among Emirati populations is understudied.

AIMS

To shed light on the mutational spectrum of NSHL in Emirati patients seen in the genetic clinic over 10 years and to capture founder mutation(s) if any were identified.

METHODS

Retrospective chart review of all Emirati patients assessed by clinical geneticists due to NSHL during the period between January 2010 to December 2020. Genetic tests were done based on clinical phenotypes of the patient and family history including targeted mutation testing, next-generation sequencing, or whole-exome sequencing (solo or trio). The authors did literature reviews using PubMed for all previously reported articles related to NSHL genes from UAE.

RESULTS

A total of 162 patients with HL, were evaluated during the period between January 2010 to December 2020. There were 82 patients with NSHL, and only 72 patients who completed the genetic evaluations were included in this retrospective study. Among the studied group, 42 (51.2%) were males and 40 (48.78%) were females. The youngest patient was 2 years old and the oldest patient was 50 years old. Consanguinity was documented in 76 patients (92.68%). A total of 14 mutations reported here are novel (23/72 i.e., 31.9%). Twelve missense mutations, 6 nonsense mutations, 6 frameshift mutations, 2 in-frame deletion mutations, and 1 splice site mutation was found. Variants in the GJB2 gene are the most commonly identified cause of NSHL, with c.35delG being the most followed by c.506G > A. The second commonly found variant is c.934C > G (p.Arg312Gly) in the CDC14A gene, found in 9 patients. This was followed by variants in OTOF and SLC26A4 genes, found in 8 patients, respectively. Chromosomal microdeletions encompassing genes causing NSHL were found in 3 patients. No mitochondrial mutations were found in this study group. A total of 11 previous reports about Emirati patients with NSHL were reviewed, with a total of 35 patients.

CONCLUSION

Emirati patients with NSHL have several mutations, most notably missense mutations. Novel mutations are worth further testing and represent the area for future researches.

Clinical evaluation and etiologic diagnosis of hearing loss: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG)

Hearing loss is a common and complex condition that can occur at any age, can be inherited or acquired, and is associated with a remarkably wide array of etiologies. The diverse causes of hearing loss, combined with the highly variable and often overlapping presentations of different forms of hearing loss, challenge the ability of traditional clinical evaluations to arrive at an etiologic diagnosis for many deaf and hard-of-hearing individuals. However, identifying the etiology of hearing loss may affect clinical management, improve prognostic accuracy, and refine genetic counseling and assessment of the likelihood of recurrence for relatives of deaf and hard-of-hearing individuals. Linguistic and cultural identities associated with being deaf or hard-of-hearing can complicate access to and the effectiveness of clinical care. These concerns can be minimized when genetic and other health care services are provided in a linguistically and culturally sensitive manner. This clinical practice resource offers information about the frequency, causes, and presentations of hearing loss and suggests approaches to the clinical and genetic evaluation of deaf and hard-of-hearing individuals aimed at identifying an etiologic diagnosis and providing informative and effective patient education and genetic counseling.

Rescue of mis-splicing of a common SLC26A4 mutant associated with sensorineural hearing loss by antisense oligonucleotides

A wide spectrum of SLC26A4 mutations causes Pendred syndrome and enlarged vestibular aqueduct, both associated with sensorineural hearing loss (SNHL). A splice-site mutation, c.919-2A>G (A-2G), which is common in Asian populations, impairs the 3′ splice site of intron 7, resulting in exon 8 skipping during pre-mRNA splicing and a subsequent frameshift that creates a premature termination codon in the following exon. Currently, there is no effective drug treatment for SHNL. For A-2G-triggered SNHL, molecules that correct mis-splicing of the mutant hold promise to treat the disease. Antisense oligonucleotides (ASOs) can promote exon inclusion when targeting specific splicing silencers. Here, we systematically screened a large number of ASOs in a minigene system and identified a few that markedly repressed exon 8 skipping. A lead ASO, which targets a heterogeneous nuclear ribonucleoprotein (hnRNP) A1/A2 intronic splicing silencer (ISS) in intron 8, promoted efficient exon 8 inclusion in cultured peripheral blood mononuclear cells derived from two homozygous patients. In a partially humanized Slc26a4 A-2G mouse model, two subcutaneous injections of the ASO at 160 mg/kg significantly rescued exon 8 splicing in the liver. Our results demonstrate that the ISS-targeting ASO has therapeutic potential to treat genetic hearing loss caused by the A-2G mutation in SLC26A4.

Concurrent newborn hearing and genetic screening of common hearing loss variants with bloodspot-based targeted next generation sequencing in Jiangxi province

BACKGROUND AND AIMS

Concurrent hearing and genetic screening of newborns have been widely adopted as an effective strategy in early diagnosis and intervention for hearing loss in many cities in China. Here, we aimed to firstly explore the efficacy of combining conventional hearing screening with genetic screening among the large-scale newborns in Jiangxi Province.

METHODS

A total of 24,349 newborns from Jiangxi Maternal and Child Health Hospital were enrolled in our study from April 2021 to June 2022. Newborn hearing screening was conducted using otoacoustic emission (OAE) and automated auditory brainstem response (AABR). Meanwhile, newborn dried blood spots were collected and twenty common variants in four genes, including GJB2, SLC26A4, MT-RNR1(12SrRNA), and GJB3, were screened using a BGISEQ-500 next generation sequencing platform. Whole coding regions sequencing of GJB2 and SLC26A4 were performed by Sanger sequencing and NGS, respectively. Following up of hearing for the newborns was undertaken by phone interviews.

RESULTS

Among the 24,349 newborns, 7.00% (1,704/24,349) were bilaterally or unilaterally referred in their initial hearing screening, whereas 1.30% (316/24,349) exhibited bilateral or unilateral hearing loss in the repeated screening. Genetic screening revealed that 4.813% (1,172/24,349) of the screened newborns were positive for at least one mutant allele (heterozygote, homozygote, or compound heterozygote in one gene, mtDNA homoplasmy or heteroplasmy and combined variants in different genes). A total of 1,146 individuals were identified with mutant allele in one gene, including 525 of GJB2, 371 of SLC26A4, 189 as homoplasmic or heteroplasmic of MT-RNR1, and 61 of GJB3, indicating that GJB2 and SLC26A4 are the most common endemic deafness-associated genes among newborns in Jiangxi Province. Nineteen newborns were detected with combined heterozygous variants in different genes, with "c.235delC heterozygous and c.919-2A > G heterozygous" as the most prevalent genotype. Additionally, seven newborns were screened as homozygotes or compound heterozygotes responsible for congenital or late-onset prelingual hearing loss, including three cases with GJB2 c.235delC homozygous and one with SLC26A4 c.919-2A > G homozygous variant, one case with compound heterozygous variants for GJB2 and two with compound heterozygous variants for SLC26A4. Coding regions sequencing of GJB2 or SLC26A4 for overall 265 infants revealed that 14 individuals were identified as compound heterozygote with a second pathogenic variant not screened by our genetic panel.

CONCLUSIONS

Herein our study firstly investigated the efficacy of concurrent hearing screening and genetic screening of common hearing impairment variants among large-scale newborns in Jiangxi Province. Concurrent screening provides a more comprehensive approach for management of congenital or delayed onset prelingual hearing loss and prevention of drug-induced hearing impairment for newborns at risk as well as their maternal relatives. An insight into the molecular epidemiology for hearing loss genes among Jiangxi population will also be beneficial to the genetic counseling and birth defect prevention.

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.

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.

Genetic architecture and phenotypic landscape of SLC26A4-related hearing loss

Mutations of coding regions and splice sites of SLC26A4 cause Pendred syndrome and nonsyndromic recessive hearing loss DFNB4. SLC26A4 encodes pendrin, a transmembrane exchanger of anions and bases. The mutant SLC26A4 phenotype is characterized by inner ear malformations, including an enlarged vestibular aqueduct (EVA), incomplete cochlear partition type II and modiolar hypoplasia, progressive and fluctuating hearing loss, and vestibular dysfunction. A thyroid iodine organification defect can lead to multinodular goiter and distinguishes Pendred syndrome from DFNB4. Pendred syndrome and DFNB4 are each inherited as an autosomal recessive trait caused by biallelic mutations of SLC26A4 (M2). However, there are some EVA patients with only one detectable mutant allele (M1) of SLC26A4. In most European-Caucasian M1 patients, there is a haplotype that consists of 12 variants upstream of SLC26A4, called CEVA (Caucasian EVA), which acts as a pathogenic recessive allele in trans to mutations affecting the coding regions or splice sites of SLC26A4. This combination of an M1 genotype with the CEVA haplotype is associated with a less severe phenotype than the M2 genotype. The phenotype in EVA patients with no mutant alleles of SLC26A4 (M0) has a very low recurrence probability and is likely to be caused by other factors.

Molecular genetic landscape of hereditary hearing loss in Pakistan

Approximately 14.5 million Pakistani individuals have a hearing loss and half of these cases may be due to genetic causes. Though significant progress has been made in uncovering genetic variants for recessively inherited nonsyndromic deafness, Pendred syndrome, and Usher syndromes, the same is not true for dominantly inherited hearing loss, most syndromic cases and deafness with complex inheritance patterns. Variants of 57 genes have been reported to cause nonsyndromic recessive deafness in Pakistan, though most are rare. Variants of just five genes GJB2, HGF, MYO7A, SLC26A4, and TMC1 together explain 57% of profound deafness while those of GJB2, MYO15A, OTOF, SLC26A4, TMC1, and TMPRSS3 account for 47% of moderate to severe hearing loss. In contrast, although variants of at least 39 genes have been implicated in different deafness syndromes, their prevalence in the population and the spectrum of mutations have not been explored. Furthermore, research on genetics of deafness has mostly focused on individuals from the Punjab province and needs to be extended to other regions of Pakistan. Identifying the genes and their variants causing deafness in all ethnic groups is important as it will pinpoint rare as well as recurrent mutations. This information may ultimately help in offering genetic counseling and future treatments.

Congenital Deafness and Recent Advances Towards Restoring Hearing Loss

Congenital hearing loss is the most common birth defect, estimated to affect 2-3 in every 1000 births. Currently there is no cure for hearing loss. Treatment options are limited to hearing aids for mild and moderate cases, and cochlear implants for severe and profound hearing loss. Here we provide a literature overview of the environmental and genetic causes of congenital hearing loss, common animal models and methods used for hearing research, as well as recent advances towards developing therapies to treat congenital deafness. © 2021 The Authors.

Genetic mutations in patients with nonsyndromic hearing impairment of minority and Han Chinese ethnicities in Qinghai, China

Objective

Mutations in GJB2, SLC26A4, and mitochondrial (mt)DNA 12S rRNA genes are the main cause of nonsyndromic hearing impairment. The present study analyzed these mutations in ethnic minority and Han Chinese patients with nonsyndromic hearing impairment from Qinghai, China.

Methods

The SNPscan assay was used to analyze mutation spectra and frequencies in the two patient groups.

Results

GJB2 mutations were detected in 9.5% (20/210) of minority patients and 20.88% (48/230) of Han Chinese patients. The most common Han Chinese GJB2 variants were c.235delC and c.299_300delAT, whereas c.235delC and c.109G > A were the most prevalent in minority patients. SLC26A4 mutations were detected in 5.71% (12/210) of minority patients and 14.35% (33/230) of Han Chinese patients, and mtDNA 12S rRNA mutations were detected in 4.28% (9/210) of minority patients and 9.13% (21/230) of Han Chinese patients.

Conclusions

These data indicate that the mutation frequencies of three deafness-associated genes were significantly higher in Han Chinese patients than in minority patients. Moreover, the GJB2 mutation spectrum was shown to differ between these two patient groups.

Transcriptomic Analysis Reveals an Altered Hcy Metabolism in the Stria Vascularis of the Pendred Syndrome Mouse Model

Purpose

Slc26a4^-/- mice exhibit severer defects in the development of the cochlea and develop deafness, while the underlying mechanisms responsible for these effects remain unclear. Our study was to investigate the potential mechanism linking SLC26A4 deficiency to hearing loss.

Materials and Methods

RNA sequencing was applied to analyze the differential gene expression of the stria vascularis (SV) from wildtype and Slc26a4^-/- mice. GO and KEGG pathway analysis were performed. Quantitative RT-PCR was applied to validate the expression of candidate genes affected by Slc26a4. ELISA and immunofluorescence technique were used to detect the homocysteine (Hcy) level in serum, brain, and SV, respectively.

Results

183 upregulated genes and 63 downregulated genes were identified in the SV associated with Slc26a4 depletion. Transcriptomic profiling revealed that Slc26a4 deficiency significantly affected the expression of genes associated with cell adhesion, transmembrane transport, and the biogenesis of multicellular organisms. The SV from Slc26a4^-/- mice exhibited a higher expression of Bhmt mRNAs, as well as altered homocysteine (Hcy) metabolism.

Conclusions

The altered expression of Bhmt results in a dramatic change in multiple biochemical reactions and a disruption of nutrient homeostasis in the endolymph which may contribute to hearing loss of Slc26a4 knockout mouse.

Genetic Epidemiology of Hearing Loss in the 22 Arab Countries: A Systematic Review

BACKGROUND

Hearing loss (HL) is a heterogeneous condition that causes partial or complete hearing impairment. Hundreds of variants in more than 60 genes have been reported to be associated with Hereditary HL (HHL). The HHL prevalence is thought to be high in the Arab population; however, the genetic epidemiology of HHL among Arab populations is understudied. This study aimed to systematically analyze the genetic epidemiology of HHL in Arab countries.

METHODS

We searched four literature databases (PubMed, Scopus, Science Direct, and Web of Science) from the time of inception until January 2019 using broad search terms to capture all the reported epidemiological and genetic data related to Arab patients with HHL.

FINDINGS

A total of 2,600 citations were obtained; 96 studies met our inclusion criteria. Our search strategy yielded 121,276 individuals who were tested for HL over 52 years (1966-2018), of whom 8,099 were clinically diagnosed with HL and belonged to 16 Arab countries. A total of 5,394 patients and 61 families with HHL were genotyped, of whom 336 patients and 6 families carried 104 variants in 44 genes and were from 17/22 Arab countries. Of these variants, 72 (in 41 genes) were distinctive to Arab patients. Arab patients manifested distinctive clinical phenotypes. The incidence of HHL in the captured studies ranged from 1.20 to 18 per 1,000 births per year, and the prevalence was the highest in Iraq (76.3%) and the lowest in Jordan (1.5%).

INTERPRETATION

This is the first systematic review to capture the prevalence and spectrum of variants associated with HHL in an Arab population. There appears to be a distinctive clinical picture for Arab patients with HHL, and the range and distribution of variants among Arab patients differ from those noted in other affected ethnic groups.

A data set of variants derived from 1455 clinical and research exomes is efficient in variant prioritization for early-onset monogenic disorders in Indians

Given the genomic uniqueness, a local data set is most desired for Indians, who are underrepresented in existing public databases. We hypothesize patients with rare monogenic disorders and their family members can provide a reliable source of common variants in the population. Exome sequencing (ES) data from families with rare Mendelian disorders was aggregated from five centers in India. The dataset was refined by excluding related individuals and removing the disease-causing variants (refined cohort). The efficiency of these data sets was assessed in a new set of 50 exomes against gnomAD and GenomeAsia. Our original cohort comprised 1455 individuals from 1203 families. The refined cohort had 836 unrelated individuals that retained 1,251,064 variants with 181,125 population-specific and 489,618 common variants. The allele frequencies from our cohort helped to define 97,609 rare variants in gnomAD and 44,520 rare variants in GenomeAsia as common variants in our population. Our variant dataset provided an additional 1.7% and 0.1% efficiency for prioritizing heterozygous and homozygous variants respectively for rare monogenic disorders. We observed additional 19 genes/human knockouts. We list carrier frequency for 142 recessive disorders. This is a large and useful resource of exonic variants for Indians. Despite limitations, datasets from patients are efficient tools for variant prioritization in a resource-limited setting.

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.

Clinical heterogeneity of the SLC26A4 gene in UAE patients with hearing loss and bioinformatics investigation of DFNB4/Pendred syndrome missense mutations

BACKGROUND

The development of next generation sequencing-based techniques showed an important progress in the identification of pathogenic variants related to monogenetic diseases with genetic and phenotypic heterogeneities. Hereditary hearing loss is considered as one of these heterogeneous diseases, given the large number of deafness causing genes, the different modes of inheritance and the phenotypic variabilities associated to the severity, age of onset and/or presence or absence of other clinical manifestations.

MATERIAL AND METHODS

In this study, we performed next-generation sequencing (NGS) in 51 UAE patients with hearing loss and no GJB2 mutations. In addition, we reviewed all reported SLC26A4 missense mutations with a confirmed DFNB4/Pendred syndrome phenotype and tried to find a genotype/phenotype correlation using different criteria.

RESULTS

By analyzing the NGS data, we identified one new SLC26A4 variant c.1150G > C (p.Glu384Gln) and one known SLC26A4 mutation c.716T > A (p.Val239Asp) in two different patients. Direct Sanger sequencing and segregation analyses confirmed the implication of both DNA variants in the deafness phenotype. Moreover, the clinical examination of both patients showed that one patient has syndromic deafness (Pendred syndrome) and the second one has non-syndromic deafness. The analysis of all confirmed missense mutations didn't reveal a complete genotype/phenotype correlation.

CONCLUSION

To the best of our knowledge, this is the first report of mutations associated with DFNB4/Pendred deafness in the GCC region.

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.

Induced Short-Term Hearing Loss due to Stimulation of Age-Related Factors by Intermittent Hypoxia, High-Fat Diet, and Galactose Injection

Age-related hearing loss (ARHL) is the most common sensory disorder among the elderly, associated with aging and auditory hair cell death due to oxidative-stress-induced mitochondrial dysfunction. Although transgenic mice and long-term aging induction cultures have been used to study ARHL, there are currently no ARHL animal models that can be stimulated by intermittent environmental changes. In this study, an ARHL animal model was established by inducing continuous oxidative stress to promote short-term aging of cells, determined on the basis of expression of hearing-loss-induced phenotypes and aging-related factors. The incidence of hearing loss was significantly higher in dual- and triple-exposure conditions than in intermittent hypoxic conditions, high-fat diet (HFD), or d-galactose injection alone. Continuous oxidative stress and HFD accelerated cellular aging. An increase in Ucp2, usually expressed during mitochondrial dysfunction, was observed. Expression of Cdh23, Slc26a4, Kcnq4, Myo7a, and Myo6, which are ARHL-related factors, were modified by oxidative stress in the cells of the hearing organ. We found that intermittent hypoxia, HFD, and galactose injection accelerated cellular aging in the short term. Thus, we anticipate that the development of this hearing loss animal model, which reflects the effects of intermittent environmental changes, will benefit future research on ARHL.

Whole exome sequencing identified mutations causing hearing loss in five consanguineous Pakistani families

Background

Hearing loss is the most common sensory defect, and it affects over 6% of the population worldwide. Approximately 50–60% of hearing loss patients are attributed to genetic causes. Currently, more than 100 genes have been reported to cause non-syndromic hearing loss. It is possible and efficient to screen all potential disease-causing genes for hereditary hearing loss by whole exome sequencing (WES).

Methods

We collected 5 consanguineous pedigrees from Pakistan with hearing loss and applied WES in selected patients for each pedigree, followed by bioinformatics analysis and Sanger validation to identify the causal genes.

Results

Variants in 7 genes were identified and validated in these pedigrees. We identified single candidate variant for 3 pedigrees: GIPC3 (c.937 T > C), LOXHD1 (c.6136G > A) and TMPRSS3 (c.941 T > C). The remaining 2 pedigrees each contained two candidate variants: TECTA (c.4045G > A) and MYO15A (c.3310G > T and c.9913G > C) for one pedigree and DFNB59 (c.494G > A) and TRIOBP (c.1952C > T) for the other pedigree. The candidate variants were validated in all available samples by Sanger sequencing.

Conclusion

The candidate variants in hearing-loss genes were validated to be co-segregated in the pedigrees, and they may indicate the aetiologies of hearing loss in such patients. We also suggest that WES may be a suitable strategy for hearing-loss gene screening in clinical detection.

Variations in the Mutational Spectrum in Nonsyndromic Hearing Impairment: A study of the Special Schools for the Deaf in Southern China

OBJECTIVES

To explore the characteristics of variations in patients with nonsyndromic hearing impairment (NSHI) in Southern China to supply a theoretical basis for screening, intervention, and prevention.

MATERIALS AND METHODS

A total of 634 hearing-impaired students from the special schools for the deaf and 220 normal-hearing individuals in South China were tested using an allele-specific polymerase chain reaction-based universal array, and the screened SLC26A4 mutation carrier was examined using computed tomography. The pathogenesis of deafness was analyzed using pathography and objective hearing tests.

RESULTS

In total, 151 patients with NSHI carried pathogenic mutations in the screening chip, and the carrier rate was 23.82% (151/634) in the studied population. Of the 151 screened carriers, 65 (10.25%) patients harbored homozygous or homoplasmy mutated genes associated with autosomal recessive hearing loss; 36 (5.68%) patients with mutant alleles were homozygous for the GJB2 c.235delC mutation and 27 (4.26%) were heterozygous. Furthermore, 18 (2.84%) patients were homozygous with mutant alleles for the SLC26A4 c.919-2A>G mutation and 43 (6.78%) were heterozygous; 7 (1.10%) patients were homoplasmy mutation carriers of MT-RNR1 gene. There was 1 SLC26A4 c.919-2A>G and 1 GJB2 c.235delC heterozygous mutant allele in the group of 220 normal-hearing individuals.

CONCLUSION

GJB2 and SLC26A4 were much more prevalent than MT-RNR1 and GJB3 in South China according to this gene chip. Minuscule differences in the mutation spectrum or prevalence of GJB2 c.235delC and SLC26A4 c.919-2A>G were found in our study; furthermore, a relatively high incidence of variations was observed among these individuals with NSHI.

DNAJC14 Ameliorates Inner Ear Degeneration in the DFNB4 Mouse Model

The His723Arg (H723R) mutation in SLC26A4, encoding pendrin, is the most prevalent mutation in East Asia, resulting in DFNB4, an autosomal recessive type of genetic hearing loss. Although the main pathological mechanism of H723R was identified as a protein-folding defect in pendrin, there is still no curative treatment for associated hearing loss. Here, we show that H723R-pendrin expression and activity are rescued by activation of the chaperonin DNAJC14. In vitro, DNAJC14 was activated via Japanese encephalitis virus (JEV) inoculation, and toxin-attenuated JEV rescued the surface expression and anion exchange activity of H723R-pendrin. Human H723R-pendrin transgenic mice (hH723R Tg) were established in a mouse slc26a4 knockout background, in which only hH723R-pendrin was expressed in the inner ear (Pax2-Cre dependent) to mimic human DFNB4 pathology. Crossing hH723R Tg with DNAJC14-overexpressing mice resulted in reduced cochlear hydrops and more preserved outer hair cells in the cochlea compared to those in hH723R Tg mice. Furthermore, the stria vascularis and spiral ligament were thicker and KCNJ10 expression was increased with DNAJC14 overexpression; however, hearing function and enlarged endolymphatic hydrops were not recovered. These results indicate that DNAJC14 overexpression ameliorates the cochlear degeneration caused by misfolded pendrin and might be a potential therapeutic target for DFNB4.

“Reversed polarization” of Na/K-ATPase—a sign of inverted transport in the human endolymphatic sac: a super-resolution structured illumination microscopy (SR-SIM) study

The human endolymphatic sac (ES) is believed to regulate inner ear fluid homeostasis and to be associated with Meniere’s disease (MD). We analyzed the ion transport protein sodium/potassium-ATPase (Na/K-ATPase) and its isoforms in the human ES using super-resolution structured illumination microscopy (SR-SIM). Human vestibular aqueducts were collected during trans-labyrinthine vestibular schwannoma surgery after obtaining ethical permission. Antibodies against various isoforms of Na/K-ATPase and additional solute-transporting proteins, believed to be essential for ion and fluid transport, were used for immunohistochemistry. A population of epithelial cells of the human ES strongly expressed Na/K-ATPase α1, β1, and β3 subunit isoforms in either the lateral/basolateral or apical plasma membrane domains. The β1 isoform was expressed in the lateral/basolateral plasma membranes in mostly large cylindrical cells, while β3 and α1 both were expressed with “reversed polarity” in the apical cell membrane in lower epithelial cells. The heterogeneous expression of Na/K-ATPase subunits substantiates earlier notions that the ES is a dynamic structure where epithelial cells show inverted epithelial transport. Dual absorption and secretion processes may regulate and maintain inner ear fluid homeostasis. These findings may shed new light on the etiology of endolymphatic hydrops and MD.

The genetic landscape of the human solute carrier (SLC) transporter superfamily

The human solute carrier (SLC) superfamily of transporters is comprised of over 400 membrane-bound proteins, and plays essential roles in a multitude of physiological and pharmacological processes. In addition, perturbation of SLC transporter function underlies numerous human diseases, which renders SLC transporters attractive drug targets. Common genetic polymorphisms in SLC genes have been associated with inter-individual differences in drug efficacy and toxicity. However, despite their tremendous clinical relevance, epidemiological data of these variants are mostly derived from heterogeneous cohorts of small sample size and the genetic SLC landscape beyond these common variants has not been comprehensively assessed. In this study, we analyzed Next-Generation Sequencing data from 141,456 individuals from seven major human populations to evaluate genetic variability, its functional consequences, and ethnogeographic patterns across the entire SLC superfamily of transporters. Importantly, of the 204,287 exonic single-nucleotide variants (SNVs) which we identified, 99.8% were present in less than 1% of analyzed alleles. Comprehensive computational analyses using 13 partially orthogonal algorithms that predict the functional impact of genetic variations based on sequence information, evolutionary conservation, structural considerations, and functional genomics data revealed that each individual genome harbors 29.7 variants with putative functional effects, of which rare variants account for 18%. Inter-ethnic variability was found to be extensive, and 83% of deleterious SLC variants were only identified in a single population. Interestingly, population-specific carrier frequencies of loss-of-function variants in SLC genes associated with recessive Mendelian disease recapitulated the ethnogeographic variation of the corresponding disorders, including cystinuria in Jewish individuals, type II citrullinemia in East Asians, and lysinuric protein intolerance in Finns, thus providing a powerful resource for clinical geneticists to inform about population-specific prevalence and allelic composition of Mendelian SLC diseases. In summary, we present the most comprehensive data set of SLC variability published to date, which can provide insights into inter-individual differences in SLC transporter function and guide the optimization of population-specific genotyping strategies in the bourgeoning fields of personalized medicine and precision public health.

Structural mechanism of the active bicarbonate transporter from cyanobacteria

Bicarbonate transporters play essential roles in pH homeostasis in mammals and photosynthesis in aquatic photoautotrophs. A number of bicarbonate transporters have been characterized, among which is BicA-a low-affinity, high-flux SLC26-family bicarbonate transporter involved in cyanobacterial CO₂-concentrating mechanisms (CCMs) that accumulate CO₂ and improve photosynthetic carbon fixation. Here, we report the three-dimensional structure of BicA from Synechocystis sp. PCC6803. Crystal structures of the transmembrane domain (BicA^TM) and the cytoplasmic STAS domain (BicA^STAS) of BicA were solved. BicA^TM was captured in an inward-facing HCO₃^--bound conformation and adopts a '7+7' fold monomer. HCO₃^- binds to a cytoplasm-facing hydrophilic pocket within the membrane. BicA^STAS is assembled as a compact homodimer structure and is required for the dimerization of BicA. The dimeric structure of BicA was further analysed using cryo-electron microscopy and physiological analysis of the full-length BicA, and may represent the physiological unit of SLC26-family transporters. Comparing the BicA^TM structure with the outward-facing transmembrane domain structures of other bicarbonate transporters suggests an elevator transport mechanism that is applicable to the SLC26/4 family of sodium-dependent bicarbonate transporters. This study advances our knowledge of the structures and functions of cyanobacterial bicarbonate transporters, and will inform strategies for bioengineering functional BicA in heterologous organisms to increase assimilation of CO₂.

A systematic review of SLC26A4 mutations causing hearing loss in the Iranian population

OBJECTIVES

The genetics of sensorineural hearing loss is characterized by a high degree of heterogeneity. In spite of this, mutations in the SLC26A4 gene, have been reported to be the second most common contributor after those of GJB2 in many populations. However, different results have been reported for the frequency of SLC26A4 mutations in Iran, which varies between 0 and 12.3%. Here, we have taken together and reviewed the spectrum and frequency of the reported SLC26A4 mutations to provide a comprehensive collection of data for SLC26A4 mutations and HL in the Iranian population and considered founder mutations.

METHODS

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

RESULTS

Nine studies involved 827 unrelated families were included and analyzed for the type and prevalence of the SLC26A4 gene mutations. Altogether 39 different genetic mutations were detected. SLC26A4 mutations were found to be 6.39% in the population studied which is significantly lower than that identified in the east Asia. However, c.1334T > G was the most common mutation accounting for 10% of the populations studied.

CONCLUSIONS

This data gives an overview of the SLC26A4 mutations in Iran, which could be used for screening, diagnostic programs of live births and genetic counseling.

Lessons From an Analysis of Newborn Hearing Screening Data for Children With Cochlear Implants

OBJECTIVES

The aims of the study are to identify the limitations of the current newborn hearing screening (NHS) programs and provide recommendations for better protocols.

STUDY DESIGN

Retrospective analysis.

SETTING

Tertiary referral center.

PATIENTS

The study participants were 185 children who received cochlear implants (CIs) at ≤5 years of age.

INTERVENTIONS

Therapeutic and rehabilitative.

MAIN OUTCOME MEASURES

The results of NHS, screening tools used, age, and hearing thresholds at which hearing loss was confirmed, causes of the hearing loss, age of CI insertion, aided pure-tone audiogram findings, and language development level were analyzed.

RESULTS

NHS data was available for 109 children, and 24 patients (22.0%) had passed NHS for both ears. Hearing loss was confirmed considerably later in children who had passed NHS than in children who were referred for further evaluation (p < 0.01). The most common cause for hearing loss in the NHS-pass group was SLC26A4 mutations (41.7%). Patients in the NHS-pass group received CIs considerably later than those in the NHS-referred group (p < 0.01). Among patients with SLC26A4 mutations, the language development level was significantly lower in the NHS-pass group than in the NHS-referred group (p < 0.01).

CONCLUSIONS

Careful counseling regarding NHS results is necessary for parents to understand that the absence of hearing loss at birth does not mean that the child will not develop hearing loss later in life. Genetic testing for SLC26A4 mutations may be necessary in regions with a high incidence of these mutations, such as East Asia.

A pathogenic variant in SLC26A4 is associated with Pendred syndrome in a consanguineous Iranian family

Objective: Hearing loss (HL) is a common sensory deficit with high phenotypic and genotypic heterogeneity. A large Iranian family with HL was genetically assessed in this study. Design: A proband from a consanguineous multiplex HL family from Iran was examined via Targeted Next-Generation Sequencing (TNGS). Sanger sequencing allowed the segregation analysis of the variant of interest and the investigation of its presence in a cohort of 50 ethnicity-matched healthy control individuals. The gene was previously associated with HL. Therefore, to determine whether the variant was specifically associated with Pendred Syndrome (PDS) or DFNB4, biochemical analyses, PTA, thyroid scans by Tc99m, perchlorate discharge test and high-resolution CT scan of the temporal bone were carried out on the affected family members. Study sample: Ten members of a large multiplex Iranian family with HL were recruited in this study. In addition, 50 unrelated healthy controls of the same ethnic group were randomly selected to genotype the variant. Results: A homozygous missense variant (NM_000441.1: c.1211C > T/p.Thr404Ile) in exon 10 was found segregating in the family. Based on the ACMG's guidelines, the variant was classified as pathogenic. Conclusion: This study expands the spectrum of SLC26A4 pathogenic variants in hearing loss.

A knock-in mouse model of Pendred syndrome with Slc26a4 L236P mutation

SLC26A4 gene mutations lead to Pendred syndrome and non-syndromic hearing loss (DFNB4). The mouse model is well used to study the pathology of Pendred syndrome, however, mice with different Slc26a4 mutations exhibit different phenotypes, and these mice have severe deafness and inner ear malformations that are not imitated less severely Human phenotype. In this study, we generated a knock-in mouse model of Pendred syndrome with Slc26a4 L236P mutation to mimic the most common mutation found in human. Some L236P mice were observed to have significant vestibular dysfunction including torticollis and circling, the giant otoconia and destruction of the otoconial membrane was observed in L236P mice. Unlike other profoundly deafness in Slc26a4 mouse model, L236P mice present mild to profound hearing loss, consistent with the hearing threshold, inner ear hair cells also lost from slight to significant. Together, these data demonstrate that the L236P mouse phenotype is more similar to the human phenotype and should be used as a tool for further research into the human Pendred syndrome.