Ultrarare heterozygous pathogenic variants of genes causing dominant forms of early-onset deafness underlie severe presbycusis

Presbycusis, or age-related hearing loss (ARHL), is a major public health issue. About half the phenotypic variance has been attributed to genetic factors. Here, we assessed the contribution to presbycusis of ultrarare pathogenic variants, considered indicative of Mendelian forms. We focused on severe presbycusis without environmental or comorbidity risk factors and studied multiplex family age-related hearing loss (mARHL) and simplex/sporadic age-related hearing loss (sARHL) cases and controls with normal hearing by whole-exome sequencing. Ultrarare variants (allele frequency [AF] < 0.0001) of 35 genes responsible for autosomal dominant early-onset forms of deafness, predicted to be pathogenic, were detected in 25.7% of mARHL and 22.7% of sARHL cases vs. 7.5% of controls (P = 0.001); half were previously unknown (AF < 0.000002). MYO6, MYO7A, PTPRQ, and TECTA variants were present in 8.9% of ARHL cases but less than 1% of controls. Evidence for a causal role of variants in presbycusis was provided by pathogenicity prediction programs, documented haploinsufficiency, three-dimensional structure/function analyses, cell biology experiments, and reported early effects. We also established Tmc1^N321I/+ mice, carrying the TMC1:p.(Asn327Ile) variant detected in an mARHL case, as a mouse model for a monogenic form of presbycusis. Deafness gene variants can thus result in a continuum of auditory phenotypes. Our findings demonstrate that the genetics of presbycusis is shaped by not only well-studied polygenic risk factors of small effect size revealed by common variants but also, ultrarare variants likely resulting in monogenic forms, thereby paving the way for treatment with emerging inner ear gene therapy.

Age-related hearing loss (ARHL), also known as presbycusis, is the most prevalent sensory impairment in the adult population and is 1 of the top 10 health conditions most frequently associated with disability in the elderly. According to the World Health Organization, 320 million people worldwide aged 65 and over currently suffer from hearing disability (1). Presbycusis is a progressive late-onset hearing impairment that begins after the age of 40 and mostly affects the perception of high-frequency sounds (2). Individuals initially encounter difficulties following conversations in noisy environments and localizing sound sources spatially, until they can no longer understand speech even in quiet environments (3). This disability leads to social isolation and desocialization, profoundly altering quality of life (4). Individuals face the threat of depression and cognitive decline (5, 6), resulting in a progressive loss of autonomy. There is growing evidence to suggest that hearing loss in and after middle age is the main modifiable risk factor for dementia (7).Patient management is currently based on prostheses—hearing aids and cochlear implants—which restore hearing to an acceptable level for understanding speech in relatively quiet environments, in most individuals (8). However, these devices are not very effective in noisy environments (9).Presbycusis was long thought to be a natural and inevitable consequence of aging, but like other aging processes, it actually depends on genetic and environmental factors and their interactions (10). Various environmental factors, such as noise overexposure, the use of ototoxic drugs and solvents, and smoking, have been identified as risk factors, as have several comorbid conditions, such as diabetes and hypertension (11, 12). The most prevalent environmental cause is noise overexposure, the impact of which is steadily increasing with the proportion of the world’s population living in overcrowded cities and inadequate controls over sound intensity, extending to recreational settings (13). Environmental factors are thought to account for about half the phenotypic variance of presbycusis (10). Heritability indices of 0.35 to 0.70 have been reported in studies based on hearing thresholds in twins (14), families (15, 16), or individuals with self-reported hearing impairment (17).Genetic traits and diseases represent a continuum, with the effect size of the variants involved being inversely related to the frequency of the disease-causing variant (18, 19). The spectrum ranges from monogenic diseases (attributable to one extremely rare variant with a very large effect size—100% penetrance), via near-Mendelian traits due to variants with incomplete penetrance, and conditions due to moderately rare variants of intermediate effect size to highly polygenic traits (hundreds of common variants involved, each having a very small effect size) (20). Genetic analyses have implicated several genes in presbycusis. Association studies have been performed with candidate genes selected on the basis of a putative or demonstrated role of the encoded proteins in the cochlea. For example, given the well-established role of oxidative stress induced by overexposure to noise, associations have been highlighted between presbycusis and null alleles or single-nucleotide polymorphisms (SNPs) of certain genes involved in redox homeostasis, such as GSTT1, GSTM1 (21, 22), NAT2 (21, 23, 24), CYP1A1 (21), and UCP2 (21). Similarly, the observation that women have better hearing than men, at least until menopause, led to the discovery of an association between ESRRG and ARHL in women (25). Association studies have also been conducted with genes responsible for early-adulthood deafness displaying autosomal dominant inheritance, autosomal dominant deafness (DFNA) forms of deafness, or congenital hearing impairment displaying autosomal recessive inheritance, autosomal recessive deafness (DFNB) forms of deafness. Indicative associations have been reported with KCNQ4 (DFNA2) (26), GRHL2 (DFNA28) (27, 28), ILDR1 (DFNB42), and EYA4 (DFNA10) (29). Pangenomic association studies were then performed in large cohorts of sporadic cases of presbycusis (30, 31). Genome-wide association studies (GWAS) were performed, assuming that presbycusis, as a common disorder, would probably involve common variants (minor allele frequency [AF] > 5%) with a small effect size. GWAS detected significant associations (P ≤ 5 × 10⁻⁸) between presbycusis and SNPs close to ISG20/ACAN (29), PCDH20 (32), ARHGEF28 (30), and SLC28A3 (32) and SNPs within TRIOBP (29), SIK3 (33), NID2 (30), CLRN2 (30), ARHGEF28 (30), EYA4 (30), and very recently, ILDR1 (30, 31). Furthermore, in a large GWAS study based on the UK Biobank (including data for more than 250,000 individuals between the ages of 40 and 69 y), 36 new loci were reported to be significantly associated with self-reported hearing difficulties or with the use of hearing aids (30). A recent analysis conducted and replicated in about 10,000 affected individuals identified associations with four additional genes (31). These candidate presbycusis-predisposing (CPP) genes were mostly identified on the basis of associations of ARHL with intragenic (mostly intronic) SNPs or SNPs located in close proximity to the gene. Finally, next-generation sequencing has identified monoallelic mutations predicted to be deleterious in NHERF1, SPATC1L (34, 35), and MYO6 (DFNB37) (36) in a few sporadic and familial cases of presbycusis. It has also been suggested that mutations affecting micro ribonucleic acids (miRNAs) (37, 38) and the mitochondrial genome (39, 40) are involved in presbycusis. Together, these studies suggest that presbycusis has a large polygenic component, involving many common genetic variants of small effect size, whereas a few reports have described monogenic or monogenic-like components involving very rare variants with a large effect size.Studies of common small-effect size variants are generally poorly efficient for achieving a mechanistic understanding of pathogenesis (41) unlike approaches based on large-effect size variants underlying Mendelian transmission. Furthermore, rapid progress has been made toward the development of inner ear gene therapy approaches, which are particularly suitable for treating monogenic forms of hearing impairment. We therefore investigated ultrarare variants as potential large-effect determinants likely to underlie monogenic forms of presbycusis. We used an approach focusing on severe ARHL with no identifiable risk factors or comorbidities. We selected variants in silico, based on both existing functional annotations and standard case–control comparisons of whole-exome sequencing (WES) (42) data, combined with various in silico and experimental functional tests to gain additional evidence of pathogenicity.     

Speech processing: from peripheral to hemispheric asymmetry of the auditory system

Language processing from the cochlea to auditory association cortices shows side-dependent specificities with an apparent left hemispheric dominance. The aim of this article was to propose to nonspeech specialists a didactic review of two complementary theories about hemispheric asymmetry in speech processing. Starting from anatomico-physiological and clinical observations of auditory asymmetry and interhemispheric connections, this review then exposes behavioral (dichotic listening paradigm) as well as functional (functional magnetic resonance imaging and positron emission tomography) experiments that assessed hemispheric specialization for speech processing. Even though speech at an early phonological level is regarded as being processed bilaterally, a left-hemispheric dominance exists for higher-level processing. This asymmetry may arise from a segregation of the speech signal, broken apart within nonprimary auditory areas in two distinct temporal integration windows--a fast one on the left and a slower one on the right--modeled through the asymmetric sampling in time theory or a spectro-temporal trade-off, with a higher temporal resolution in the left hemisphere and a higher spectral resolution in the right hemisphere, modeled through the spectral/temporal resolution trade-off theory. Both theories deal with the concept that lower-order tuning principles for acoustic signal might drive higher-order organization for speech processing. However, the precise nature, mechanisms, and origin of speech processing asymmetry are still being debated. Finally, an example of hemispheric asymmetry alteration, which has direct clinical implications, is given through the case of auditory aging that mixes peripheral disorder and modifications of central processing.     

Cochlear neuropathy in the rat exposed for a long period to moderate‐intensity noises

Damaging effects on the cochlea of high‐intensity acoustic overexposures have been extensively documented, but only few works have focused on the danger of moderate noise levels. Using scanning and transmission electron microscopy, we explored the noise‐induced neuroepithelial changes that occur in the cochlea of rats subjected to moderate intensities, 70 and 85 dB SPL, for an extended period of time (6 hr/day over 3 months). Although the full quota of outer and inner sensory hair cells remained present, we detected discrete abnormalities, likely resulting from metabolic impairment, in both types of hair cell within the basal region of the cochlea. In contrast, important noise‐dependent losses of spiral ganglion neurons had occurred. In addition, we found cytoplasmic accumulations of lipofuscin‐like aggregates in most of the surviving cochlear neurons. These results strongly suggest that noise levels comparable to those of certain working environments, with sufficient exposure duration, pose a severe risk to the cochlea. Moreover, our data support the notion that long‐duration exposure to moderate noise is a causative factor of presbycusis. © 2015 Wiley Periodicals, Inc.     

中医肾主耳理论的现代生物学研究进展与思路

“肾主耳”理论是中医藏象学说的重要内容,对耳鸣、耳聋的中医药治疗有重要的指导价值。以往的研究认为,甲状腺素、醛固酮、钙和铁等物质可能是中医肾与耳相关的物质基础。但长期以来受方法及技术手段的限制,肾主耳的研究仍然停留在这几个孤立的物质上,没有取得新的进展,不能很好地阐释中医肾主耳理论的现代生物学机制及科学内涵。近年来,’肾本质的研究进展以及现代生物学技术的飞速发展为中医肾主耳理论的研究提供了良好的契机。本文在对前期研究进展进行总结和分析的基础上,对肾主耳理论的现代生物学研究思路进行新的探讨。基于衰老是生理性肾虚的观点,本文认为,老年性聋是由于听觉系统衰老而产生的一种退行性疾病,也是机体衰老表现的一部分,老年性聋也可以看作是一种肾虚耳聋的模型。因此,结合肾本质的研究进展和思路,充分利用系统生物学技术,探讨老年性聋与中医肾虚的相关性及其物质基础,将为中医肾主耳理论的现代生物学研究提供崭新的内容。     

Progression of hearing loss and choice of hearing aids by patients in their 60s, 70s,and 80s and older: experience in the Japanese super-aged era

Abstract

Background: Demographic data of patients with sensorineural hearing loss (SNHL) in super-aged societies are still limited.

Aims/objectives: To report audiometric statistics of SNHL and hearing aid (HA) use in patients in their 60s, 70s, and 80s and older during the super-aged era.

Material and methods: Medical charts and audiograms of 2064 older patients with SNHL who visited a Japanese University Hospital in 2007–2018 were retrospectively reviewed. Among 270 patients referred to the HA service unit (HASU), the percentage of final decisions to continue using HAs was calculated.

Results: The average pure tone thresholds on initial visit to the clinic were 56.9, 60.6, 69.4, and 82.4?dB HL in patients in their 60s, 70s, 80s, and 90s, respectively. The rates of progression were 0.25, 0.87, 1.19, and 1.37?dB/year in patients in their 50s, 60s, 70s, and 80s, respectively. The percentage of patients in HASU who chose to use HAs did not differ among the 60s (59.3%), 70s (51.2%), and 80s and older (58.2%).

Conclusions and significance: The clinical picture of patients with SNHL in their 70s and 80s differs because progression accelerates exponentially through these ages. HAs can be recommended to older adult patients in all the age groups.     

Age-related changes in glycine receptor subunit composition and binding in dorsal cochlear nucleus

Age-related hearing loss, presbycusis, can be thought of, in part, as a slow progressive peripheral deafferentation. Previous studies suggest that certain deficits seen in presbycusis may partially result from functional loss of the inhibitory neurotransmitter glycine in dorsal cochlear nucleus (DCN). The present study assessed age-related behavioral gap detection changes and neurochemical changes of postsynaptic glycine receptor (GlyRs) subunits and their anchoring protein gephyrin in fusiform cells of young (7–11 months) and aged (28–33 months) Fischer brown Norway (FBN) rats. Aged rats showed significantly (20–30 dB) elevated auditory brainstem-evoked response thresholds across all tested frequencies and worse gap detection ability compared to young FBN rats. In situ hybridization and quantitative immunocytochemistry were used to measure GlyR subunit message and protein levels. There were significant age-related increases in the α₁ subunit message with significant age-related decreases in α₁ subunit protein. Gephyrin message and protein showed significant increases in aged DCN fusiform cells. The pharmacologic consequences of these age-related subunit changes were assessed using [³H] strychnine binding. In support of the age-related decrease of α₁ subunit protein levels in DCN, there was a significant age-related decrease in the total number of GlyR binding sites with no significant change in affinity. These age-related changes may reflect an effort to reestablish a homeostatic balance between excitation and inhibition impacting on DCN fusiform cells by downregulation of inhibitory function in the face of an age-related loss of peripheral input. Age-related decrease in presynaptic glycine release results in altered subunit composition and this may correlate with loss of temporal coding of the aged fusiform cell in DCN. The previously reported role for gephyrin in retrograde intracellular receptor subunit trafficking could contribute to the α₁ decrease in the face of increased message.     

RAGE和NF-kB及p21在小鼠螺旋神经节细胞的表达研究

目的：通过研究晚期糖基化终产物受体（RAGE）、核转录因子NF-xB、p21在幼、老年C57BL／6j小鼠螺旋神经节细胞（SGC）的表达，探讨老年性聋的发病机制。方法：将C57BL／6j小鼠分为2月龄、10月龄组各25只，分别行组织学切片观察耳蜗SGC形态结构，免疫组织化学检测RAGE、NF_xB、p21在SGC中的表达，利用IPP6图像分析软件计算平均光密度值，值越大，表达量越多。结果：①10月龄小鼠SGC数目明显比2月龄少，分别为（20±6）个和（39±5）个，差异有统计学意义（P〈0．01）；②RAGE在2月龄和10月龄小鼠耳蜗SGC平均光密度值分别为0．179±0．025和0．308±0．050；NF-”B在2月龄和lO月龄小鼠耳蜗SGC平均光密度值分别为0．181±0．045和0．335±0．120；p21在2月龄和10月龄小鼠耳蜗SGC平均光密度值分别为0．160±0．023和0．365±0．031，两组分别比较，差异均有统计学意义（P〈O．05）。结论：RAGE、NF-kB、p21在SGC中有表达且随年龄增大表达增多，推测RAGE、NF-xB、p21可能参与老年性聋的发病过程。     

老年性聋病因学研究进展及启示

PCR和分子杂交等技术的应用，使线粒体疾病的研究取得了重大进展，衰老和老年性聋与线粒体DNA突变的关系受到了许多研究人员的关注，线粒体功能的研究更使结构与功能研究结合起来。其中包含的辩证思想更带给我们启迪和思索。     

Early investigational drugs for hearing loss

Introduction: Sensorineural hearing loss (HL) is becoming a global phenomenon at an alarming rate. Nearly 600 million people have been estimated to have significant HL in at least one ear. There are several different causes of sensorineural HL included in this review of new investigational drugs for HL. They are noise-induced, drug-induced, sudden sensorineural HL, presbycusis and HL due to cytomegalovirus infections.

Areas covered: This review presents trends in research for new investigational drugs encompassing a variety of causes of HL. The studies presented here are the latest developments either in the research laboratories or in preclinical, Phase 0, Phase I or Phase II clinical trials for drugs targeting HL.

Expert opinion: While it is important that prophylactic measures are developed, it is extremely crucial that rescue strategies for unexpected or unavoidable cochlear insult be established. To achieve this goal for the development of drugs for HL, innovative strategies and extensive testing are required for progress from the bench to bedside. However, although a great deal of research needs to be done to achieve the ultimate goal of protecting the ear against acquired sensorineural HL, we are likely to see exciting breakthroughs in the near future.