Isolation of novel and known genes from a human fetal cochlear cDNA library using subtractive hybridization and differential screening

Demyelination and Na+ Channel Redistribution Underlie Auditory and Vestibular Dysfunction in PMP22-Null Mice

Altered expression of peripheral myelin protein 22 (PMP22) results in demyelinating peripheral neuropathy. PMP22 exhibits a highly restricted tissue distribution with marked expression in the myelinating Schwann cells of peripheral nerves. Auditory and vestibular Schwann cells and the afferent neurons also express PMP22, suggesting a unique role in hearing and balancing. Indeed, neuropathic patients diagnosed with PMP22-linked hereditary neuropathies often present with auditory and balance deficits, an understudied clinical complication. To investigate the mechanism by which abnormal expression of PMP22 may cause auditory and vestibular deficits, we studied gene-targeted PMP22-null mice. PMP22-null mice exhibit an unsteady gait, have difficulty maintaining balance, and live for only ∼3-5 weeks relative to unaffected littermates. Histological analysis of the inner ear revealed reduced auditory and vestibular afferent nerve myelination and profound Na+ channel redistribution without PMP22. Yet, Na+ current density was unaltered, in stark contrast to increased K+ current density. Atypical postsynaptic densities and a range of neuronal abnormalities in the organ of Corti were also identified. Analyses of auditory brainstem responses (ABRs) and vestibular sensory-evoked potential (VsEP) revealed that PMP22-null mice had auditory and vestibular hypofunction. These results demonstrate that PMP22 is required for hearing and balance, and the protein is indispensable for the formation and maintenance of myelin in the peripheral arm of the eighth nerve. Our findings indicate that myelin abnormalities and altered signal propagation in the peripheral arm of the auditory nerve are likely causes of auditory deficits in patients with PMP22-linked neuropathies.

Genetic background in late-onset sensorineural hearing loss patients

Genetic testing for congenital or early-onset hearing loss patients has become a common diagnostic option in many countries. On the other hand, there are few late-onset hearing loss patients receiving genetic testing, as late-onset hearing loss is believed to be a complex disorder and the diagnostic rate for genetic testing in late-onset patients is lower than that for the congenital cases. To date, the etiology of late-onset hearing loss is largely unknown. In the present study, we recruited 48 unrelated Japanese patients with late-onset bilateral sensorineural hearing loss, and performed genetic analysis of 63 known deafness gene using massively parallel DNA sequencing. As a result, we identified 25 possibly causative variants in 29 patients (60.4%). The present results clearly indicated that various genes are involved in late-onset hearing loss and a significant portion of cases of late-onset hearing loss is due to genetic causes. In addition, we identified two interesting cases for whom we could expand the phenotypic description. One case with a novel MYO7A variant showed a milder phenotype with progressive hearing loss and late-onset retinitis pigmentosa. The other case presented with Stickler syndrome with a mild phenotype caused by a homozygous frameshift COL9A3 variant. In conclusion, comprehensive genetic testing for late-onset hearing loss patients is necessary to obtain accurate diagnosis and to provide more appropriate treatment for these patients.

LCCL peptide cleavage after noise exposure exacerbates hearing loss and is associated with the monocyte infiltration in the cochlea

Acoustic trauma induces an inflammatory response in the cochlea, resulting in debilitating hearing function. Clinically, amelioration of inflammation substantially prevents noise-induced hearing loss. The Limulus factor C, Cochlin, and Lgl1 (LCCL) peptide plays an important role in innate immunity during bacteria-induced inflammation in the cochlea. We aimed to investigate the LCCL-induced innate immune response to noise exposure and its impact on hearing function.

METHODS

We used Coch (encodes cochlin harboring LCCL peptide) knock-out and p.G88E knock-in mice to compare the immune responses before and after noise exposure. We explored their hearing function and hair cell degeneration. Moreover, we investigated distinct characteristics of immune responses upon noise exposure using flow cytometry and RNA sequencing.

RESULTS

One day after noise exposure, the LCCL peptide cleaved from cochlin increased over time in the perilymph space. Both Coch^-/- and Coch^G88E/G88E mutant mice revealed more preserved hearing following acoustic trauma compared to wild-type mice. The outer hair cells were more preserved in Coch^-/- than in wild-type mice upon noise exposure. The RNA sequencing data demonstrated significantly upregulated cell migration gene ontology in wild-type mice than in Coch^-/- mice following noise exposure, indicating that the infiltration of immune cells was dependent on cochlin. Notably, infiltrated monocytes from blood (C11b⁺/Ly6G^-/Ly6C⁺) were remarkably higher in wild-type mice than in Coch^-/- mice at 1 day after noise exposure.

CONCLUSIONS

Noise-induced hearing loss was attributed to over-stimulated cochlin, and led to the cleavage and secretion of LCCL peptide in the cochlea. The LCCL peptide recruited more monocytes from the blood vessels upon noise stimulation, thus highlighting a novel therapeutic target for noise-induced hearing loss.

Genotype-phenotype Correlation Study in a Large Series of Patients Carrying the p.Pro51Ser (p.P51S) Variant in COCH (DFNA9): Part I-A Cross-sectional Study of Hearing Function in 111 Carriers

INTRODUCTION

DFNA9 is characterized by adult-onset progressive sensorineural hearing loss (SNHL) and vestibular impairment. More than 15 years ago, genotype-phenotype correlation studies estimated the initial age of hearing deterioration in the fourth to fifth decade (ranging from 32 to 43 years). However, these analyses were based on relatively limited numbers of mainly symptomatic carriers using markedly different methodologies. The starting point for the hearing deterioration is more correctly determined with larger numbers of carriers and with a more clearly defined starting point of the hearing deterioration.

AIM

The aim of this study was to determine milestone ages (start and maximal hearing deterioration, potential eligibility for hearing aids and cochlear implants based on pure-tone average [PTA]) in a large series of p.Pro51Ser COCH variant carriers. The degree of individual interaural asymmetry and the degree of variability (interquartile range) with which the hearing deterioration progresses across ages were also studied, and age-related typical audiograms (ARTA) were constructed.

MATERIAL AND METHODS

One hundred eleven Belgian and Dutch p.P51S variant carriers were identified and recruited for audiological investigation. Their hearing thresholds were compared with p50th, p95th, and p97.5th percentile values of presbyacusis (ISO 7029 standards). The onset and degree of hearing deterioration were defined and assessed for each frequency and with three PTAs (PTA0.5-4 [0.5, 1, 2, and 4 kHz]; PTA4-8 [4 and 8 kHz]; and PTA6-8 [6 and 8 kHz]). The milestones ages were derived from nonlinear regression model of hearing thresholds against age, for male and female carriers separately, because of different age-referenced limits. Interaural right-left asymmetry was assessed, and variability of hearing thresholds were calculated using interquartile range. ARTAs were built with both observed data and a prediction model.

RESULTS

Hearing dysfunction in p.P51S carriers begins at about 38 years of age (ranging from 28 to 43 years) on average in female and 46 years (ranging from 42 to 49 years) in male carriers (third decade: female, fifth decade: male carriers), depending on the hearing frequency and with differences in deterioration sequence between both genders. These differences, however, were mainly due to more stringent age-referenced limits for men. In contrast, predictions (ARTA) did not show any difference of phenotypic expression between genders. At about 48 to 50 years of age on average, the majority of DFNA9 patients may need conventional hearing aids (PTA ≥ 40 dB HL), whereas this is about 56 to 59 years for cochlear implants (PTA ≥ 70 dB HL). There is a high degree of individual interaural asymmetry and interindividual variability throughout all ages.

CONCLUSION

This study demonstrates that the onset of sensorineural hearing deterioration starts in the third decade and probably even earlier. Regardless of differences in estimates, DFNA9 expresses similarly in male and female carriers, but male carriers are much more difficult to identify in early stages of the disease. Comprehensive assessment of the natural course of DFNA9 is of particular interest to predict the age of onset or critical period of most significant function deterioration in individual carriers of the pathogenic variant. This will help to design studies in the search for disease-modifying therapies.

Genotype-Phenotype Correlation Study in a Large Series of Patients Carrying the p.Pro51Ser (p.P51S) Variant in COCH (DFNA9) Part II: A Prospective Cross-Sectional Study of the Vestibular Phenotype in 111 Carriers

INTRODUCTION

DFNA9 is characterized by adult-onset hearing loss and evolution toward bilateral vestibulopathy (BVP). The genotype-phenotype correlation studies were conducted 15 years ago. However, their conclusions were mainly based on symptomatic carriers and the vestibular data exclusively derived from the horizontal (lateral) semicircular canal (SCC). The last decade was marked by the emergence of new clinical diagnostic tools, such as the video head impulse test (vHIT) and vestibular-evoked myogenic evoked potentials (VEMPs), expanding our evaluation to all six SCCs and the otolith organs (saccule and utricule).

AIM

The aim of this study was to comprehensively evaluate vestibular function in the largest series presymptomatic as well as symptomatic p.P51S variant carriers, to determine which labyrinthine part shows the first signs of deterioration and which SCC function declines at first and to determine the age at which p.P51S variant carriers develop caloric areflexia on VNG and vHIT vestibulo-ocular reflex (VOR)-gain dysfunction as defined by the Barany Society criteria for BVP.

MATERIAL AND METHODS

One hundred eleven p.P51S variant carriers were included. The following vestibular function tests were applied in two different centers: ENG/VNG, vHIT, and VEMPs. The following parameters were analyzed: age (years), hearing loss (pure-tone average of 0.5-4 kHz [PTA0.5-4, dB HL]), sum of maximal peak slow-phase eye velocity obtained with bi-thermal (30°C and 44°C, water irrigation; 25°C and 44°C, air irrigation) caloric test (°/s), vHIT VOR-gain on LSCC, superior SCC and posterior SCC, C-VEMP both numerical (threshold, dB nHL) and categorical (present or absent), and O-VEMP as categorical (present or absent). The age of onset of vestibular dysfunction was determined both with categorical (onset in decades using Box & Whisker plots) and numeric approach (onset in years using regression analysis). The same method was applied for determining the age at which vestibular function declined beyond the limits of BVP, as defined by the Barany Society.

RESULTS

With the categorical approach, otolith function was declining first (3rd decade), followed by caloric response (5th decade) and vHIT VOR-gains (5th-6th decade). Estimated age of onset showed that the deterioration began with C-VEMP activity (31 years), followed by caloric responses (water irrigation) (35 years) and ended with vHIT VOR-gains (48-57 years). Hearing deterioration started earlier than vestibular deterioration in female carriers, which is different from earlier reports. BVP was predicted at about 53 years of age on average with VNG caloric gain (water irrigation) and between 47 and 57 years of age for the three SCCs. Loss of C-VEMP response was estimated at about 46 years of age.

CONCLUSION

Former hypothesis of vestibular decline preceding hearing deterioration by 9 years was confirmed by the numeric approach, but this was less obvious with the categorical approach. Wide confidence intervals of the regression models may explain deviation of the fits from true relationship. There is a typical vestibular deterioration hierarchy in p.P51S variant carriers. To further refine the present findings, a prospective longitudinal study of the auditory and vestibular phenotype may help to get even better insights in this matter.

Cochlin-cleaved LCCL is a dual-armed regulator of the innate immune response in the cochlea during inflammation

The inner ear is a complex and delicate structure composed of the cochlea and the vestibular system. To maintain normal auditory function, strict homeostasis of the inner ear is needed. A proper immune response against infection, thus, is crucial. Also, since excessive immune reaction can easily damage the normal architecture within the inner ear, the immune response should be fine regulated. The exact mechanism how the inner ear’s immune response, specifically the innate immunity, is regulated was unknown. Recently, we reported a protein selectively localized in the inner ear during bacterial infection, named cochlin, as a possible mediator of such regulation. In this review, the immunological function of cochlin and the mechanism behind its role within inner ear immunity is sum-marized. Cochlin regulates innate immunity by physically en-trapping pathogens within scala tympani and recruiting innate immune cells. Such mechanism enables efficient removal of pathogen while preserving the normal inner ear structure from inflammatory damage.

Predictive Sensitivity and Concordance of Machine-learning Tools for Diagnosing DFNA9 in a Large Series of p.Pro51Ser Variant Carriers in the COCH-gene

OBJECTIVE

In this study we aimed to evaluate the predictive cross-sectional sensitivity and longitudinal concordance of a machine-learning algorithm in a series of genetically confirmed p.(Pro51Ser) variant carriers (DFNA9).

STUDY DESIGN

Cross-sectional study.

SETTING

Tertiary and secondary referral center.

PATIENTS

Audiograms of 111 subjects with the p.(Pro51Ser) mutation in the COCH-gene were analyzed cross-sectionally. A subset of 17 subjects with repeated audiograms were used for longitudinal analysis.

INTERVENTIONS

All audiological thresholds were run through the web-based AudioGene v4.0 software.

MAIN OUTCOME MEASURES

Sensitivity for accurate prediction of DFNA9 for cross-sectional data and concordance of correct prediction for longitudinal auditory data.

RESULTS

DFNA9 was predicted with a sensitivity of 93.7% in a series of 222 cross-sectionally collected audiological thresholds (76.1% as first gene locus). When using the hearing thresholds of the best ear, the sensitivity was 94.6%. The sensitivity was significantly higher in DFNA9 patients aged younger than 40 and aged 60 years or older, compared to the age group of 40 to 59 years, with resp. 97.6% (p < 0.0001) and 98.8% (p < 0.0001) accurate predictions. An average concordance of 91.6% was found to show the same response in all successive longitudinal audiometric data per patient.

CONCLUSIONS

Audioprofiling software can accurately predict DFNA9 in an area with a high prevalence of confirmed carriers of the p.(Pro51Ser) variant in the COCH-gene. This algorithm yields high promises for helping clinicians in directing genetic testing in case of a strong family history of progressive hearing loss, especially for very young and old carriers.

Cochlin Deficiency Protects Against Noise-Induced Hearing Loss

Cochlin is the most abundant protein in the inner ear. To study its function in response to noise trauma, we exposed adolescent wild-type (Coch +/+ ) and cochlin knock-out (Coch -/-) mice to noise (8-16 kHz, 103 dB SPL, 2 h) that causes a permanent threshold shift and hair cell loss. Two weeks after noise exposure, Coch-/- mice had substantially less elevation in noise-induced auditory thresholds and hair cell loss than Coch + / + mice, consistent with cochlin deficiency providing protection from noise trauma. Comparison of pre-noise exposure thresholds of auditory brain stem responses (ABRs) and distortion product otoacoustic emissions (DPOAEs) in Coch-/- mice and Coch + / + littermates revealed a small and significant elevation in thresholds of Coch-/- mice, overall consistent with a small conductive hearing loss in Coch-/- mice. We show quantitatively that the pro-inflammatory component of cochlin, LCCL, is upregulated after noise exposure in perilymph of wild-type mice compared to unexposed mice, as is the enzyme catalyzing LCCL release, aggrecanase1, encoded by Adamts4. We further show that upregulation of pro-inflammatory cytokines in perilymph and cochlear soft-tissue after noise exposure is lower in cochlin knock-out than wild-type mice. Taken together, our data demonstrate for the first time that cochlin deficiency results in conductive hearing loss that protects against physiologic and molecular effects of noise trauma.

A Novel COCH Mutation Affects the vWFA2 Domain and Leads to a Relatively Mild DFNA9 Phenotype

OBJECTIVE

To study the genotype and phenotype of a Dutch family with autosomal dominantly inherited hearing loss.

STUDY DESIGN

Genotype-phenotype correlation study. Genetic analysis consisted of linkage analysis, variable number of tandem repeats analysis, and Sanger sequencing. Audiovestibular function was examined. Regression analysis was performed on pure tone audiometry and speech recognition scores and correlated with the age and/or level of hearing loss.

SETTING

Tertiary referral center.

PATIENTS

A large Dutch family presenting with sensorineural hearing loss.

MAIN OUTCOME MEASURES

Identification of the underlying genetic defect of the hearing loss in this family. Results of pure tone and speech audiometry, onset age, progression of hearing loss and vestibular (dys)function.

RESULTS

A novel mutation in COCH, c.1312C > T p.(Arg438Cys), cosegregates with hearing loss and a variable degree of vestibular (dys)function in this family. The reported mean age of onset of hearing loss is 33 years (range, 18-49 yr). Hearing loss primarily affects higher frequencies and its progression is relatively mild (0.8 dB/yr). Speech perception is remarkably well preserved in affected family members when compared with other DFNA9 families with different COCH mutations.

CONCLUSION

These findings expand the genotypic and phenotypic spectrum of DFNA9. The c.1312C > T mutation, which affects the vWFA2 domain, causes a relatively mild audiovestibular phenotype when compared with other COCH mutations.

Novel loss-of-function mutations in COCH cause autosomal recessive nonsyndromic hearing loss

COCH is the most abundantly expressed gene in the cochlea. Unsurprisingly, mutations in COCH underly hearing loss in mice and humans. Two forms of hearing loss are linked to mutations in COCH, the well-established autosomal dominant nonsyndromic hearing loss, with or without vestibular dysfunction (DFNA9) via a gain-of-function/dominant-negative mechanism, and more recently autosomal recessive nonsyndromic hearing loss (DFNB110) via nonsense variants. Using a combination of targeted gene panels, exome sequencing, and functional studies, we identified four novel pathogenic variants (two nonsense variants, one missense, and one inframe deletion) in COCH as the cause of autosomal recessive hearing loss in a multi-ethnic cohort. To investigate whether the non-truncating variants exert their effect via a loss-of-function mechanism, we used minigene splicing assays. Our data showed both the missense and inframe deletion variants altered RNA splicing by creating an exon splicing silencer and abolishing an exon splicing enhancer, respectively. Both variants create frameshifts and are predicted to result in a null allele. This study confirms the involvement of loss-of-function mutations in COCH in autosomal recessive nonsyndromic hearing loss, expands the mutational landscape of DFNB110 to include coding variants that alter RNA splicing, and highlights the need to investigate the effect of coding variants on RNA splicing.

Cochlear involvement in patients with systemic autoimmune rheumatic diseases: a clinical and laboratory comparative study

PURPOSE

Inner ear involvement has been reported in systemic rheumatic disease while detection of cochlin-specific antibodies has been reported in patients with idiopatic sensorineural hearing loss, suggesting cochlin's strong link to autoimmune hearing loss. The aim of this cross-sectional study was to calculate the prevalence of sensorineural hearing loss (SNHL) in patients with systemic rheumatic diseases, and to investigate any potential correlation with human antibodies to cochlin.

METHODS

Patients with rheumatoid arthritis (RA), systemic lupus erythematosus (SLE), Sjogren's syndrome (SS) and systemic sclerosis (SSc) according to the criteria of American College of Rheumatology were included in the study. All patients underwent a complete ear-nose-throat physical examination and audiological evaluation with pure tone audiometry and impedance audiometry. Pure tone average was calculated, taking as a starting point the hearing loss in dB according to the recommendation 02/1 of "Bureau International d' Audiophonologie" (BIAP) so as an average hearing threshold value. Sera of all patients were tested for the presence of IgG antibodies to human cochline (COCH-IgG). Sex and age-matched healthy subjects were included as controls to each group.

RESULTS

A total of 133 patients were studied; 60 with RA, 41 with SLE, 24 with SS and 8 with SSc. 61.4% of patients reported vertigo, 41% hyperacousis, 39% hearing loss, 38% tinnitus, 37.9% headache and 2.1% sensation of ear pressure with unremarkable otoscopy. The prevalence of SNHL calculated for patients affected by RA, SLE, SS and SSc was 66.6%, 31.71%, 54.17%, and 75% respectively. The calculated average hearing thresholds value in RA was increased in comparison to SLE (p < 0.05). In addition it was also higher in patients with RA and secondary SS, in comparison to RA patients (p > 0.05). There was statistically significant correlation of average hearing threshold with disease activity score 28 (DAS28) in RA, but no correlation observed with disease activity index (SLEDAI) in SLE. COCH-IgG antibodies were detected in only two samples. The results were compared with those of their respective sex and age-matched healthy subjects.

CONCLUSION

Our study revealed increased prevalence of SNHL in patients with systemic autoimmune rheumatic disease but no correlation of hearing loss with COCHIgG antibodies. The mechanism of inner ear damage remains unknown; thus, additional prospective studies will be needed to elucidate its pathogenesis.

Genetic Hearing Loss and Gene Therapy

Genetic hearing loss crosses almost all the categories of hearing loss which includes the following: conductive, sensory, and neural; syndromic and nonsyndromic; congenital, progressive, and adult onset; high-frequency, low-frequency, or mixed frequency; mild or profound; and recessive, dominant, or sex-linked. Genes play a role in almost half of all cases of hearing loss but effective treatment options are very limited. Genetic hearing loss is considered to be extremely genetically heterogeneous. The advancements in genomics have been instrumental to the identification of more than 6,000 causative variants in more than 150 genes causing hearing loss. Identification of genes for hearing impairment provides an increased insight into the normal development and function of cells in the auditory system. These defective genes will ultimately be important therapeutic targets. However, the auditory system is extremely complex which requires tremendous advances in gene therapy including gene vectors, routes of administration, and therapeutic approaches. This review summarizes and discusses recent advances in elucidating the genomics of genetic hearing loss and technologies aimed at developing a gene therapy that may become a treatment option for in the near future.

Intracellular Regulome Variability Along the Organ of Corti: Evidence, Approaches, Challenges, and Perspective

The mammalian hearing organ is a regular array of two types of hair cells (HCs) surrounded by six types of supporting cells. Along the tonotopic axis, this conserved radial array of cell types shows longitudinal variations to enhance the tuning properties of basilar membrane. We present the current evidence supporting the hypothesis that quantitative local variations in gene expression profiles are responsible for local cell responses to global gene manipulations. With the advent of next generation sequencing and the unprecedented array of technologies offering high throughput analyses at the single cell level, transcriptomics will become a common tool to enhance our understanding of the inner ear. We provide an overview of the approaches and landmark studies undertaken to date to analyze single cell variations in the organ of Corti and discuss the current limitations. We next provide an overview of the complexity of known regulatory mechanisms in the inner ear. These mechanisms are tightly regulated temporally and spatially at the transcription, RNA-splicing, mRNA-regulation, and translation levels. Understanding the intricacies of regulatory mechanisms at play in the inner ear will require the use of complementary approaches, and most probably, a combinatorial strategy coupling transcriptomics, proteomics, and epigenomics technologies. We highlight how these data, in conjunction with recent insights into molecular cell transformation, can advance attempts to restore lost hair cells.

Bi-allelic inactivating variants in the COCH gene cause autosomal recessive prelingual hearing impairment

Pathogenic variant in COCH are a known cause of DFNA9 autosomal dominant progressive hearing loss and vestibular dysfunction with adult onset. Hitherto, only dominant nonsynonymous variants and in-frame deletions with a presumed dominant negative or gain-of-function effect have been described. Here, we describe two brothers with congenital prelingual deafness and a homozygous nonsense c.292C>T(p.Arg98*) COCH variant, suggesting a loss-of-function effect. Vestibular dysfunction starting in the first decade was observed in the older patient. The heterozygous parents and sibling have normal hearing and vestibular function, except for the mother, who shows vestibular hyporeflexia and abnormal smooth pursuit tests, most likely due to concomitant disease. This is the first report of autosomal recessive inheritance of cochlea-vestibular dysfunction caused by a pathogenic variant in the COCH gene. An earlier onset of hearing impairment and vestibular dysfunction compared to the dominant hearing loss causing COCH variants is observed.

Molecular study of patients with auditory neuropathy

Auditory neuropathy is a type of hearing loss that constitutes a change in the conduct of the auditory stimulus by the involvement of inner hair cells or auditory nerve synapses. It is characterized by the absence or alteration of waves in the examination of brainstem auditory evoked potentials, with otoacoustic and/or cochlear microphonic issues. At present, four loci associated with non‑syndromic auditory neuropathy have been mapped: Autosomal recessive deafness‑9 [DFNB9; the otoferlin (OTOF) gene] and autosomal recessive deafness‑59 [DFNB59; the pejvakin (PJVK) gene], associated with autosomal recessive inheritance; the autosomal dominant auditory neuropathy gene [AUNA1; the diaphanous‑3 (DIAPH3) gene]; and AUNX1, linked to chromosome X. Furthermore, mutations of connexin 26 [the gap junction β2 (GJB2) gene] have also been associated with the disease. OTOF gene mutations exert a significant role in auditory neuropathy. In excess of 80 pathogenic mutations have been identified in individuals with non‑syndromic deafness in populations of different origins, with an emphasis on the p.Q829X mutation, which was found in ~3% of cases of deafness in the Spanish population. The identification of genetic alterations responsible for auditory neuropathy is one of the challenges contributing to understand the molecular bases of the different phenotypes of hearing loss. Thus, the present study aimed to investigate molecular changes in the OTOF gene in patients with auditory neuropathy, and to develop a DNA chip for the molecular diagnosis of auditory neuropathy using mass spectrometry for genotyping. Genetic alterations were investigated in 47 patients with hearing loss and clinical diagnosis of auditory neuropathy, and the c.35delG mutation in the GJB2 gene was identified in three homozygous patients, and the heterozygous parents of one of these cases. Additionally, OTOF gene mutations were tracked by complete sequencing of 48 exons, although these results are still preliminary. Studying the genetic basis of auditory neuropathy is of utmost importance for obtaining a differential diagnosis, developing more specific treatments and more accurate genetic counseling.

A Novel Locus Harbouring a Functional CD164 Nonsense Mutation Identified in a Large Danish Family with Nonsyndromic Hearing Impairment

Nonsyndromic hearing impairment (NSHI) is a highly heterogeneous condition with more than eighty known causative genes. However, in the clinical setting, a large number of NSHI families have unexplained etiology, suggesting that there are many more genes to be identified. In this study we used SNP-based linkage analysis and follow up microsatellite markers to identify a novel locus (DFNA66) on chromosome 6q15-21 (LOD 5.1) in a large Danish family with dominantly inherited NSHI. By locus specific capture and next-generation sequencing, we identified a c.574C>T heterozygous nonsense mutation (p.R192*) in CD164. This gene encodes a 197 amino acid transmembrane sialomucin (known as endolyn, MUC-24 or CD164), which is widely expressed and involved in cell adhesion and migration. The mutation segregated with the phenotype and was absent in 1200 Danish control individuals and in databases with whole-genome and exome sequence data. The predicted effect of the mutation was a truncation of the last six C-terminal residues of the cytoplasmic tail of CD164, including a highly conserved canonical sorting motif (YXXФ). In whole blood from an affected individual, we found by RT-PCR both the wild-type and the mutated transcript suggesting that the mutant transcript escapes nonsense mediated decay. Functional studies in HEK cells demonstrated that the truncated protein was almost completely retained on the plasma cell membrane in contrast to the wild-type protein, which targeted primarily to the endo-lysosomal compartments, implicating failed endocytosis as a possible disease mechanism. In the mouse ear, we found CD164 expressed in the inner and outer hair cells of the organ of Corti, as well as in other locations in the cochlear duct. In conclusion, we have identified a new DFNA locus located on chromosome 6q15-21 and implicated CD164 as a novel gene for hearing impairment.

Cochlin in normal middle ear and abnormal middle ear deposits in DFNA9 and Coch (G88E/G88E) mice

DFNA9 sensorineural hearing loss and vestibular disorder, caused by mutations in COCH, has a unique identifying histopathology including prominent acellular deposits in cochlear and vestibular labyrinths. A recent study has shown presence of deposits also in middle ear structures of DFNA9-affected individuals (McCall et al., J Assoc Res Otolaryngol 12:141-149, 2004). To investigate the possible role of cochlin in the middle ear and in relation to aggregate formation, we evaluated middle ear histopathology in our Coch knock-in (Coch (G88E/G88E) ) mouse model, which harbors one of the DFNA9-causative mutations. Our findings reveal accumulation of acellular deposits in the incudomalleal and incudostapedial joints in Coch (G88E/G88E) mice, similar to those found in human DFNA9-affected temporal bones. Aggregates are absent in negative control Coch (+/+) and Coch (-/-) mice. Thickening of the tympanic membrane (TM) found in humans with DFNA9 was not appreciably detected in Coch (G88E/G88E) mice at the evaluated age. We investigated cochlin localization first in the Coch (+/+)mouse and in normal human middle ears, and found prominent and specific cochlin staining in the incudomalleal joint, incudostapedial joint, and the pars tensa of the TM, which are the three sites where abnormal deposits are detected in DFNA9-affected middle ears. Cochlin immunostaining of Coch (G88E/G88E) and DFNA9-affected middle ears showed mutant cochlin localization within areas of aggregates. Cochlin staining was heterogeneous throughout DFNA9 middle ear deposits, which appear as unorganized and overlapping mixtures of both eosinophilic and basophilic substances. Immunostaining for type II collagen colocalized with cochlin in pars tensa of the tympanic membrane. In contrast, immunostaining for type II collagen did not overlap with cochlin in interossicular joints, where type II collagen was localized in the region of the chondrocytes, but not in the thin layer of the articular surface of the ossicles nor in the eosinophilic deposits with specific cochlin staining.

Cochlin produced by follicular dendritic cells promotes antibacterial innate immunity

Cochlin, an extracellular matrix protein, shares homologies with the Factor C, a serine protease found in horseshoe crabs, which is critical for antibacterial responses. Mutations in the COCH gene are responsible for human DFNA9 syndrome, a disorder characterized by neurodegeneration of the inner ear that leads to hearing loss and vestibular impairments. The physiological function of cochlin, however, is unknown. Here, we report that cochlin is specifically expressed by follicular dendritic cells and selectively localized in the fine extracellular network of conduits in the spleen and lymph nodes. During inflammation, cochlin was cleaved by aggrecanases and secreted into blood circulation. In models of lung infection with Pseudomonas aeruginosa and Staphylococcus aureus, Coch(-/-) mice show reduced survival linked to defects in local cytokine production, recruitment of immune effector cells, and bacterial clearance. By producing cochlin, FDCs thus contribute to the innate immune response in defense against bacteria.

Research resource: identification of novel coregulators specific for thyroid hormone receptor-β2

Thyroid hormone receptors (TRs) are expressed as a series of interrelated isoforms that perform distinct biological roles. The TRβ2 isoform is found predominantly in the hypothalamus, pituitary, retina, and cochlea and displays unique transcriptional properties relative to the other TR isoforms. To more fully understand the isoform-specific biological and molecular properties of TRβ2, we have identified a series of previously unrecognized proteins that selectively interact with TRβ2 compared with the more widely expressed TRβ1. Several of these proteins preferentially enhance the transcriptional activity of TRβ2 when coexpressed in cells and are likely to represent novel, isoform-specific coactivators. Additional proteins were also identified in our screen that bind equally to TRβ1 and TRβ2 and may function as isoform-independent auxiliary proteins for these and/or other nuclear receptors. We propose that a combination of isoform-specific recruitment and tissue-specific expression of these newly identified coregulator candidates serves to customize TR function for different biological purposes in different cell types.

RNA preservation in decalcified cochlear samples

HYPOTHESIS

Decalcification of cochlear samples in Morse's solution after methacarn fixation provides greater RNA quantification and morphologic preservation of cochlear structures as compared with EDTA and formic acid decalcifying solutions after methacarn fixation.

BACKGROUND

A variety of fixatives and decalcifying agents can fragment or chemically alter RNA in samples inhibiting their isolation and quantification. Morphologic alterations can also be observed in light microscopy analyses. The cochlea is embedded in the bone; hence, fixation and decalcification steps are mandatory to obtain histologic sections and preserve the cochlea for morphologic evaluation.

METHODS

Cochlear samples obtained in a RNase-free environment were processed in 4 combinations of decalcifying agents in combination with methacarn fixation. Samples in Protocols 1, 2, and 3 were fixed in methacarn for 4 hours at 4°C, followed by decalcification at 4°C with Morse's solution, 10% ethylenediaminetetraacetic acid, and 5% formic acid solution, respectively. Samples processed with protocol 4 were decalcified in Morse's solution at 4°C followed by fixation for 4 hours at 4°C. Real-time PCR analysis was performed on total RNA extracted. Histology sections were evaluated for morphology preservation of cochlear structures.

RESULTS

RNA was isolated in all samples. Relative expression levels were greatest with Protocol 1 and lowest with Protocol 3. Morphology preservation was adequate with Protocols 1, 2, and 3.

CONCLUSION

Of the 4 protocols evaluated, methacarn fixation followed by decalcification in Morse's solution provided the greatest genetic expression levels as well as the best tissue morphology preservation in the cochlea.

A novel deletion in SMPX causes a rare form of X-linked progressive hearing loss in two families due to a founder effect

X-linked hearing loss is the rarest form of genetic hearing loss contributing to <1% of cases. We identified a multiplex family from Newfoundland (Family 2024) segregating X-linked hearing loss. Haplotyping of the X chromosome and sequencing of positional candidate genes revealed a novel point deletion (c.99delC) in SMPX which encodes a small muscle protein responsible for reducing mechanical stress during muscle contraction. This novel deletion causes a frameshift and a premature stop codon (p.Arg34GlufsX47). We successfully sequenced both SMPX wild-type and mutant alleles from cDNA of a lymphoblastoid cell line, suggesting that the mutant allele may not be degraded via nonsense-mediated mRNA decay. To investigate the role of SMPX in other subpopulations, we fully sequenced SMPX in 229 Canadian probands with hearing loss and identified a second Newfoundland Family (2196) with the same mutation, and a shared haplotype on the X chromosome, suggesting a common ancestor.

The DMD locus harbours multiple long non-coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms

The 2.2 Mb long dystrophin (DMD) gene, the largest gene in the human genome, corresponds to roughly 0.1% of the entire human DNA sequence. Mutations in this gene cause Duchenne muscular dystrophy and other milder X-linked, recessive dystrophinopathies. Using a custom-made tiling array, specifically designed for the DMD locus, we identified a variety of novel long non-coding RNAs (lncRNAs), both sense and antisense oriented, whose expression profiles mirror that of DMD gene. Importantly, these transcripts are intronic in origin and specifically localized to the nucleus and are transcribed contextually with dystrophin isoforms or primed by MyoD-induced myogenic differentiation. Furthermore, their forced ectopic expression in both human muscle and neuronal cells causes a specific and negative regulation of endogenous dystrophin full length isoforms and significantly down-regulate the activity of a luciferase reporter construct carrying the minimal promoter regions of the muscle dystrophin isoform. Consistent with this apparently repressive role, we found that, in muscle samples of dystrophinopathic female carriers, lncRNAs expression levels inversely correlate with those of muscle full length DMD isoforms. Overall these findings unveil an unprecedented complexity of the transcriptional pattern of the DMD locus and reveal that DMD lncRNAs may contribute to the orchestration and homeostasis of the muscle dystrophin expression pattern by either selective targeting and down-modulating the dystrophin promoter transcriptional activity.

Proteomic analysis of the organ of corti using nanoscale liquid chromatography coupled with tandem mass spectrometry

The organ of Corti (OC) in the cochlea plays an essential role in auditory signal transduction in the inner ear. For its minute size and trace amount of proteins, the identification of the molecules in pathophysiologic processes in the bone-encapsulated OC requires both delicate separation and a highly sensitive analytical tool. Previously, we reported the development of a high resolution metal-free nanoscale liquid chromatography system for highly sensitive phosphoproteomic analysis. Here this system was coupled with a LTQ-Orbitrap XL mass spectrometer to investigate the OC proteome from normal hearing FVB/N male mice. A total of 628 proteins were identified from six replicates of single LC-MS/MS analysis, with a false discovery rate of 1% using the decoy database approach by the OMSSA search engine. This is currently the largest proteome dataset for the OC. A total of 11 proteins, including cochlin, myosin VI, and myosin IX, were identified that when defective are associated with hearing impairment or loss. This study demonstrated the effectiveness of our nanoLC-MS/MS platform for sensitive identification of hearing loss-associated proteins from minute amount of tissue samples.

High throughput gene expression analysis of the inner ear

The mouse auditory and vestibular epithelia consist of a complex array of many different cell types. Over the last decade microarrays were used to characterize gene expression in the inner ear. Studies were performed on wild type mice to identify deafness genes, transcriptional networks activated during development, or identify miRNA with a functional role in the ear. Other studies focused on the molecular response of the inner ear to stimuli ranging from ototoxic medications to hypergravity and caloric restriction. Finally, microarrays were used to identify transcriptional networks activated downstream of deafness genes. As template-free high throughput gene expression profiling methods such as RNA-seq are increasingly popular, we offer a critical review of the data generated over the last decade relating to microarrays for gene expression profiling of the inner ear. Moreover, as most of the published data is available through the gene expression omnibus (GEO), we demonstrate the feasibility of integrating data from independent experiments to reach novel insights.

A novel mutation within the MIR96 gene causes non-syndromic inherited hearing loss in an Italian family by altering pre-miRNA processing

The miR-96, miR-182 and miR-183 microRNA (miRNA) family is essential for differentiation and function of the vertebrate inner ear. Recently, point mutations within the seed region of miR-96 were reported in two Spanish families with autosomal dominant non-syndromic sensorineural hearing loss (NSHL) and in a mouse model of NSHL. We screened 882 NSHL patients and 836 normal-hearing Italian controls and identified one putative novel mutation within the miR-96 gene in a family with autosomal dominant NSHL. Although located outside the mature miR-96 sequence, the detected variant replaces a highly conserved nucleotide within the companion miR-96*, and is predicted to reduce the stability of the pre-miRNA hairpin. To evaluate the effect of the detected mutation on miR-96/mir-96* biogenesis, we investigated the maturation of miR-96 by transient expression in mammalian cells, followed by real-time reverse-transcription polymerase chain reaction (PCR). We found that both miR-96 and miR-96* levels were significantly reduced in the mutant, whereas the precursor levels were unaffected. Moreover, miR-96 and miR-96* expression levels could be restored by a compensatory mutation that reconstitutes the secondary structure of the pre-miR-96 hairpin, demonstrating that the mutation hinders precursor processing, probably interfering with Dicer cleavage. Finally, even though the mature miR-96 sequence is not altered, we demonstrated that the identified mutation significantly impacts on miR-96 regulation of selected targets. In conclusion, we provide further evidence of the involvement of miR-96 mutations in human deafness and demonstrate that a quantitative defect of this miRNA may contribute to NSHL.

Molecular genetic epidemiology of age-related hearing impairment

Genetic epidemiology focuses on the genetic determinants in the etiology of disease among populations and seeks to elucidate the role of genetic factors and their interaction with environmental factors in disease occurrence. In recent years, genetic epidemiological research has become more focused on complex diseases, and human genome analysis technology has made remarkable advances. Age-related hearing impairment (ARHI) is a complex trait, which results from a multitude of confounding intrinsic and extrinsic factors. Although the number of genetic investigations of ARHI is increasing at a surprising rate, the etiology of ARHI is not firmly established. In this article, we review (1) the methodological strategies used to analyze genetic factors that contribute to human ARHI, (2) several representative investigations, and (3) specific genetic risk factors for human ARHI identified in previous work.

A novel mutation in COCH-implications for genotype-phenotype correlations in DFNA9 hearing loss

OBJECTIVES/HYPOTHESIS

To determine the cause of autosomal dominant hearing loss segregating in an American family.

STUDY DESIGN

Family study.

METHODS

Otologic and audiometric examination was performed on affected family members. Genome wide parametric multipoint linkage mapping using a dominant model was performed with Affymetrix 50K GeneChip data. Direct sequencing was used to confirm the causative mutation.

RESULTS

In American family 467, segregating autosomal dominant nonsyndromic hearing loss, a novel heterozygous missense mutation (c.362T>C; p.F121S) was identified in the COCH gene. This mutation was also associated with vestibular dysfunction typical of other DFNA9 families. However, affected family members also exhibited memory loss and night blindness.

CONCLUSIONS

The novel COCH mutation affects the functionally important limulus factor C, Coch-5b2 and Lgl1 domain where most DFNA9 mutations have been localized. The onset of the hearing loss, in the 2nd or 3rd decade of life, is earlier than in most DFNA9 families. The progression of hearing loss and vestibular dysfunction in the American family is typical of other DFNA9 families with mutations in this domain. Memory loss and night blindness have not been previously reported in DFNA9 families.

Extralabyrinthine manifestations of DFNA9

DFNA9 is an autosomal dominant cause of non-syndromic adult-onset sensorineural hearing loss with associated variable vestibular dysfunction caused by mutations in the COCH gene. DFNA9 has previously been characterized by the presence of unique histopathologic features limited to the cochlear and vestibular labyrinth. This report describes newly discovered extralabyrinthine findings within the middle ear in DFNA9 and discusses their implications. The histopathologic anatomy of extralabyrinthine structures was reviewed in 12 temporal bones from seven individuals with DFNA9 and compared with age-matched controls. All temporal bones with DFNA9 had abnormal deposits within the tympanic membrane, incudomalleal joint, and incudostapedial joint. Hematoxylin and eosin stain and Movat's pentachrome stain both revealed different staining patterns of the extralabyrinthine deposits compared with the intralabyrinthine deposits suggesting that the composition of the deposits varies with location. The deposits within the tympanic membrane resembled cartilage morphologically and stained positively for aggrecan, an extracellular matrix protein found in cartilage. However, the cellular component of the tympanic membrane deposits did not stain with immunomarkers for chondrocytes (s100 and connective tissue growth factor). These novel findings in DFNA9 have implications for the phenotypic expression of the disorder and the clinical workup of adult-onset sensorineural hearing loss.

Molecular cloning of the Coch gene of guinea pig inner ear and its expression analysis in cultured fibrocytes of the spiral ligament

CONCLUSIONS

We have cloned guinea pig Coch cDNA and the sequence information will be useful for future molecular study combined with physiological experiments. Proper Coch gene expression appears to be dependent on the unique extracellular micro-environment of the inner ear in vivo. These results provide insight into the Coch gene expression and its regulation.

OBJECTIVE

To characterize the guinea pig Coch gene, we performed molecular cloning and expression analysis in the inner ear and cultured fibrocytes of the spiral ligament.

METHODS

The Coch cDNA was isolated using RACE. Cochlin isofoms were studied by Western blot using three different types of mammalian inner ear. The cochlear fibrocytes were cultured and characterized by immunostaining. Coch gene expression in the fibrocytes was investigated and the influence of cytokine stimulation was evaluated.

RESULTS

The full-length 1991 bp Coch cDNA that encodes a 553 amino acid protein was isolated. The sequence had significant homology with other mammals, and the sizes of the Cochlin isoforms were identical. In the cultured fibrocytes, Coch mRNA was expressed in a very small amount and the isoform production was different, compared with the results in vivo. Cytokine stimulation did not alter the level of mRNA expression or isoform formation.

A genome-wide association study for age-related hearing impairment in the Saami

This study aimed at contributing to the elucidation of the genetic basis of age-related hearing impairment (ARHI), a common multifactorial disease with an important genetic contribution as demonstrated by heritability studies. We conducted a genome-wide association study (GWAS) in the Finnish Saami, a small, ancient, genetically isolated population without evidence of demographic expansion. The choice of this study population was motivated by its anticipated higher extent of LD, potentially offering a substantial power advantage for association mapping. DNA samples and audiometric measurements were collected from 352 Finnish Saami individuals, aged between 50 and 75 years. To reduce the burden of multiple testing, we applied principal component (PC) analysis to the multivariate audiometric phenotype. The first three PCs captured 80% of the variation in hearing thresholds, while maintaining biologically important audiometric features. All subjects were genotyped with the Affymetrix 100 K chip. To account for multiple levels of relatedness among subjects, as well as for population stratification, association testing was performed using a mixed model. We summarised the top-ranking association signals for the three traits under study. The top-ranked SNP, rs457717 (P-value 3.55 x 10(-7)), was associated with PC3 and was localised in an intron of the IQ motif-containing GTPase-activating-like protein (IQGAP2). Intriguingly, the SNP rs161927 (P-value 0.000149), seventh-ranked for PC1, was positioned immediately downstream from the metabotropic glutamate receptor-7 gene (GRM7). As a previous GWAS of a European and Finnish sample set already suggested a role for GRM7 in ARHI, this study provides further evidence for the involvement of this gene.

Expression of Pou3f3/Brn-1 and its genomic methylation in developing auditory epithelium

In the mammalian cochlea, both the sensory cells-called hair cells (HCs)-and nonsensory cells such as supporting cells (SCs) and mesenchymal cells participate in proper auditory function through the expression of various functional molecules. During development, expression of certain genes is repressed through genomic methylation, one of the major epigenetic regulatory mechanisms. We explored the genomic regions that were differentially methylated in rat auditory epithelium at postnatal day 1 (P1) and P14 using amplification of intermethylated sites (AIMS). An AIMS fragment was mapped to the 3'-flanking region of Pou3f3/Brn-1. Bisulfite-converted PCR and quantitative methylation-specific PCR showed that the methylation frequency of the AIMS region and the adjacent CpG island was increased at P14, when the expression of Pou3f3 and the noncoding RNAs nearby decreased. Expression of de novo DNA methyltransferases 3a and 3b also suggests a role of epigenetic regulation during postnatal inner ear development. Immunohistochemical analysis showed that Pou3f3 was expressed specifically in the SCs and mesenchymal cells in the cochlea and established that Pou3f3 is a new cell-type marker for studying inner ear development. Mice deficient in Pou3f3 or Pou3f2 plus Pou3f3 did not exhibit any abnormality in the embryonic cochlea. Absence of Pou3f3 affected neither the proliferation nor the differentiation activities of HC progenitor cells. Pou3f3 may, however, be important for the maintenance or functional development of the postnatal cochlea. This is the first report to study involvement of an epigenetic regulatory mechanism in the developing mammalian auditory epithelium.

Analysis of cochlear protein profiles of Wistar, Sprague-Dawley, and Fischer 344 rats with normal hearing function

Differences in the expression of cochlear proteins are likely to affect the susceptibility of different animal models to specific types of auditory pathology. However, little is currently known about proteins that are abundantly expressed in inner ear. Identification of these proteins may facilitate the search for biomarkers of susceptibility and intervention targets. To begin to address this issue, we analyzed cochlear protein profiles of three strains of rats, Wistar, Sprague-Dawley, and Fischer 344, using a broad spectrum antibody microarray. Normal hearing function of the animals was ascertained using distortion product otoacoustic emissions (DPOAE). Of 725 proteins screened in whole cochlea, more than 80% were detected in all three strains. However, there were striking differences in the levels at which they occur. Among 213 proteins expressed at levels>or=2 fold of actin, only 7.5% were detected at these levels in all three strains. Myosin light chain kinase (MLCK) was immunolocalized in cuticular plate of outer hair cells (OHC) while mitogen activated protein (MAP) kinase-extracellular-signal regulated kinase1/2 (ERK1/2) was detected as foci in OHC, pillar cells, strial marginal cells, and fibroblasts of spiral ligament. A review of literature indicated that the expression of 7 (44%) of these 16 proteins were detected for the first time in the inner ear, although there were implications of the presence of some of these proteins. One of these abundant, but unstudied, proteins, MAP kinase activated protein kinase2 (MAPKAPK2), shows strong immunolabeling in pillar cells and inner hair cells (IHC). There was moderate MAPKAPK2 labeling in OHC, supporting cells, neurons, and marginal, intermediate, and basal cells. The current study provides the first, large cochlear protein profile of multiple rat strains. The diversity in expression of abundant proteins in these strains may contribute to differences in susceptibility of these strains to aging, noise, or ototoxic drugs.

Identities and frequencies of mutations of the otoferlin gene (OTOF) causing DFNB9 deafness in Pakistan

Mutations in OTOF, encoding otoferlin, cause non-syndromic recessive hearing loss. The goal of our study was to define the identities and frequencies of OTOF mutations in a model population. We screened a cohort of 557 large consanguineous Pakistani families segregating recessive, severe-to-profound, prelingual-onset deafness for linkage to DFNB9. There were 13 families segregating deafness consistent with linkage to markers for DFNB9. We analyzed the genomic nucleotide sequence of OTOF and detected probable pathogenic sequence variants among all 13 families. These include the previously reported nonsense mutation p.R708X and 10 novel variants: 3 nonsense mutations (p.R425X, p.W536X, and p.Y1603X), 1 frameshift (c.1103_1104delinsC), 1 single amino acid deletion (p.E766del) and 5 missense substitutions of conserved residues (p.L573R, p.A1090E, p.E1733K, p.R1856Q and p.R1939W). OTOF mutations thus account for deafness in 13 (2.3%) of 557 Pakistani families. This overall prevalence is similar, but the mutation spectrum is different from those for Western populations. In addition, we demonstrate the existence of an alternative splice isoform of OTOF expressed in the human cochlea. This isoform must be required for human hearing because it encodes a unique alternative C-terminus affected by some DFNB9 mutations.

A genome-wide analysis identifies genetic variants in the RELN gene associated with otosclerosis

Otosclerosis is a common form of progressive hearing loss, characterized by abnormal bone remodeling in the otic capsule. The etiology of the disease is largely unknown, and both environmental and genetic factors have been implicated. To identify genetic factors involved in otosclerosis, we used a case-control discovery group to complete a genome-wide association (GWA) study with 555,000 single-nucleotide polymorphisms (SNPs), utilizing pooled DNA samples. By individual genotyping of the top 250 SNPs in a stepwise strategy, we were able to identify two highly associated SNPs that replicated in two additional independent populations. We then genotyped 79 tagSNPs to fine map the two genomic regions defined by the associated SNPs. The region with the strongest association signal, p(combined) = 6.23 x 10(-10), is on chromosome 7q22.1 and spans intron 1 to intron 4 of reelin (RELN), a gene known for its role in neuronal migration. Evidence for allelic heterogeneity was found in this region. Consistent with the GWA data, expression of RELN was confirmed in the inner ear and in stapes footplate specimens. In conclusion, we provide evidence that implicates RELN in the pathogenesis of otosclerosis.

Molecular and functional characterization of choline transporter in rat renal tubule epithelial NRK-52E cells

Homeostatic regulation of the plasma choline concentration depends on the effective functioning of a choline transporter in the kidney. However, the nature of the choline transport system in the kidney is poorly understood. In this study, we examined the molecular and functional characterization of choline uptake in the rat renal tubule epithelial cell line NRK-52E. Choline uptake was saturable and mediated by a single transport system, with an apparent Michaelis-Menten constant (K(m)) of 16.5 microM and a maximal velocity (V(max)) of 133.9 pmol/mg protein/min. The V(max) value of choline uptake was strongly enhanced in the absence of Na(+) without any change in K(m) values. The increase in choline uptake under Na(+)-free conditions was inhibited by Na(+)/H(+) exchanger (NHE) inhibitors. Choline uptake was inhibited by the choline uptake inhibitor hemicholinium-3 (HC-3) and organic cations, and was decreased by acidification of the extracellular medium and by intracellular alkalinization. Collapse of the plasma membrane H(+) electrochemical gradient by a protonophore inhibited choline uptake. NRK-52E cells mainly express mRNA for choline transporter-like proteins (CTL1 and CTL2), and NHE1 and NHE8. CTL1 protein was recognized in both plasma membrane and mitochondria. CTL2 protein was mainly expressed in mitochondria. The biochemical and pharmacological data indicated that CTL1 is functionally expressed in NRK-52E cells and is responsible for choline uptake. This choline transport system uses a directed H(+) gradient as a driving force, and its transport functions in co-operation with NHE8. Furthermore, the presence of CTL2 in mitochondria provides a potential site for the control of choline oxidation.

Novel autosomal recessive non-syndromic hearing impairment locus (DFNB71) maps to chromosome 8p22-21.3

A novel autosomal recessive nonsyndromic hearing impairment (ARNSHI) locus, DFNB71 was localized to 8p22-21.3. In order to map the locus, a whole genome scan was carried out using DNA samples from a consanguineous seven-generational Pakistani family with profound prelingual ARNSHI. A maximum multipoint LOD score of 4.2 occurred at marker D8S261. The DFNB71 region of homozygosity and 3-unit support interval is flanked by markers D8S1130 and D8S1786. This region has a genetic distance of 19.1 cM and contains 10.6 Mb of sequence.

Positional cloning of deafness genes

The identification of the majority of the known causative genes involved in nonsyndromic sensorineural hearing loss (NSHL) started with linkage analysis as part of a positional cloning procedure. The human and mouse genome projects in combination with technical developments on genotyping, transcriptomics, proteomics, and the creation of animal models have greatly enhanced the speed of disease gene identification. In the present chapter, we first discuss the possibilities for exclusion of known NSHL loci and genes. Subsequently, methods are described to determine the genomic regions that contain the genetic defects. These include linkage analysis with genotyping and statistical evaluation and the determination of copy number variations. In the case of a large genomic region, candidate genes are selected and prioritized using gene expression analysis, protein network data, and phenotypes of animal models. A number of algorithms are described to automate the process of candidate gene selection. The novel high-throughput sequencing techniques might make gene selection and prioritization unnecessary in the near future. Once genetic variants are identified, questions on pathogenicity need to be addressed, which is the topic of the last section of this chapter.

Cochlin expression in anterior segment organ culture models after TGFbeta2 treatment

PURPOSE

To determine the effect of transforming growth factor (TGF)-beta2 treatment on intraocular pressure (IOP), outflow facility, and cochlin expression in vitro in monkey and pig organ-cultured anterior segments (MOCAS and POCAS).

METHODS

MOCAS (rhesus and cynomolgus) or POCAS were infused with media containing 10 ng/mL TGFbeta2 to one segment of each pair and 0.1% BSA (vehicle) to the contralateral segment for up to 14 days at a constant rate. Cochlin expression was determined by immunohistochemical study, ELISA, and Western blot analysis using chicken polyclonal antibodies against different regions of cochlin.

RESULTS

TGFbeta2 infusion produced elevated IOP in MOCAS (usually after 5 days), that was approximately 45% greater than baseline and compared to control segments. Outflow facility (OF) was decreased by approximately 40% compared with pretreatment baseline (n=5). In POCAS (n=7), IOP was increased (approximately 3 days) by approximately 75% compared with baseline and contralateral changes. The IOP elevation subsided thereafter. Cochlin levels increased with duration of TGFbeta2 treatment in the media and in the region of the trabecular meshwork in both species.

CONCLUSIONS

TGFbeta2-induced IOP elevation was associated with an increase in cochlin secretion into the media and expression in the tissue of MOCAS and POCAS. Whether cochlin overexpression contributes to elevated IOP or is a consequence of other changes relevant to IOP elevation remains to be determined.

A targeted Coch missense mutation: a knock-in mouse model for DFNA9 late-onset hearing loss and vestibular dysfunction

Mutations in COCH (coagulation factor C homology) are etiologic for the late-onset, progressive, sensorineural hearing loss and vestibular dysfunction known as DFNA9. We introduced the G88E mutation by gene targeting into the mouse and have created a Coch(G88E/G88E) mouse model for the study of DFNA9 pathogenesis and cochlin function. Vestibular-evoked potential (VsEP) thresholds of Coch(G88E/G88E) mice were elevated at all ages tested compared with wild-type littermates. At the oldest ages, two out of eight Coch(G88E/G88E) mice had no measurable VsEP. Auditory brainstem response (ABR) thresholds of Coch(G88E/G88E) mice were substantially elevated at 21 months but not at younger ages tested. At 21 months, four of eight Coch(G88E/G88E) mice had absent ABRs at all frequencies tested and two of three Coch(G88E)(/+) mice had absent ABRs at three of four frequencies tested. Distortion product otoacoustic emission amplitudes of Coch(G88E/G88E) mice were substantially lower than Coch(+/+) mice and absent in the same Coch(G88E/G88E) mice with absent ABRs. These results suggest that vestibular function is affected beginning as early as 11 months when cochlear function appears to be normal, and dysfunction increases with age. Hearing loss declines substantially at 21 months of age and progresses to profound hearing loss at some to all frequencies tested. This is the only mouse model developed to date where hearing loss begins at such an advanced age, providing an opportunity to study both progressive age-related hearing loss and possible interventional therapies.

Glucose transporter 5 is undetectable in outer hair cells and does not contribute to cochlear amplification

Glucose transporter 5 (Glut5) is a high-affinity fructose transporter. It was proposed to be a motor protein or part of the motor complex required for cochlear amplification in outer hair cells (OHCs). Here we show that, in contrast to previous reports, Glut5 is undetectable, and possibly absent, in OHCs harvested from wildtype mice. Further, Glut5-deficient mice display normal OHC morphology and motor function (i.e., nonlinear capacitance and electromotility) and normal cochlear sensitivity and frequency selectivity. We conclude that Glut5 is not required for OHC motility or cochlear amplification.

Expression studies of osteoglycin/mimecan (OGN) in the cochlea and auditory phenotype of Ogn-deficient mice

Genes involved in the hearing process have been identified through both positional cloning efforts following genetic linkage studies of families with heritable deafness and by candidate gene approaches based on known functional properties or inner ear expression. The latter method of gene discovery may employ a tissue- or organ-specific approach. Through characterization of a human fetal cochlear cDNA library, we have identified transcripts that are preferentially and/or highly expressed in the cochlea. High expression in the cochlea may be suggestive of a fundamental role for a transcript in the auditory system. Herein we report the identification and characterization of a transcript from the cochlear cDNA library with abundant cochlear expression and unknown function that was subsequently determined to represent osteoglycin (OGN). Ogn-deficient mice, when analyzed by auditory brainstem response and distortion product otoacoustic emissions, have normal hearing thresholds.

Cochlin isoforms and their interaction with CTL2 (SLC44A2) in the inner ear

Choline transporter-like protein 2 (CTL2) is a multi-transmembrane protein expressed on inner ear supporting cells that was discovered as a target of antibody-induced hearing loss. Its function is unknown. A 64 kDa band that consistently co-precipitates with CTL2 from inner ear extracts was identified by mass spectroscopy as cochlin. Cochlin is an abundant inner ear protein expressed as multiple isoforms. Its function is also unknown, but it is suspected to be an extracellular matrix component. Cochlin is mutated in individuals with DFNA9 hearing loss. To investigate the CTL2-cochlin interaction, antibodies were raised to a cochlin-specific peptide. The antibodies identify several cochlin polypeptides on western blots and are specific for cochlin. We show that the heterogeneity of the cochlin isoforms is caused, in part, by in vivo post-translational modification by N-glycosylation and, in part, caused by alternative splicing. We verified that antibody to CTL2 co-immunoprecipitates cochlin from the inner ear and antibody to cochlin co-immunoprecipitates CTL2. Using cochlear cross-sections, we show that CTL2 is more widely distributed than previously described, and its prominent expression on cells facing the scala media suggests a possible role in homeostasis. A prominent but previously unreported ribbon-like pattern of cochlin in the basilar membrane was demonstrated, suggesting an important role for cochlin in the structure of the basilar membrane. CTL2 and cochlin are expressed in close proximity in the inner sulcus, the spiral prominence, vessels, limbus, and spiral ligament. The possible functional significance of CTL2-cochlin interactions remains unknown.

Quantitative analysis of mRNA in human temporal bones

CONCLUSION

Well-preserved mRNA could be extracted from frozen human inner ears. Therefore, this study demonstrates that analysis of mRNA could be performed to study the molecular mechanisms of inner ear disorders using human specimens.

OBJECTIVES

Analysis of RNA as well DNA is requisite to study the molecular mechanisms of inner ear disorders. Methods of isolating RNA from experimental animals have been established, while isolation of RNA from human inner ears is much more challenging. In the present study, we demonstrate a method by which messenger RNA (mRNA) was extracted from human inner ears and quantitatively analyzed.

MATERIALS AND METHODS

COCH mRNA as well as GAPDH mRNA was extracted from membranous labyrinths dissected from three formalin-fixed and three frozen human temporal bones, removed at autopsy. The length of COCH mRNA and quantity of GAPDH mRNA was compared between the two groups by quantitative RT-PCR.

RESULTS

COCH mRNA could be amplified as much as 976 bp in all three frozen specimens. By contrast, it was amplified to 249 bp in two of the three formalin-fixed specimens, with no amplification observed in the remaining. The quantity of amplifiable GAPDH mRNA in the formalin specimens was only 1% of that of the frozen specimens.

Cochlin in the eye: functional implications

Aqueous humor is actively produced in the ciliary epithelium of the anterior chamber and has important functions for the eye. Under normal physiological conditions, the inflow and outflow of the aqueous humor are tightly regulated, but in the pathologic state this balance is lost. Aqueous outflow involves structures of the anterior chamber and experiences most resistance at the level of the trabecular meshwork (TM) that acts as a filter. The modulation of the TM structure regulates the filter and its mechanism remains poorly understood. Proteomic analyses have identified cochlin, a protein of poorly understood function, in the glaucomatous TM but not in healthy control TM from human cadaver eyes. The presence of cochlin has subsequently been confirmed by Western and immunohistochemical analyses. Functionally, cochlin undergoes multimerization induced by shear stress and other changes in the microenvironment. Cochlin along with mucopolysaccharide deposits has been found in the TM of glaucoma patients and in the inner ear of subjects affected by the hearing disorder DNFA9, a late-onset, progressive disease that also involves alterations in fluid shear regimes. In vitro, cochlin induces aggregation of primary TM cells suggesting a role in cell adhesion, possibly in mechanosensation, and in modulation of the TM filter.

Methylthioadenosine phosphorylase (MTAP) in hearing: gene disruption by chromosomal rearrangement in a hearing impaired individual and model organism analysis

Genes with a role in the auditory system have been mapped by genetic linkage analysis of families with heritable deafness and then cloned through positional candidate gene approaches. Another positional method for gene discovery is to ascertain deaf individuals with balanced chromosomal translocations and identify disrupted or disregulated genes at the site(s) of rearrangement. We report herein the use of fluorescence in situ hybridization (FISH) to map the breakpoint regions on each derivative chromosome of a de novo apparently balanced translocation, t(8;9)(q12.1;p21.3)dn, in a deaf individual. Chromosomal breakpoints were assigned initially by GTG-banding of metaphase chromosomes and then BAC probes chosen to map precisely the breakpoints by FISH experiments. To facilitate cloning of the breakpoint sequences, further refinement of the breakpoints was performed by FISH experiments using PCR products and by Southern blot analysis. The chromosome 9 breakpoint disrupts methylthioadenosine phosphorylase (MTAP); no known or predicted genes are present at the chromosome 8 breakpoint. Disruption of MTAP is hypothesized to lead to deafness due to the role of MTAP in metabolizing an inhibitor of polyamine synthesis. Drosophila deficient for the MTAP ortholog, CG4,802, were created and their hearing assessed; no hearing loss phenotype was observed. A knockout mouse model for MTAP deficiency was also created and no significant hearing loss was detected in heterozygotes for Mtap. Homozygous Mtap-deficient mice were embryonic lethal.