Genome sequencing identifies coding and non-coding variants for non-syndromic hearing loss.

Hearing loss (HL) is a common heterogeneous trait that involves variants in more than 200 genes. In this study, we utilized exome (ES) and genome sequencing (GS) to effectively identify the genetic cause of presumably non-syndromic HL in 322 families from South and West Asia and Latin America. Biallelic GJB2 variants were identified in 58 probands at the time of enrollment these probands were excluded. In addition, upon review of phenotypic findings, 38/322 probands were excluded based on syndromic findings at the time of ascertainment and no further evaluation was performed on those samples. We performed ES as a primary diagnostic tool on one or two affected individuals from 212/226 families. Via ES we detected a total of 78 variants in 30 genes and showed their co-segregation with HL in 71 affected families. Most of the variants were frameshift or missense and affected individuals were either homozygous or compound heterozygous in their respective families. We employed GS as a primary test on a subset of 14 families and a secondary tool on 22 families which were unsolved by ES. Although the cumulative detection rate of causal variants by ES and GS is 40% (89/226), GS alone has led to a molecular diagnosis in 7 of 14 families as the primary tool and 5 of 22 families as the secondary test. GS successfully identified variants present in deep intronic or complex regions not detectable by ES.

Mutations in MINAR2 encoding membrane integral NOTCH2-associated receptor 2 cause deafness in humans and mice.

Discovery of deafness genes and elucidating their functions have substantially contributed to our understanding of hearing physiology and its pathologies. Here we report on DNA variants in MINAR2, encoding membrane integral NOTCH2-associated receptor 2, in four families underlying autosomal recessive nonsyndromic deafness. Neurologic evaluation of affected individuals at ages ranging from 4 to 80 y old does not show additional abnormalities. MINAR2 is a recently annotated gene with limited functional understanding. We detected three MINAR2 variants, c.144G > A (p.Trp48*), c.412_419delCGGTTTTG (p.Arg138Valfs*10), and c.393G > T, in 13 individuals with congenital- or prelingual-onset severe-to-profound sensorineural hearing loss (HL). The c.393G > T variant is shown to disrupt a splice donor site. We show that Minar2 is expressed in the mouse inner ear, with the protein localizing mainly in the hair cells, spiral ganglia, the spiral limbus, and the stria vascularis. Mice with loss of function of the Minar2 protein (Minar2tm1b/tm1b) present with rapidly progressive sensorineural HL associated with a reduction in outer hair cell stereocilia in the shortest row and degeneration of hair cells at a later age. We conclude that MINAR2 is essential for hearing in humans and mice and its disruption leads to sensorineural HL. Progressive HL observed in mice and in some affected individuals and as well as relative preservation of hair cells provides an opportunity to interfere with HL using genetic therapies.

A truncating CLDN9 variant is associated with autosomal recessive nonsyndromic hearing loss.

While the importance of tight junctions in hearing is well established, the role of Claudin- 9 (CLDN9), a tight junction protein, in human hearing and deafness has not been explored. Through whole-genome sequencing, we identified a one base pair deletion (c.86delT) in CLDN9 in a consanguineous family from Turkey with autosomal recessive nonsyndromic hearing loss. Three affected members of the family had sensorineural hearing loss (SNHL) ranging from moderate to profound in severity. The variant is predicted to cause a frameshift and produce a truncated protein (p.Leu29ArgfsTer4) in this single-exon gene. It is absent in public databases as well as in over 1000 Turkish individuals, and co-segregates with SNHL in the family. Our in vitro studies demonstrate that the mutant protein does not localize to cell membrane as demonstrated for the wild-type protein. Mice-lacking Cldn9 have been shown to develop SNHL. We conclude that CLDN9 is essential for proper audition in humans and its disruption leads to SNHL in humans.

Three cases of Chronic Suppurative Otitis Media (CSOM) caused by Kerstersia gyiorum and a review of the literature.

New identification techniques such as gene sequencing and mass spectrometry have increased the incidence of novel agents such as Kerstersia gyiorum. As a new member of the Alcaligenaceae family, K. gyiorum was isolated from wounds, respiratory tract, urine specimens and most frequently from chronic suppurative otitis media (CSOM). We isolated three K. gyiorum strains from three CSOM cases over a one-year period. The strains were analyzed by mass spectrometry and identified by Bruker Biotyper 3.1 (Bruker Daltonics, USA). The cases were young patients without chronic diseases and immunodeficiencies. Two strains were resistant to ciprofloxacin.

Comprehensive analysis via exome sequencing uncovers genetic etiology in autosomal recessive nonsyndromic deafness in a large multiethnic cohort.

PURPOSE: Autosomal recessive nonsyndromic deafness (ARNSD) is characterized by a high degree of genetic heterogeneity, with reported mutations in 58 different genes. This study was designed to detect deafness-causing variants in a multiethnic cohort with ARNSD by using whole-exome sequencing (WES). METHODS: After excluding mutations in the most common gene, GJB2, we performed WES in 160 multiplex families with ARNSD from Turkey, Iran, Mexico, Ecuador, and Puerto Rico to screen for mutations in all known ARNSD genes. RESULTS: We detected ARNSD-causing variants in 90 (56%) families, 54% of which had not been previously reported. Identified mutations were located in 31 known ARNSD genes. The most common genes with mutations were MYO15A (13%), MYO7A (11%), SLC26A4 (10%), TMPRSS3 (9%), TMC1 (8%), ILDR1 (6%), and CDH23 (4%). Nine mutations were detected in multiple families with shared haplotypes, suggesting founder effects. CONCLUSION: We report on a large multiethnic cohort with ARNSD in which comprehensive analysis of all known ARNSD genes identifies causative DNA variants in 56% of the families. In the remaining families, WES allows us to search for causative variants in novel genes, thus improving our ability to explain the underlying etiology in more families.Genet Med 18 4, 364-371.

Evidence for genotype-phenotype correlation for OTOF mutations.

OBJECTIVES: The aim of this study is to evaluate the auditory phenotype in subjects with OTOF gene mutations to describe genotype-phenotype correlations. METHODS: Twenty-two affected members from three families with homozygous OTOF mutations were included. Nine subjects were evaluated audiologically with otoscopic examination, pure-tone audiometry, tympanometry with acoustic reflex testing, auditory brain stem responses, and otoacoustic emission tests. RESULTS: Homozygous c.4718T>C (p.Ile1573Thr) mutation was associated with the auditory neuropathy/auditory dys-synchrony (AN/AD) phenotype and with progressive sensorineural hearing loss in four siblings in one family, while homozygous c.4467dupC (p.I1490HfsX19) was associated with severe to profound sensorineural hearing loss without AN/AD in four relatives in another family. Homozygous c.1958delC (p.Pro653LeufsX13) mutation was associated with moderate sensorineural hearing loss without AN/AD in one affected person in an additional family. CONCLUSIONS: The audiological phenotype associated with different OTOF mutations appears to be consistently different suggesting the presence of a genotype-phenotype correlation.

The pathology of silent otitis media: a predecessor to tympanogenic meningitis in infants.

OBJECTIVE: To determine the association of bacteria embedded within a fibrous matrix in the middle and inner ear in infants with tympanogenic meningitis. METHODS: Thirty-one cases with meningitis from the human temporal bone collection at the University of Minnesota were screened to select those with tympanogenic meningitis. Inclusion criteria for tympanogenic meningitis were acute meningitis with histopathological evidence of chronic otitis media, and no other source of infection. The presence of labyrinthitis and pathologic changes such as granulation tissue, fibrosis, cholesterol granuloma, cholesteatoma, tympanic membrane perforation, tympanosclerosis, and the type of effusion were noted. The extent and location of bacteria embedded in a fibrous matrix were also explored. RESULTS: Seventeen temporal bones, from nine cases that included two females and seven males, ranging in age from five to twenty-three months, met our criteria of tympanogenic meningitis. Eighty two percent of these temporal bones had bacteria within the fibrous matrices (BFM). BFM were located in one anatomical region in one temporal bone and multiple anatomic regions in sixteen temporal bones. The most common locations were the areas near the oval and round windows. They were also commonly seen in the epitympanum, facial recess, and supratubal recess. BFM within the inner ear were observed in the scala tympani and modiolus in the middle and basal turns of the cochleae of nine temporal bones. In one of these temporal bones, BFM were seen in the internal auditory canal. Labyrinthitis was seen in all ears. The tympanic membrane was intact in all cases. BFM were not seen in three temporal bones from two patients. In one case only one side was available for study. CONCLUSIONS: Our findings show an association between the presence of BFM in the ear with chronic pathologic changes and tympanogenic meningitis. Potential pathways of bacteria from the middle ear include hematogeous spread and/or direct spread to dura through the tympanic tegmen, and/or to the inner ear through the oval and round windows, and from there to the modiolus and the meninges. Chronic pathologic changes in the middle ear behind an intact tympanic membrane and the lack of ear symptoms may result in potentially serious sequelae and complications in infant age groups. There should be a heightened awareness of this condition.

An evaluation of preoperative computed tomography on patients with chronic otitis media.

This study aimed to compare the veracity of computed tomography findings on patients undergoing surgery for chronic otitis media (COM) with the surgical findings, and to determine to what extent the preoperative computerized tomography (CT) findings are useful to the surgeon. A series of 56 patients with COM undergoing preoperative CT scanning followed by surgical exploration of the middle ear and mastoid. Operative notes were recorded and data collected on the nature of soft tissue masses, the status of the ossicles, presence or absence of facial canal dehiscence and semicircular canal (SCC) dehiscence and the presence or absence of dural plate erosion, and sigmoid sinus thrombosis. Fifty-six patients were recruited in the study, 30 males and 26 females. The age range was from 16 to 67 years with a mean of 26.51 ± 1.4 years. The preoperative CT scan imaging in cases of cholesteatoma, ossicular chain erosion and SCC dehiscence have good correlation with the intraoperative findings. The specificity of preoperative CT scan in detecting facial canal dehiscence, dural plate erosion and sigmoid sinus thrombosis in patient of COM were weak. Preoperative computed tomography evaluation is fairly useful especially in cases of cholesteatoma. According to the results of this study, CT is of value particularly in the definition of cholesteatoma, and in determining ossicular chain erosion and semicircular canal fistula.

Association between type 1 diabetes mellitus and deposits in the semicircular canals.

OBJECTIVE: To compare the prevalence of cupular and free-floating deposits in the semicircular canals between temporal bones of type 1 diabetes mellitus patients and normal controls. STUDY DESIGN: Case-control histopathologic human temporal bone study. SETTING: Otopathology laboratory in a tertiary academic medical center. SUBJECTS AND METHODS: Twenty-eight temporal bones from 14 patients with type 1 diabetes mellitus and 56 normal temporal bones from 28 age-matched individuals were histopathologically examined. The cupula and lumina of the semicircular canals were examined for evidence of deposits. RESULTS: The prevalence of cupular and free-floating deposits in the lateral and posterior semicircular canals was significantly higher in type 1 diabetes mellitus patients compared with normal temporal bones (lateral, cupular deposits, odds ratio [OR], 5.47; 95% confidence interval [CI], 1.43 to 21.02; free-floating deposits, OR, 8.25; 95% CI, 2.42 to 27.85; posterior, cupular deposits, OR, 41.73; 95% CI, 5.96 to 275.50; free-floating deposits, OR, 7.44; 95% CI, 1.91 to 28.53). The prevalence of these deposits was associated with the duration of disease rather than with aging. CONCLUSION: The findings suggest that type 1 diabetes mellitus is associated with cupular and free-floating deposits in the semicircular canals. The patients with type 1 diabetes mellitus with a longer duration of disease have an increased probability of suffering from benign paroxysmal positional vertigo.

[A rare cause of dysphagia: Forestier's disease]. / Disfajinin nadir bir nedeni: Forestier hastaligi.

Forestier's disease is a rare rheumatologic disease characterized by ossification in various spinal and extraspinal ligaments especially the anterior longitudinal ligament. The hypertrophic bone proliferations seen in cervical involvement may be so extensive causing dysphagia. We present Forestier's disease as a rare cause of dysphagia with clinical and radiological findings. An 80-year-old male was admitted for 2-3 months' increasing dysphagia and sore throat. Examination of the oropharynx revealed a 3 cm painless, hard swelling posterior to the epiglottis. A large area of ossification was detected in the anterior portion of the C2-7 vertebrae on lateral cervical roentgenogram. Neck computed tomography revealed bridging hyperosseous changes in the anterior longitudinal ligament between the C2-7 vertebrae and narrowing of the pharyngeal passage. A lesion with similar intensity to adjacent vertebrae and heterogeneous appearance lying along the anterior longitudinal ligament was seen on cervical magnetic resonance imaging. We interpreted the large osseous lesion to be an ossified anterior longitudinal ligament causing dysphagia, and a diagnosis of Forestier's disease was based on these findings. Forestier's disease must be kept in mind as a rare etiology in the differential diagnosis of dysphagia.