Otitis media susceptibility and shifts in the head and neck microbiome due to SPINK5 variants

BACKGROUND

Otitis media (OM) susceptibility has significant heritability; however, the role of rare variants in OM is mostly unknown. Our goal is to identify novel rare variants that confer OM susceptibility.

METHODS

We performed exome and Sanger sequencing of >1000 DNA samples from 551 multiethnic families with OM and unrelated individuals, RNA-sequencing and microbiome sequencing and analyses of swabs from the outer ear, middle ear, nasopharynx and oral cavity. We also examined protein localisation and gene expression in infected and healthy middle ear tissues.

RESULTS

A large, intermarried pedigree that includes 81 OM-affected and 53 unaffected individuals cosegregates two known rare A2ML1 variants, a common FUT2 variant and a rare, novel pathogenic variant c.1682A>G (p.Glu561Gly) within SPINK5 (LOD=4.09). Carriage of the SPINK5 missense variant resulted in increased relative abundance of Microbacteriaceae in the middle ear, along with occurrence of Microbacteriaceae in the outer ear and oral cavity but not the nasopharynx. Eight additional novel SPINK5 variants were identified in 12 families and individuals with OM. A role for SPINK5 in OM susceptibility is further supported by lower RNA counts in variant carriers, strong SPINK5 localisation in outer ear skin, faint localisation to middle ear mucosa and eardrum and increased SPINK5 expression in human cholesteatoma.

CONCLUSION

SPINK5 variants confer susceptibility to non-syndromic OM. These variants potentially contribute to middle ear pathology through breakdown of mucosal and epithelial barriers, immunodeficiency such as poor vaccination response, alteration of head and neck microbiota and facilitation of entry of opportunistic pathogens into the middle ear.

A2ML1 and otitis media: novel variants, differential expression, and relevant pathways

A genetic basis for otitis media is established, however, the role of rare variants in disease etiology is largely unknown. Previously a duplication variant within A2ML1 was identified as a significant risk factor for otitis media in an indigenous Filipino population and in US children. In this report exome and Sanger sequencing was performed using DNA samples from the indigenous Filipino population, Filipino cochlear implantees, US probands, Finnish, and Pakistani families with otitis media. Sixteen novel, damaging A2ML1 variants identified in otitis media patients were rare or low-frequency in population-matched controls. In the indigenous population, both gingivitis and A2ML1 variants including the known duplication variant and the novel splice variant c.4061 + 1 G>C were independently associated with otitis media. Sequencing of salivary RNA samples from indigenous Filipinos demonstrated lower A2ML1 expression according to the carriage of A2ML1 variants. Sequencing of additional salivary RNA samples from US patients with otitis media revealed differentially expressed genes that are highly correlated with A2ML1 expression levels. In particular, RND3 is upregulated in both A2ML1 variant carriers and high-A2ML1 expressors. These findings support a role for A2ML1 in keratinocyte differentiation within the middle ear as part of otitis media pathology and the potential application of ROCK inhibition in otitis media.

FUT2 Variants Confer Susceptibility to Familial Otitis Media

Non-secretor status due to homozygosity for the common FUT2 variant c.461G>A (p.Trp154∗) is associated with either risk for autoimmune diseases or protection against viral diarrhea and HIV. We determined the role of FUT2 in otitis media susceptibility by obtaining DNA samples from 609 multi-ethnic families and simplex case subjects with otitis media. Exome and Sanger sequencing, linkage analysis, and Fisher exact and transmission disequilibrium tests (TDT) were performed. The common FUT2 c.604C>T (p.Arg202∗) variant co-segregates with otitis media in a Filipino pedigree (LOD = 4.0). Additionally, a rare variant, c.412C>T (p.Arg138Cys), is associated with recurrent/chronic otitis media in European-American children (p = 1.2 × 10-5) and US trios (TDT p = 0.01). The c.461G>A (p.Trp154∗) variant was also over-transmitted in US trios (TDT p = 0.01) and was associated with shifts in middle ear microbiota composition (PERMANOVA p < 10-7) and increased biodiversity. When all missense and nonsense variants identified in multi-ethnic US trios with CADD > 20 were combined, FUT2 variants were over-transmitted in trios (TDT p = 0.001). Fut2 is transiently upregulated in mouse middle ear after inoculation with non-typeable Haemophilus influenzae. Four FUT2 variants-namely p.Ala104Val, p.Arg138Cys, p.Trp154∗, and p.Arg202∗-reduced A antigen in mutant-transfected COS-7 cells, while the nonsense variants also reduced FUT2 protein levels. Common and rare FUT2 variants confer susceptibility to otitis media, likely by modifying the middle ear microbiome through regulation of A antigen levels in epithelial cells. Our families demonstrate marked intra-familial genetic heterogeneity, suggesting that multiple combinations of common and rare variants plus environmental factors influence the individual otitis media phenotype as a complex trait.

Middle ear microbiome differences in indigenous Filipinos with chronic otitis media due to a duplication in the A2ML1 gene

Background

Previously rare A2ML1 variants were identified to confer otitis media susceptibility in an indigenous Filipino community and in otitis-prone US children. The goal of this study is to describe differences in the middle ear microbiome between carriers and non-carriers of an A2ML1 duplication variant that increases risk for chronic otitis media among indigenous Filipinos with poor health care access.

Methods

Ear swabs were obtained from 16 indigenous Filipino individuals with chronic otitis media, of whom 11 carry the A2ML1 duplication variant. Ear swabs were submitted for 16S rRNA gene sequencing.

Results

Genotype-based differences in microbial richness, structure, and composition were identified, but were not statistically significant. Taxonomic analysis revealed that the relative abundance of the phyla Fusobacteria and Bacteroidetes, and genus Fusobacterium were nominally increased in carriers compared to non-carriers, but were non-significant after correction for multiple testing. We also detected rare bacteria including Oligella that was reported only once in the middle ear.

Conclusions

These findings suggest that A2ML1-related otitis media susceptibility may be mediated by changes in the middle ear microbiome. Knowledge of middle ear microbial profiles according to genetic background can be potentially useful for therapeutic and prophylactic interventions for otitis media and can guide public health interventions towards decreasing otitis media prevalence within the indigenous Filipino community.

Electronic supplementary material

The online version of this article (doi:10.1186/s40249-016-0189-7) contains supplementary material, which is available to authorized users.

Genetic and Environmental Determinants of Otitis Media in an Indigenous Filipino Population

OBJECTIVE

To identify genetic and environmental risk factors for otitis media in an indigenous Filipino population.

STUDY DESIGN

Cross-sectional study.

SETTING

Indigenous Filipino community.

SUBJECTS AND METHODS

Clinical history and information on breastfeeding, tobacco smoke exposure, and swimming were obtained from community members. Heads of households were interviewed for family history and personal beliefs on ear health. Height and weight were measured. Otoscopic findings were described for the presence and character of perforation or discharge. An A2ML1 duplication variant that confers otitis media susceptibility was Sanger sequenced in all DNA samples. Co-occurrence of middle ear bacteria detected by 16S rRNA gene sequencing was determined according to A2ML1 genotype and social cluster.

RESULTS

The indigenous Filipino population has a ~50% prevalence of otitis media. Young age was associated with otitis media (4 age strata; P = .004); however, age was nonsignificant as a bistratal or continuous variable. There was no association between otitis media and sex, body mass index, breastfeeding, tobacco exposure, or deep swimming. In multivariate analyses, A2ML1 genotype is the strongest predictor of otitis media, with an odds ratio of 3.7 (95% confidence interval: 1.3-10.8; P = .005). When otitis media diagnoses were plotted across ages, otitis media was observed within the first year of life, and chronic otitis media persisted up to adulthood, particularly in A2ML1-variant carriers.

CONCLUSION

Among indigenous Filipinos, A2ML1 genotype is the primary risk factor for otitis media and main determinant of disease progression, although age, the middle ear microbiome, and social clusters might modulate the effect of the A2ML1 genotype.

Validity of a filipino translation of the Tinnitus Handicap Inventory

OBJECTIVE

To determine the validity and reliability of a Filipino translation of the Tinnitus Handicap Inventory (THI), a self-report measure of tinnitus handicap.

DESIGN

Psychometric cross-sectional validation Study sample: Seventy-five patients, aged 18-82 with tinnitus recruited consecutively at the Ear Unit of the Philippine General Hospital after receiving assessment at the Ear, Nose, and Throat-Out Patient Department.

RESULTS

The THI-PH showed robust internal consistency reliability (Cronbach's alpha = 0.92), only slightly lower than the original version (THI-US Cronbach's alpha = 0.93), and its Danish (Cronbach's alpha = 0.93), Portuguese (Cronbach's alpha = 0.94), and German (Cronbach's alpha = 0.93) translations. Two of the subscales, the Functional and Emotional subscales, also showed good internal consistency reliability (Cronbach's alpha = 0.86 and Cronbach's alpha = 0.82, respectively). The Catastrophic subscale showed poorer internal consistency reliability (Cronbach's alpha = 0.63) due to the shorter number of items in that scale.

CONCLUSION

The results of the present study suggest that the THI-PH is a valid and reliable tool that can be used to quantify the effects of tinnitus on the quality of life of Filipino tinnitus patients.

Echinococcosis presenting as an otogenic brain abscess: an unusual lesion of the middle ear cleft and temporal lobe

This paper presents a case of a 28-year-old male with a seizure episode and a 4-year history of intermittent tinnitus on the left ear. On computed tomography and magnetic resonance imaging, a density with rim enhancement was found at the temporal lobe, associated with mastoid tegmen destruction and middle ear mass, indicating cholesteatoma with complicating brain abscess. Evacuation of the brain abscess was performed with a combined otolaryngologic and neurosurgical procedures (canal wall-down mastoidectomy and temporal craniotomy). The pathology turned out to be infestation with Echinococcus granulosus.

Training of nurses in ear examination and hearing screening in the school setting

The objectives of this study were to determine the agreement between the ear examination findings of the otorhinolaryngologist (trainer) and the elementary school nurse (trainee) after training with the use of a penlight and to determine the mean sound pressure level (SPL) produced by school nurses as a standard parameter for hearing screening using a 512 tuning fork after training on tuning fork testing by the otorhinolaryngologist. Training workshops in ear examination using a penlight and hearing screening using a 512 tuning fork were conducted for school nurses. Data for assessment of ear examination skills and production of SPL were collected by questionnaire and observation of performance. Kappa statistics were used to assess agreement between trainees' and trainer's responses. Mean and standard deviation were determined for the assessment of the SPL produced. Results showed an excellent agreement between the school nurses' and otorhinolaryngologist's observations on ear examination. These included observations of the ear canal, visualization of the tympanic membrane and identification of unusual findings such as wax and discharge. The majority of nurses responded positively in terms of the ease and confidence in performance of the procedure. Regarding tuning fork testing, the nurses were able to produce significant SPL. The mean SPL produced by the nurses using a 512 tuning fork was 56.316 dB.

Evoked otoacoustic emissions and auditory brainstem responses: concordance in hearing screening among high-risk children

OBJECTIVE

Evoked otoacoustic emissions (OAEs) and diagnostic auditory brainstem responses (ABRs) were determined in 379 high-risk children referred for hearing screening.

MATERIAL AND METHODS

This was a retrospective, cross-sectional study. The records of 379 children referred for hearing screening between January 2002 and March 2003 at the Ear Unit of the Philippine General Hospital were evaluated.

RESULTS

Of the 379 children, 53.6% were male and 46.4% were female and the mean age was 41+/-47 months. The age distribution was as follows: < or = 12 months, 32.2%; 12-24 months, 52.2%; and > 24 months, 11%. Out of 229 right and 232 left ears, 111 (48.5%) and 112 (48.3%) had "pass" responses and 113 (49.3%) and 116 (50.5%) had "refer" responses, respectively. Five right and four left ears had "noise" responses. Out of 266 right and 209 left ears, the ABR results showed 72 (27.1%) and 30 (14.4%) with normal auditory pathways and 194 (72.9%) and 179 (85.6%) with abnormal auditory pathways, respectively. Of the 131 children whose parents gave their consent for concomitant OAE and ABR testing, agreements were observed between the two tests in terms of classifying the results as normal or abnormal of 78.9% (kappa = 0.51; p = 0.00) in right and 78.6% (kappa = 0.51; p = 0.00) in left ears. When the children were classified as either "with hearing loss-bilateral abnormal ABRs" or "at least one normal ABR", there was an observed agreement of 81% (kappa = 0.6; p = 0.00). OAEs had a sensitivity of 76.9% (95% CI 66.7-84.8%) and a specificity of 90% (95% CI 75.4-96.7%).

CONCLUSION

There is good concordance between OAE and ABR results among high-risk children referred for hearing screening.