Genome-wide screen of otosclerosis in population biobanks: 27 loci and shared associations with skeletal structure

Abstract

Otosclerosis is one of the most common causes of conductive hearing loss, affecting 0.3% of the population. It typically presents in adulthood and half of the patients have a positive family history. The pathophysiology of otosclerosis is poorly understood. A previous genome-wide association study (GWAS) identified a single association locus in an intronic region of RELN. Here, we report a meta-analysis of GWAS studies of otosclerosis in three population-based biobanks comprising 3504 cases and 861,198 controls. We identify 23 novel risk loci (p < 5 × 10^-8) and report an association in RELN and three previously reported candidate gene or linkage regions (TGFB1, MEPE, and OTSC7). We demonstrate developmental stage-dependent immunostaining patterns of MEPE and RUNX2 in mouse otic capsules. In most association loci, the nearest protein-coding genes are implicated in bone remodelling, mineralization or severe skeletal disorders. We highlight multiple genes involved in transforming growth factor beta signalling for follow-up studies.

Fig. 1. Meta-analysis of the genome-wide association studies of otosclerosis in FinnGen, EstBB and UKBB.

GWAS for each individual study cohort was performed using a generalized mixed model with the saddlepoint approximation using SAIGE v0.20, using a kinship matrix as a random effect and covariates as fixed effects. Results are presented for a fixed-effect meta-analysis of effect estimates from the three cohorts, including a total of 3504 cases and 861,198 controls. In the Manhattan plot, chromosomal positions are indicated on the x-axis and -log₁₀(p-value) is presented on the y-axis for each variant. Twenty-seven loci reached genome-wide significance (two-sided p-value < 5×10⁻⁸ to account for multiple comparisons, marked by the dashed line). The included variants were present in at least two cohorts with a cross-cohort minor allele frequency > 0.1% and imputation INFO score ≥ 0.7. The loci are annotated by the names of the coding genes nearest to the lead variants. The exact p-values corresponding to lead variants in each locus are presented in Table 2. Blue and gray colours are used to visually separate chromosomes.

Fig. 2. Localization of RUNX2 and MEPE proteins in the murine cochlea.

a Cross-section through a P12 mouse cochlea stained with anti-MEPE-antibody (brown) and counterstained with hematoxylin (blue). b Immunofluorescent staining for RUNX2 (green) was observed in the nuclei (blue) of P2 osteoblasts. g Lack of RUNX2 expression in the adult otic capsule. c – f Immunofluorescence for MEPE (green) developed from more diffuse (c white arrowhead) to more clearly cellularly localized (f white arrows) with age. SL Spiral ligament. Representative images of N = 3 animals per age group. Scale bars: a: 500 µm, b–g 50 µm.