Burden of novel and ultra-rare missense variants in the NF-κB pathway genes associated to Ménière's disease.

INTRODUCTION: Ménière's disease (MD) is an inner ear disorder characterised by tinnitus, sensorineural hearing loss and dizziness, although around 60% of patients also exhibit and immune dysregulation. Transcriptomic studies have identified three distinct immune phenotypes in MD, classified based on systemic inflammation, cytokine profiles and association to autoinflammatory/autoimmune comorbidities. Furthermore, genetic studies have shown aggregation of rare variants in MD patients; however, the relationship between genetic factors and immune responses remains poorly understood.

METHODS: In this study, we analysed exome data pertaining to NF-κB pathway genes to identify ultrarare variants that could contribute to the immune phenotypes observed in MD. Furthermore, we retrieved MD epigenetic and transcriptomic data to search for the associated molecular signature. We performed protein modelling and receptor-ligand docking, as well as differential transcript usage (DTU) and splicing prediction.

RESULTS: We identified ultrarare heterozygous variants in TLR9 (chr3:52222299 G>C and chr3:52223761 C>A), TNFRSF1B (chr1:12167150 C>T and chr1:12202100 G>A), and FAS (chr10:89003139 G>A and chr10:89008919 C>T) in MD patients. Splicing predictions suggested potential creation of cryptic donor/acceptor sites for TLR9 and TNFRSF1B variants. Protein modelling predicted destabilising effects for all three proteins, with altered atomic interactions in TNFRSF1B and FAS. When docked, the TLR9-TLR9 dimer and FAS-FASGL models, redistributed interfacial contacts, potentially reducing binding efficiency, whereas docked TNFRSF1B-TRAF2 interactions were partially maintained.

CONCLUSION: These findings suggest that MD distinct immune phenotypes based on systemic inflammation and may be linked to comorbid autoimmune/autoinflammatory disorders, with rare variants in TLR9, TNFRSF1B and FAS likely contributing to autoinflammation.