Biological insights from multi-omic analysis of 31 genomic risk loci for adult hearing difficulty

• Published in: PLoS genetics Vol. 16; no. 9; p. e1009025
• Main Authors: Kalra, Gurmannat, Milon, Beatrice, Casella, Alex M., Herb, Brian R., Humphries, Elizabeth, Song, Yang, Rose, Kevin P., Hertzano, Ronna, Ament, Seth A.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 28.09.2020; Public Library of Science (PLoS)
• Subjects: Adult; Age; Aging (Biology); Animals; Auditory system; Biobanks; Biological Specimen Banks; Biology and Life Sciences; Chromatin; Chromatin - genetics; Cochlea; Cochlea - cytology; Cohort Studies; Deafness; Epigenome; Epithelial cells; Epithelial Cells - physiology; Evolutionary conservation; Female; Gene mapping; Gene regulation; Genes; Genetic aspects; Genetic Loci; Genetic Predisposition to Disease; Genome-Wide Association Study; Genomes; Genomic analysis; Hair cells; Hair Cells, Auditory - cytology; Hair Cells, Auditory - physiology; Health aspects; Hearing aids; Hearing disorders; Hearing loss; Hearing Loss - genetics; Humans; Hypotheses; Medicine; Medicine and Health Sciences; Mice, Inbred ICR; Mice, Inbred Strains; mRNA; Mutation; Neurosciences; Noise; Otolaryngology; Polymorphism, Single Nucleotide; Proteins; Quantitative trait loci; Regulatory sequences; Risk factors; Sensory epithelium; Single-Cell Analysis; Software; Statistical analysis; Supervision; Surgery; Tinnitus; United Kingdom; United Kingdom; United States; United Kingdom > UK; United States > US; Baltimore Maryland
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1009025

Age-related hearing impairment (ARHI), one of the most common medical conditions, is strongly heritable, yet its genetic causes remain largely unknown. We conducted a meta-analysis of GWAS summary statistics from multiple hearing-related traits in the UK Biobank (n = up to 330,759) and identified 31 genome-wide significant risk loci for self-reported hearing difficulty (p < 5x10-8), of which eight have not been reported previously in the peer-reviewed literature. We investigated the regulatory and cell specific expression for these loci by generating mRNA-seq, ATAC-seq, and single-cell RNA-seq from cells in the mouse cochlea. Risk-associated genes were most strongly enriched for expression in cochlear epithelial cells, as well as for genes related to sensory perception and known Mendelian deafness genes, supporting their relevance to auditory function. Regions of the human genome homologous to open chromatin in epithelial cells from the mouse were strongly enriched for heritable risk for hearing difficulty, even after adjusting for baseline effects of evolutionary conservation and cell-type non-specific regulatory regions. Epigenomic and statistical fine-mapping most strongly supported 50 putative risk genes. Of these, 39 were expressed robustly in mouse cochlea and 16 were enriched specifically in sensory hair cells. These results reveal new risk loci and risk genes for hearing difficulty and suggest an important role for altered gene regulation in the cochlear sensory epithelium.