scRNA-seq of P2 mouse cochlea

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 323,978) and identified 31 genome-wide significant risk loci for self-reported hearing difficulty (p < 5e-8), of which 30 have not been reported previously at genome-wide significance. We interpreted these loci in the context of newly generated ATAC-seq and single-cell RNA-seq from cells in the mouse cochlea. Risk-associated genes were enriched for expression in cochlear epithelial and non-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 sensory 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, at least 45 were expressed in mouse cochlea and 15 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. Examination of expression patterns of genes expressed in day 2 mouse cochlea.年龄相关性听力损失（Age-related hearing impairment, ARHI）是最常见的医学病症之一，具有高度可遗传性，但其遗传病因在很大程度上仍未明确。我们对英国生物银行（UK Biobank）中多项听力相关性状的全基因组关联研究（Genome-Wide Association Study, GWAS）汇总统计数据开展了荟萃分析，样本量最高达323,978例，最终鉴定出31个与自我报告的听力困难相关的全基因组显著性风险位点（p < 5×10^-8），其中30个此前未被报道达到全基因组显著性水平。 我们结合新生成的小鼠耳蜗细胞的转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing, ATAC-seq）与单细胞RNA测序（single-cell RNA-seq）数据，对上述位点进行了功能注释。风险关联基因在耳蜗上皮细胞与非上皮细胞中呈现表达富集，同时也富集于与感觉感知相关的基因以及已知的孟德尔式耳聋基因，这佐证了这些基因与听觉功能的相关性。 即便是在校正了进化保守性和细胞类型非特异性调控区域的基础效应后，与小鼠感觉上皮细胞开放染色质同源的人类基因组区域，仍显著富集听力困难的遗传风险位点。 通过表观基因组学与统计学精细定位分析，我们最终筛选出50个潜在风险基因。其中至少45个可在小鼠耳蜗中检测到表达，15个特异性富集于感觉毛细胞。 本研究揭示了多个与听力困难相关的新型风险位点与风险基因，提示耳蜗感觉上皮的基因调控异常在年龄相关性听力损失中发挥关键作用。本研究同时对小鼠出生后第2天耳蜗组织的基因表达模式进行了分析。