Genetic and epigenomic determinants of hearing loss in Hispanic populations

摘要[最初与R01DC019642一起提交，经最小修改后包含在此处]： 感音神经性听力损失(SNHL)是导致残疾的主要原因，全球约有14亿人受到影响， 包括不同的年龄段和种族。虽然大约150个基因已经被确定为SNHL，但 拉美裔人群对SNHL的研究仍然不足，大多数拉美裔研究集中在单个基因GJB2上。 一些被研究的国家--智利、墨西哥/西班牙裔美国人、菲律宾--GJB2的患病率较低 变种，这表明这些国家的SNHL队列有新的基因或变种可供发现。 此外，西班牙裔儿童在环境中暴露于可能导致表观遗传的化学物质的风险 修改并引起SNHL。我们的主要假设是SNHL有一个独特的，特定于人群的 西班牙裔人群的等位基因和表观遗传谱。我们召集了一个国际小组， 在耳科学、遗传学、表观基因组学和功能基因组学方面具有互补专业知识的研究人员， 以前的协作经验表明，这个项目将具有很高的生产力。在我们之前的研究中，我们 在患有SNHL的西班牙裔美国人和菲律宾人中发现了新的变异，包括 与颞骨异常相关，并预测人工耳蜗术后的结果。我们已经就位 鉴定家系和差异甲基化区域中新的SNHL基因的有效途径 (DMRS)在病例对照队列中，以及在动物模型和上皮细胞中的验证方法。我们的目标是 目的：确定西班牙裔儿童SNHL的遗传和表观遗传危险因素。对于目标1，我们将确定 SNHL变体来自使用分层方法的下一代序列数据，其包括Sanger测序， 筛选、纯合性作图、连锁分析和传递不平衡测试。我们将招募500人 西班牙裔家庭，包括足以在全基因组范围内显著连锁的大家庭，并提交DNA 对样品进行测序和分析。在这些家族中发现的新的SNHL基因和变种将被跟踪 在小鼠和斑马鱼模型中的蛋白质定位和听力研究，以及 上皮细胞。对于目标2，我们将进行表观基因组范围的关联研究，方法是分析一个 根据年龄、性别和人口匹配的500名SNHL先证者和500名听力正常儿童组成的强大队列 以识别与SNHL相关联的DMR。对于排名靠前的DMR，我们将使用CRISPR-dCas9 对上皮细胞的技术，以确定靶向甲基化位置是否会影响基因表达。整合 使用甲基化数量性状基因座分析的甲基化图谱和遗传数据将有助于 了解遗传和环境对SNHL的贡献。总体而言，该项目将影响基因 筛查方案和遗传咨询，特别是在西班牙裔人口中，以及改善 了解听力机制，为SNHL治疗的发展提供新的靶点。 在这项为期两年的多样性补充文件中，工作重点将放在目标1和目标2的开始。

ABSTRACT [originally submitted with R01DC019642 and included here with minimal modifications]: Sensorineural hearing loss (SNHL) is a leading cause of disability and affects ~1.4 billion people globally, including different age groups and ethnicities. Although around 150 genes have been identified for SNHL, the Hispanic population remains understudied for SNHL, with most Hispanic studies focused on a single gene GJB2. A few countries studied – Chile, Mexico/Hispanic-American, the Philippines – have a low prevalence of GJB2 variants, suggesting that SNHL cohorts from these countries have novel genes or variants for discovery. Additionally, Hispanic children are at risk for environmental exposures to chemicals that may lead to epigenetic modifications and cause SNHL. Our overarching hypothesis is that SNHL has a unique, population-specific allelic and epigenetic spectrum in Hispanic-descent populations. We assembled an international group of researchers with complementary expertise in otology, genetics, epigenomics and functional genomics, with previous collaborative experience that signals this project will be highly productive. In our previous studies, we identified novel variants in Hispanic-American and Filipino patients with SNHL, including genetic variants that were associated with temporal bone anomalies and predictive of cochlear implant outcomes. We have in place efficient pipelines for the identification of novel SNHL genes in families and differentially methylated regions (DMRs) in case-control cohorts, as well as validation methods in animal models and epithelial cells. Our goal is to determine genetic and epigenetic risk factors in Hispanic children with SNHL. For Aim 1, we will identify SNHL variants from next-generation sequence data using a tiered approach, which includes Sanger sequencing, filtering, homozygosity mapping, linkage analysis and transmission disequilibrium tests. We will recruit 500 Hispanic families, including large families sufficient for genome-wide significant linkage, and submit DNA samples to sequencing and analyses. Novel SNHL genes and variants identified in these families will be followed up with protein localization and hearing studies in mouse and zebrafish models, and mutation constructs in epithelial cells. For Aim 2, we will perform an epigenome-wide association study by profiling the methylome of a well-powered cohort of 500 SNHL probands and 500 hearing children matched by age, sex and population, in order to identify DMRs that are associated with SNHL. For the top identified DMRs, we will utilize CRISPR-dCas9 technology on epithelial cells to determine if targeting the methylation site will affect gene expression. Integration of methylation profiles and genetic data using methylation quantitative trait locus analysis will aid in understanding genetic vs. environmental contributions to SNHL. Overall, this project will impact genetic screening protocols and genetic counseling particularly in Hispanic populations, as well as improve understanding of the hearing mechanism and lead to new targets for the development of treatment of SNHL. For this two-year diversity supplement, work will focus on Aim 1 and the beginning of Aim 2.