Uncovering novel biological processes and pathogenic mechanisms for glaucoma

揭示青光眼的新生物过程和致病机制

• 批准号: 10171860
• 负责人: Ayellet Vered Segre
• 金额: $ 74.47万
• 依托单位: MASSACHUSETTS EYE AND EAR INFIRMARY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-06-01 至 2025-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10171860
• 关键词: ATAC-seq; Affect; Alleles; Alternative Splicing; Autopsy; Biological; Biological Process; Blindness; Cell Death; Cells; Chromatin; Ciliary Body; Complex; Computing Methodologies; DNA; DNA sequencing; Data; Disease; Disease susceptibility; Drug Targeting; Etiology; Eye; Eye diseases; Functional disorder; Gene Expression; Gene Expression Regulation; Gene set enrichment analysis; Genes; Genetic; Genetic Transcription; Genetic study; Genomic Segment; Genomics; Genotype; Genotype-Tissue Expression Project; Glaucoma; Goals; Heritability; Human; Human Genetics; Investigation; Lead; Link; Linkage Disequilibrium; Maps; Measures; Methods; Molecular; Nerve Degeneration; Online Systems; Optic Nerve; Pathogenicity; Pathway interactions; Patients; Physiologic Intraocular Pressure; Predisposition; Prevention; Primary Open Angle Glaucoma; Primary Prevention; Protein Isoforms; QTL Genes; Regulation; Research; Research Support; Resources; Retina; Retinal Degeneration; Retinal Ganglion Cells; Risk; Risk Factors; Statistical Data Interpretation; Statistical Methods; Structure of sinus venosus of sclera; Systems Biology; Testing; Therapeutic; Tissue Sample; Tissues; Trabecular meshwork structure; Translating; Untranslated RNA; Variant; Work; causal variant; cell type; disorder risk; functional genomics; gene expression variation; gene therapy; genetic association; genetic risk factor; genetic variant; genome sequencing; genome wide association study; genomic locus; improved; insight; macula; new therapeutic target; novel; novel therapeutics; optic nerve disorder; sharing platform; single-cell RNA sequencing; statistics; therapeutic development; therapy design; trait; transcriptome; transcriptome sequencing; web site; whole genome

Project Summary/Abstract Glaucoma is a leading cause of irreversible vision loss affecting 60 million people world-wide. Despite this, prevention and treatment of glaucoma are limited. Primary open angle glaucoma (POAG), the most common form, is characterized by progressive retinal ganglion cell death leading to optic neuropathy, often caused by elevated intraocular pressure (IOP). The long-term goals of the proposed research are to identify genomic regions that affect gene expression in glaucoma-relevant eye tissues, and in combination with large-scale human genetic association studies, to uncover novel causal genes and key biological processes that can lead to glaucoma, which may serve as effective drug targets for novel therapies. Genome-wide association studies (GWAS) have led to the discovery of over 20 genomic loci associated with POAG and over 100 loci associated with IOP, however extracting biological insights from these genetic associations has been challenging, largely due to the fact that the associated variants lie in noncoding regions. Furthermore, much of the heritability of glaucoma has yet to be detected. The Genotype-Tissue Expression (GTEx) project has shown that genetic variants associated with gene expression variation (eQTLs) substantially contribute to disease risk, however GTEx does not contain data for ocular tissues. The working hypothesis of the proposed research, supported by our preliminary results, is that hundreds of regulatory effects will contribute to the pathogenicity of glaucoma and will explain much of its heritability, and that the affected genes will cluster in disease-relevant biological processes. We thus propose in Aim 1, to create a high-quality map of the transcriptome and open chromatin regions (indicative of transcriptional activity), and to identify genetic variants associated with gene expression (eQTLs) and alternative splicing (sQTLs) in four key pathogenic tissues for glaucoma: outflow pathway (trabecular meshwork and Schlemm’s canal), ciliary body, optic nerve, and macular retina, collected from 100 postmortem donors. We will use RNA-seq, ATAC-seq, and whole genome sequencing on bulk tissue and we will further identify cell type-specific eQTLs and sQTLs using cell type-specific gene expression profiles from single cell RNA-seq studies that are available to us. In Aim 2, we will apply novel computational and statistical methods that integrate data from Aim 1 with GWAS data of high or normal-tension glaucoma and several risk factor traits, with the goal of identifying new genetic associations, and the underlying causal genes, pathways, and pathogenic cell types for glaucoma. To broaden the impact of our work, we will build a web-based platform for sharing, browsing, and inspecting gene expression and genetic regulation data from the different eye tissues in relation to genetic associations with glaucoma and other complex eye traits (Aim 3). The proposed research is expected to significantly improve our understanding of the pathophysiology of glaucoma, uncover novel genetic risk factors, and open new avenues for therapeutic development. Our genomics eye resource will also be valuable for studying the molecular causes of other eye diseases, such as retinal degeneration diseases, and for tissue-targeted gene therapy design.

项目概要/摘要 青光眼是影响全球 6000 万人的不可逆转视力丧失的主要原因。尽管如此， 青光眼的预防和治疗有限。原发性开角型青光眼 (POAG)，最常见的形式， 其特征是进行性视网膜神经节细胞死亡，导致视神经病变，通常由升高引起 眼压（IOP）。拟议研究的长期目标是确定基因组区域 影响青光眼相关眼组织的基因表达，并与大规模人类遗传相结合 关联研究，揭示可能导致青光眼的新致病基因和关键生物过程， 可以作为新疗法的有效药物靶点。全基因组关联研究（GWAS）已导致 发现了超过 20 个与 POAG 相关的基因组位点和超过 100 个与 IOP 相关的基因座，但是提取 从这些遗传关联中获得生物学见解一直具有挑战性，很大程度上是因为相关的事实 变体位于非编码区。此外，青光眼的大部分遗传性尚未被发现。这 基因型组织表达 (GTEx) 项目表明，遗传变异与基因表达相关 变异（eQTL）极大地增加了疾病风险，但 GTEx 不包含眼组织的数据。 拟议研究的工作假设得到我们初步结果的支持，即数百个 调节作用将导致青光眼的致病性，并解释其遗传性的大部分原因，并且 受影响的基因将聚集在与疾病相关的生物过程中。因此，我们在目标 1 中建议，创建 转录组和开放染色质区域（表明转录活性）的高质量图谱，以及 识别与基因表达 (eQTL) 和选择性剪接 (sQTL) 相关的四个关键基因变异 青光眼的致病组织：流出通路（小梁网和施累姆氏管）、睫状体、 视神经和黄斑视网膜，取自 100 名死后捐献者。我们将使用 RNA-seq、ATAC-seq 和 对大块组织进行全基因组测序，我们将使用以下方法进一步鉴定细胞类型特异性的 eQTL 和 sQTL 我们可以获得来自单细胞 RNA-seq 研究的细胞类型特异性基因表达谱。在目标 2 中，我们 将应用新颖的计算和统计方法，将目标 1 的数据与高或低水平的 GWAS 数据相结合 正常眼压性青光眼和一些危险因素特征，目的是确定新的遗传关联，以及 青光眼的潜在致病基因、途径和致病细胞类型。为了扩大我们的影响 工作中，我们将建立一个基于网络的平台，用于共享、浏览和检查基因表达和遗传 来自不同眼组织的与青光眼和其他复杂疾病的遗传关联相关的调节数据 眼睛特征（目标 3）。拟议的研究预计将显着提高我们对 青光眼的病理生理学，发现新的遗传危险因素，并开辟新的治疗途径 发展。我们的眼睛基因组学资源对于研究其他眼睛的分子原因也很有价值 疾病，例如视网膜变性疾病，以及组织靶向基因治疗设计。