Circular RNAs and their interactions with RNA-binding proteins to modulate AD-related neuropathology

环状RNA及其与RNA结合蛋白的相互作用调节AD相关神经病理学

• 批准号: 10436271
• 负责人: Benjamin L Wolozin
• 金额: $ 76.93万
• 依托单位: BOSTON UNIVERSITY MEDICAL CAMPUS
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10436271
• 关键词: 3-Dimensional; Affect; Aging; Alzheimer' s Disease; Alzheimer' s disease brain; Alzheimer' s disease model; Alzheimer' s disease related dementia; Amyotrophic Lateral Sclerosis; Astrocytes; Atlases; Back; Binding; Binding Proteins; Binding Sites; Biogenesis; Biology; Brain; Brain region; C9ORF72; Code; Data; Deposition; Diagnosis; Disease; Elements; Evaluation; Exhibits; Exons; Experimental Designs; Frontotemporal Dementia; Frontotemporal Lobar Degenerations; Functional disorder; Future; Gene Expression Profile; Gene Proteins; Genes; Genetic; Genetic Diseases; Genetic Polymorphism; Genetic Risk; Genome; Genomics; Human; Informatics; Investigation; Late Onset Alzheimer Disease; Link; Location; Mediating; Messenger RNA; Methods; MicroRNAs; Microglia; Molecular; Mutation; Nerve Degeneration; Neurons; Nucleotides; Organoids; Pathology; Pattern; Porifera; Process; Production; Protein Isoforms; Proteins; Proteomics; Publishing; Quantitative Trait Loci; RNA; RNA Binding; RNA Splicing; RNA metabolism; RNA-Binding Proteins; Recording of previous events; Regulation; Research Design; Ribosomal RNA; Site; Spliced Genes; Susceptibility Gene; System; Tissues; Untranslated RNA; Variant; Work; age related; axonal degeneration; circular RNA; crosslinking and immunoprecipitation sequencing; disorder control; frontotemporal lobar dementia-amyotrophic lateral sclerosis; genetic variant; genome wide association study; genome-wide; genomic data; high throughput screening; knock-down; multi-ethnic; neuropathology; novel; novel marker; prevent; protein TDP-43; protein aggregation; protein metabolism; stathmin; synaptic function; tau Proteins; therapeutic target; transcriptome sequencing

SUMMARY New variants, especially in non-coding regions, are expected to be discovered through the ongoing AD Sequencing Project (ADSP). This proposal will investigate circular RNAs (circRNAs) and RNA binding proteins (RBPs) that regulate or are regulated by these circRNAs. Recent genomic studies have discovered thousands of circRNAs produced from both protein-coding genes and non-coding regions of the genome via a process known as back-splicing. CircRNAs are more enriched in neuronal tissues and are often derived from genes specific for neuronal and synaptic function. The discovery of these circRNAs demands a coordinated investigation of RBPs that interact with the circRNAs. Mutations in and dysfunction of RBPs are known to be major mechanisms contributing to the pathophysiology in frontotemporal dementia, ALS and AD. However, the contributions of the circRNA:RBP network to these disease mechanisms are largely unknown. The novel biology of circRNAs opens an entirely new window into mechanisms of neurodegeneration in ADRD. CircRNAs could contribute to neurodegeneration by acting as sponges that sequester miRNA/RBPs away from normal mRNA targets, altering splicing or expression. RBPs also regulate circRNA production by binding to the flanking intronic sequences of circRNAs which contain many conserved binding sites of splicing factors/RBPs. Thus, sequestration of RBPs in protein aggregates could cause dysfunctional regulation of circRNAs. The history of genomics indicate that discovery of each new nucleotide species expands our understanding of disease mechanisms. The discovery of circRNA presents a major unexplored avenue of RNA metabolism that demands investigation. We hypothesize that changes in the levels of circRNAs contributes to the pathophysiology of ADRD, and that discovery of key circRNAs or circRNA-RBP interactions in aging human brains could uncover novel biomarkers, disease mechanisms or therapeutic targets. In this proposal, by leveraging large public and our own RNA-seq data (rRNA-depleted), we will apply several methods to detect and characterize AD-related circRNAs from multiple human brain regions, and integrate them with ADSP genetic findings (Aim 1). In Aim 2, aside from discovering AD-related RBPs from human brain RNA-seq, proteomics and ADSP WES/WGS data, we will leverage the ENCODE CLIP-seq data for RBP binding to identify putative RBP-circRNA interactions with AD, i.e. AD-related functional RNA elements. Finally, in Aim 3, we will select the top 10% of the circRNAs (~200) and RBPs (~150) for further high-throughput functional evaluation with a novel, powerful 3D human organoid model of ADRD, termed AstAD that exhibits the full range of tau pathology and neurodegeneration. We anticipate that our integrative analyses of ADSP genetics, circRNA, mRNA, RBP and the high-throughput AstAD functional screen readouts can help generate testable hypothesis for future molecular mechanisms experimental design.

总结 新的变异，特别是在非编码区，有望通过正在进行的AD发现 测序项目（ADSP）。本论文将研究环状RNA和RNA结合蛋白 （RBP）调节这些circRNA或由这些circRNA调节。最近的基因组研究发现了数千个 从蛋白质编码基因和基因组的非编码区通过一个过程产生的circRNA 称为反向拼接。CircRNA在神经元组织中更富集，通常来源于基因 对神经元和突触功能有特异性这些circRNA的发现需要一个协调的 研究与circRNA相互作用的RBP。已知RBPs的突变和功能障碍是 额颞叶痴呆、ALS和AD的病理生理学的主要机制。但 circRNA：RBP网络对这些疾病机制的贡献在很大程度上是未知的。小说 circRNA的生物学为ADRD中神经退行性变的机制打开了一扇全新的窗户。CircRNA 可能通过充当海绵将miRNA/RBP从正常细胞中隔离出来而导致神经退行性变 mRNA靶点，改变剪接或表达。RBP还通过结合到CircRNA来调节CircRNA的产生 circRNA的侧翼内含子序列，其含有许多剪接因子/RBP的保守结合位点。 因此，RBP在蛋白质聚集体中的螯合可能导致circRNA的功能失调。的 基因组学的历史表明，每一个新核苷酸物种的发现都扩展了我们对 疾病机制。circRNA的发现为RNA代谢提供了一条尚未探索的主要途径， 需要调查我们假设circRNA水平的变化有助于 ADRD病理生理学，以及衰老中关键circRNA或circRNA-RBP相互作用的发现 人类大脑可以发现新的生物标志物、疾病机制或治疗靶点。在这 建议，通过利用大量的公共和我们自己的RNA-seq数据（rRNA耗尽），我们将应用几个 检测和表征来自多个人脑区域的AD相关circRNA的方法， 他们与ADSP基因发现（目的1）。在目标2中，除了从人脑中发现AD相关的RBP外， RNA测序、蛋白质组学和ADSP WES/WGS数据，我们将利用ENCODE CLIP-seq数据进行RBP 结合以鉴定推定的RBP-circRNA与AD的相互作用，即AD相关的功能性RNA元件。最后， 在目标3中，我们将选择前10%的circRNA（~200）和RBP（~150）用于进一步的高通量 功能评价与一种新的，强大的三维人体器官模型ADRD，称为AstAD，表现出 tau蛋白病理学和神经退行性变的全部范围。我们预计，我们的综合分析ADSP 遗传学，circRNA，mRNA，RBP和高通量AstAD功能筛选读数可以帮助产生 未来分子机制实验设计的可检验假设。