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

基本信息

批准号：
10217628
负责人：
Benjamin L Wolozin
金额：
$ 77.35万
依托单位：
BOSTON UNIVERSITY MEDICAL CAMPUS
依托单位国家：
美国
项目类别：
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/10217628
关键词：
3-Dimensional Affect Aging Alzheimer&apos s Disease Alzheimer&apos s disease model Alzheimer&apos s disease related dementia Amyotrophic Lateral Sclerosis Astrocytes Atlases Axon 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 Synapses System Tissues Untranslated RNA Variant Work age related 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 synaptic function tau Proteins therapeutic target transcriptome sequencing

项目摘要

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.

概括期望通过正在进行的广告发现新的变体，尤其是在非编码区域测序项目（ADSP）。该建议将研究圆形RNA（CIRCRNA）和RNA结合蛋白（RBP）由这些ciRCRNA调节或调节。最近的基因组研究发现了数千个由基因组的蛋白质编码基因和非编码区域产生的ciRCRNA通过一个过程被称为后拼图。 CircrNA在神经元组织中更富集，并且通常源自基因特定于神经元和突触功能。这些circrnas的发现需要协调与CIRCRNA相互作用的RBP的研究。 RBP的突变和功能障碍已知额颞痴呆，ALS和AD的病理生理学的主要机制。但是， 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中神经退行性的机制打开了一个全新的窗口。 circrnas 可以通过充当海绵，从而使miRNA/rbps脱离正常 mRNA靶标，改变剪接或表达。 RBP还通过与 CIRCRNA的内含子序列，其中包含许多保守的剪接因子/RBP的结合位点。因此，蛋白质聚集体中RBP的固换可能导致CIRCRNA功能失调的调节。这基因组学史表明，每种新核苷酸物种的发现都扩大了我们对疾病机制。 Circrna的发现提出了RNA代谢的主要未开发的大道需要调查。我们假设CIRCRNA水平的变化有助于 ADRD的病理生理，以及在衰老中发现关键的CircrNA或Circrna-RBP相互作用人的大脑可以发现新颖的生物标志物，疾病机制或治疗靶标。在这个提案，通过利用大型公众和我们自己的RNA-seq数据（耗尽RRNA），我们将应用几个从多个人脑区域检测和表征与广告相关的CIRCRNA的方法，并整合它们具有ADSP遗传发现（AIM 1）。在AIM 2中，除了发现与人脑的广告相关的RBP之外 RNA-seq，蛋白质组学和ADSP WES/WGS数据，我们将利用RBP的编码剪辑数据结合以鉴定推定的RBP-CIRCRNA与AD的相互作用，即与AD相关的功能RNA元素。最后，在AIM 3中，我们将选择CIRCRNA（〜200）和RBP（〜150）的前10％具有新型，强大的3D人体器官ADRD的功能评估，称为Astad TAU病理和神经退行性的全部范围。我们预计我们对ADSP的综合分析遗传学，Circrna，mRNA，RBP和高通量Astad功能屏幕读数可以帮助产生未来分子机制实验设计的可检验假设。