Systems biology analysis of RNA-binding protein aggregation during cellular aging

细胞衰老过程中RNA结合蛋白聚集的系统生物学分析

• 批准号: 10211598
• 负责人: Nan Hao
• 金额: $ 45.32万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-15 至 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10211598
• 关键词: Affect; Age; Aging; Alzheimer' s Disease; Binding Proteins; Biochemical; Biological Models; Biophysics; Cell Aging; Cell physiology; Cells; Communities; Complement; Complex; Controlled Environment; Data; Deacetylase; Disease; Foundations; Gene Expression; Gene Expression Regulation; Genes; Genomics; Imaging technology; Individual; Libraries; Light; Link; Liquid substance; Longevity; Lysine; Malignant Neoplasms; Measurement; Mediating; Messenger RNA; Methods; Microfluidic Microchips; Microfluidics; Microscopy; Neurodegenerative Disorders; Pathologic; Pathway interactions; Phase; Phase Transition; Phenotype; Play; Post-Transcriptional Regulation; Prevention strategy; Process; Property; Proteins; Proteome; Proteomics; RNA analysis; RNA metabolism; RNA-Binding Proteins; Ribonucleoproteins; Role; Saccharomyces cerevisiae; Solid; Structure; System; Systems Biology; Technology; Testing; Time; Yeasts; age related; cellular imaging; data integration; data sharing; design; experimental study; functional decline; innovation; insight; microfluidic technology; mutant; overexpression; population based; prion-like; protein aggregation; proteostasis; response; screening; sensor; therapeutic development; tool; transcriptome; web site

Project Summary RNA-binding proteins (RBPs) play key roles in regulating gene expression and many cellular functions. A lot of RBPs are aggregation-prone due to their low complexity, prion-like domains. While naturally-occurring aggregation of RBPs is important for the compartmentalized control of RNA metabolism, aberrant aggregation is detrimental and is associated with many diseases, in particular, age-related diseases such as neurodegenerative diseases and cancers. However, a systematic analysis of RBP aggregation and its functional consequences during aging remains lacking. Here we propose to conduct a systems biology analysis of age- dependent RBP aggregation using the replicative aging of S.cerevisiae as a model system. Our initial screen has identified positive RBP candidates that aggregate upon aging-related perturbations. Building upon these findings, we will combine innovative microfluidics with single-cell imaging technologies to systematically characterize these RBP aggregates during aging and to evaluate how these aggregates influence gene expression, aging phenotypes and the lifespan of individual living cells. In Aim 1, we will systematically characterize each of the identified RBPs that aggregate during aging. We will determine the biophysical and biochemical properties, material state and phase transition of RBP aggregates at different stages of the lifespan, which will provide important clues about how these aggregates influence cell physiology during aging. In Aim 2, we will investigate the interplay between RBP aggregation and cellular aging, focusing on how aggregation of RBPs is regulated by conserved aging-related pathways or factors, and how these aggregates contribute to age- dependent cellular changes and the final lifespan. In Aim 3, we will evaluate how RBP aggregation contributes to the proteomic changes during aging. We will use a newly-developed high-throughput microfluidic platform to identify target genes that are regulated by RBP aggregation and will examine their influences on aging, establishing the functional links among RBP aggregation, proteomic changes and aging phenotypes. Finally, we will integrate all the data generated in Aims 1, 2 and 3, delineate a systems-level regulatory network of RBP aggregation during yeast replicative aging, and develop a dedicated website for sharing the data to the scientific community. The RBP-regulated network will provide mechanistic insights into the causes, control and consequences of pathological RBP aggregation in aging and will be used to guide the design of new hypotheses and experiments, laying the foundation for the development of therapeutic and preventive strategies towards age-associated diseases.

项目摘要 RNA结合蛋白（RBP）在调节基因表达和许多细胞功能中起着关键作用。很多 RBP由于其低复杂性、朊病毒样结构域而易于聚集。虽然是自然发生的 RBP的聚集对于RNA代谢的区室化控制、异常聚集和细胞内的细胞外基质的形成是重要的。 是有害的，并且与许多疾病有关，特别是与年龄有关的疾病， 神经退行性疾病和癌症。然而，系统分析RBP聚集及其功能， 衰老的后果仍然缺乏。在这里，我们建议对年龄进行系统生物学分析- 使用酿酒酵母的复制老化作为模型系统的依赖性RBP聚集。我们的初始屏幕 已经确定了积极的RBP候选人聚集在老化相关的扰动。在此基础上， 研究结果，我们将联合收割机与单细胞成像技术相结合， 在老化过程中表征这些RBP聚集体，并评估这些聚集体如何影响基因表达， 表达、老化表型和个体活细胞的寿命。在目标1中，我们将系统地 表征老化过程中聚集的每种已识别的RBP。我们将确定生物物理和 RBP聚集体在生命周期不同阶段的生物化学性质、物质状态和相变， 这将提供关于这些聚集体如何在衰老过程中影响细胞生理学的重要线索。在目标2中， 我们将研究RBP聚集和细胞衰老之间的相互作用，重点是RBP聚集是如何发生的。 RBP受保守的衰老相关途径或因子的调节，以及这些聚集体如何影响年龄- 依赖细胞变化和最终寿命。在目标3中，我们将评估RBP聚合如何贡献 衰老过程中蛋白质组的变化。我们将使用新开发的高通量微流控平台， 确定由RBP聚集调节的靶基因，并将检查它们对衰老的影响， 建立RBP聚集、蛋白质组变化和衰老表型之间的功能联系。最后我们 将整合目标1、2和3中产生的所有数据，描绘限制性商业惯例的系统级监管网络 聚合在酵母复制老化，并开发一个专门的网站，分享数据的科学 社区限制性商业惯例监管网络将提供对原因、控制和 的病理性RBP聚集在衰老的后果，并将用于指导新的假设设计 为制定治疗和预防战略奠定基础， 与年龄相关的疾病。