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: 10661772
• 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/10661772
• 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; Dedications; 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; 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(RNAbindingProteins，RBPs)在调控基因表达和多种细胞功能中起着关键作用。很多 限制性商业惯例是易于聚集的，因为它们的低复杂性，类病毒结构域。而自然发生的 限制性商业惯例的聚集对于RNA代谢的区隔调控、异常聚集、 是有害的，并与许多疾病有关，特别是与年龄有关的疾病，如 神经退行性疾病和癌症。然而，对RBP聚集及其功能的系统分析 衰老过程中的后果仍然是未知的。在这里，我们建议对年龄进行系统生物学分析- 以酿酒酵母复制老化为模型系统的依赖RBP聚集。我们的初始屏幕 已经确定了积极的RBP候选对象，这些候选对象在老化相关的扰动下聚合在一起。建立在这些基础上 我们将把创新的微流控技术与单细胞成像技术相结合，系统地 描述这些RBP聚集体在衰老过程中的特征，并评估这些聚集体如何影响基因 表达、衰老表型和单个活细胞的寿命。在目标1中，我们将系统地 描述在老化过程中聚集的每个已识别的限制性商业惯例的特征。我们将确定生物物理和 RBP聚集体在寿命的不同阶段的生化性质、物质状态和相变， 这将为这些聚集体在衰老过程中如何影响细胞生理提供重要线索。在目标2中， 我们将研究RBP聚集和细胞老化之间的相互作用，重点是如何聚集 限制性商业惯例受到保守的衰老相关途径或因素的调节，以及这些聚集体是如何促进衰老的。 依赖细胞的变化和最终寿命。在目标3中，我们将评估RBP聚合如何做出贡献 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来 确定受RBP聚集调控的靶基因，并将研究它们对衰老的影响， 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、目标2和目标3产生的所有数据，勾勒出RBP的系统级监管网络 酵母复制老化过程中的聚合，并开发一个专门的网站，以便将数据分享给科学人员 社区。RBP监管的网络将提供对原因、控制和 病理性RBP聚集在衰老中的后果，并将用于指导新假说的设计 和实验，为制定治疗和预防策略奠定了基础 与年龄相关的疾病。