Deciphering dynamic signals in control of cell fate decisions

破译控制细胞命运决定的动态信号

• 批准号: 10656487
• 负责人: Robin E. C. Lee
• 金额: $ 40.2万
• 依托单位: UNIVERSITY OF PITTSBURGH AT PITTSBURGH
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10656487
• 关键词: Biological; Cell Culture Techniques; Cell Death; Cell Fate Control; Cell Line; Cell Nucleus; Cell membrane; Cells; Cellular Structures; Coculture Techniques; Code; Computational Technique; Cytoplasm; Data; Data Set; Decision Making; Disease; Frequencies; Genetic Transcription; Goals; Heterogeneity; Hybrids; Immune; Inflammation; Inflammatory; Knowledge; Learning; Ligand Binding; Link; Measurement; Mediating; Modeling; Pathway interactions; Process; Proliferating; Property; Protein translocation; Proteins; Reporter; Robot; Signal Induction; Signal Pathway; Signal Transduction; Stimulus; Structure; System; Testing; Time; Tumor Necrosis Factor Receptor; cancer cell; computer framework; experimental study; high dimensionality; in vivo; information processing; live cell microscopy; molecular dynamics; protein complex; quantitative imaging; rate of change; rational design; response; therapy design

PROJECT SUMMARY In the long-term, our goal is to understand how single cells integrate and process information to make irreversible decisions such as whether to proliferate, differentiate or die. Inflammatory factors that participate in many normal and diseased cell fate decisions initiate signals by dynamically re-organizing proteins within the cell. For example, ligand-bound TNF receptors transiently organize large protein complexes near the plasma membrane, and these are visible within the cell as discrete punctate structures, whereas other proteins translocate between cellular compartments such as the cytoplasm and the nucleus. It is an emerging principle that dynamic properties of molecules within signal transduction circuits provide temporal codes (including rate of change, amplitude, duration or frequency among others) that are critical to each cell’s response to stimulus. Given that there is substantial cell-to-cell heterogeneity, even in clonal cell lines, static measurements at fixed time points cannot reveal the mechanisms of dynamic information processing. We hypothesize that components of the same signaling pathway are deterministically linked to one another in a single cell, even though there is substantial heterogeneity between cells. Here, we propose to multiplex expression of live-cell fluorescent reporters for up- and down-stream components of the same signaling pathway in the same cell, and correlate time-varying signals from live-cell microscopy data. We will also multiplex expression for reporters between pathways predicted to have crosstalk. Using a hybrid of quantitative imaging, robot-controlled cell cultures, and computational techniques, we will extract time-varying data from single cells in a broad range of experimental condition that reflect what cells may encounter in vivo. We will also compare cellular responses across different inflammatory factors that share signaling modules and converge on the NF-κB transcriptional system, and we will learn how immune and cancer cells communicate these signals in co-cultures and higher-dimensional cellular structures. Using a rich single-cell dataset, we will identify emergent properties of signal transduction, and infer transfer functions that connect signaling mechanisms and correlate with cell fate. Data from live-cell experiments will be incorporated into mechanistic models to formalize our understanding of how information is relayed through the signaling network into transcription, and suggest perturbations to test predicted mechanisms. We anticipate that increasingly accurate models may lead to non-intuitive strategies to manipulate decisions in single cells. Through a detailed understanding of how dynamic molecular signals encode, process, and decode information, we have the potential to understand biological problems that are deeply rooted in disease, and use this knowledge to rationally design therapies that impact cell fate decisions.

项目总结

项目成果

A variable-gain stochastic pooling motif mediates information transfer from receptor assemblies into NF-κB.

• DOI: 10.1126/sciadv.abi9410
• 发表时间: 2021-07
• 期刊: Science advances
• 影响因子: 13.6
• 作者: Cruz JA;Mokashi CS;Kowalczyk GJ;Guo Y;Zhang Q;Gupta S;Schipper DL;Smeal SW;Lee REC
• 通讯作者: Lee REC

Label and quantify mRNA molecules in live cell experiments using SunRISER and dNEMO.

• DOI: 10.1016/j.xpro.2022.101630
• 发表时间: 2022-09-16
• 期刊: STAR PROTOCOLS
• 作者: Guo, Yue;Kowalczyk, Gabriel J.;Lee, Robin E. C.
• 通讯作者: Lee, Robin E. C.

Long-term imaging of individual mRNA molecules in living cells.

• DOI: 10.1016/j.crmeth.2022.100226
• 发表时间: 2022-06-20
• 期刊: Cell reports methods