Modeling transcriptional and post-transcriptional systems for regulating non-genetic heterogeneity in mammalian cells

模拟转录和转录后系统以调节哺乳动物细胞中的非遗传​​异质性

• 批准号: 10623648
• 负责人: Tian Hong
• 金额: $ 33.05万
• 依托单位: UNIVERSITY OF TENNESSEE KNOXVILLE
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-01 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10623648
• 关键词: Binding; Cells; Computing Methodologies; Data; Degenerative Disorder; Development; Disease; Epithelial Cells; Epithelium; Foundations; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Heterogeneity; Malignant Neoplasms; Mammalian Cell; Measurement; Mesenchymal; Methods; MicroRNAs; Modeling; Molecular; Motor Neurons; Neuronal Differentiation; Pattern; Pattern Formation; Physiology; Play; Role; Signal Transduction; Site; Spinal Cord; Stem Cell Factor; System; Techniques; Testing; Therapeutic; cancer cell; cancer drug resistance; developmental disease; epithelial to mesenchymal transition; experimental study; gene regulatory network; insight; lung cancer cell; mathematical model; non-genetic; novel; posttranscriptional; stem; stem cells; success; theories; tissue degeneration; tumor; tumor progression

PROJECT SUMMARY Recent advances of experimental techniques allow quantitative and systems‐wide measurements of non‐ genetic heterogeneity of mammalian cells, which serves as a crucial factor for stem cell dynamics and differentiation potentials, as well as drug resistance of cancer cells. However, it remains challenging to understand many puzzling observations regarding this type of heterogeneity in terms of underlying gene regulatory networks. For example, progenitor cells restore their heterogeneity on timescales of days from subpopulation with extreme gene expression patterns, and these cells switch from plasticity‐enabling dynamics to robust commitment and pattern formation during differentiation; epithelial cells can be distributed in a stable continuum in the epithelial‐mesenchymal spectrum upon receiving signals in tumors. Existing theories provide very limited insights into these important dynamics and patterns. We propose to combine mathematical modeling, new methods of analyzing gene regulatory networks and gene expression data, and experiments in a motor neuron differentiation system, and systems involving epithelial‐mesenchymal transition to study transcriptional and post‐transcriptional mechanisms underlying non‐genetic heterogeneity in mammalian cells. We propose to test a novel theoretical framework of a diverging oscillator for controlling progenitor cell dynamics with both computational methods and experimental systems. We will rigorously formulate and test a new hypothesis of an oscillator‐to‐switch transition for motor neuron differentiation in the developing spinal cord. Stemming from our recent results on surprising post‐transcriptional mechanisms for multistability and oscillation, we will use novel algebraic approaches to establish the relationship between the number of microRNA bindings sites and biologically plausible cell states. We will test the roles of microRNA binding in epithelial cell plasticity experimentally. We will examine the roles of epithelial plasticity and microRNAs in dynamics of lung cancer cells. The success of the proposed study will provide a new theoretical basis and new methods for interpreting and understanding dynamical gene expression data on non‐genetic heterogeneity in mammalian cells. The theories and methods can used as a foundation to develop therapeutics for diseases related to development, tissue degeneration and cancer.

项目总结 实验技术的最新进展使定量和系统范围内的非 哺乳动物细胞的遗传异质性，这是干细胞动力学和 癌细胞的分化潜能以及耐药性。然而，它仍然具有挑战性， 从潜在基因的角度理解关于这种异质性的许多令人费解的观察结果 监管网络。例如，祖细胞在几天的时间尺度上恢复其异质性 具有极端基因表达模式的亚群，这些细胞从使能可塑性 分化过程中强健的承诺和模式形成的动力学；上皮细胞可以 在上皮-间充质光谱中以稳定的连续体分布 肿瘤。现有的理论对这些重要的动态和模式提供的洞察力非常有限。我们 建议将数学建模、分析基因调控网络的新方法和 基因表达数据和运动神经元分化系统中的实验，以及涉及 上皮-间充质转化研究转录和转录后机制 哺乳动物细胞中潜在的非遗传异质性。 我们建议测试一种用于控制祖细胞的发散振荡器的新理论框架 具有计算方法和实验系统的动力学。我们将严格制定和实施 测试振荡器到开关转换用于运动神经元分化的新假说 发育中的脊髓。源于我们最近关于令人惊讶的转录后机制的结果 对于多稳定性和振荡，我们将使用新的代数方法来建立关系 MicroRNA结合位点的数量和生物学上可信的细胞状态之间的关系。我们将测试 微小RNA结合在上皮细胞可塑性实验中的作用。我们将研究这些角色 肺癌细胞动力学中的上皮可塑性和microRNAs拟议研究的成功 将为解释和理解动力基因提供新的理论基础和新的方法 哺乳动物细胞中非遗传异质性的表达数据。本文的理论和方法可以作为 为开发与发育、组织退化和癌症相关的疾病的治疗方法奠定基础。