Modulating Stochastic Gene Expression for Cell-fate Control and Therapeutics

调节随机基因表达以控制细胞命运和治疗

• 批准号: 10211509
• 负责人: Leor S Weinberger
• 金额: $ 96.28万
• 依托单位: J. DAVID GLADSTONE INSTITUTES
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-06-01 至 2026-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10211509
• 关键词: Address; Affect; Architecture; Attenuated; Award; Bacteria; Cell Fate Control; Cells; Cellular biology; Chemosensitization; Circadian Rhythms; Clinical; Data; Development; Electrophysiology (science); Embryo; Embryonic Development; Engineering; Enhancers; Evolution; FDA approved; Feedback; Flow Cytometry; Gene Expression; Genes; Genetic; Genetic Transcription; Goals; HIV; Heterogeneity; Intervention; Knowledge; Lead; Literature; Malignant Neoplasms; Mammalian Cell; Maps; Modeling; Molecular; Neurosciences; Noise; Nuclear Export; Outcome; Pathway interactions; Pharmacology; Regulator Genes; Reporter; Research; Rest; Role; Safety; Science; Sensorimotor functions; Source; Starvation; Stress; System; T-Lymphocyte; TNF gene; Testing; Therapeutic; Therapeutic Effect; Transcription Coactivator; Translations; Viral; Virus Diseases; Virus Latency; Work; Yeasts; base; biological systems; cell fate specification; circadian; clinical translation; drug repurposing; effective therapy; embryonic stem cell; improved; in vivo; knock-down; mathematical model; molecular modeling; mutant; novel; novel therapeutic intervention; predictive modeling; reactivation from latency; stem cell therapy; stem cells; therapeutic development; therapeutic target; tool; transcriptome

PROJECT SUMMARY Stochastic fluctuations in gene expression are unavoidable at the single-cell level and affect fate decisions from HIV to embryonic development. Yet, there remain fundamental gaps in our understanding of the mechanisms generating and regulating expression fluctuations in mammalian cells. Addressing this gap in knowledge is critical to therapeutic development in systems where fluctuations and heterogeneity present treatment barriers, such as in HIV, stem-cell therapeutics, and cancer. Our long-term goal is to develop therapeutics that target mechanisms of cellular heterogeneity to overcome barriers to precise control of cell fate. During the past 5 years, our work established mechanistic roles for noise and heterogeneity, demonstrating that noise is a feature, rather than a bug, of biological systems that can be modulated for therapeutic effect. Specifically, we: (i) elucidated a viral transcriptional-feedback circuit that harnesses noise to regulate HIV latency, (ii) found this circuit to be optimized by evolution to function as a viral bet-hedging circuit, (iii) made contributions to cell biology showing that transcriptional fluctuations are, in general, amplified by nuclear export and translation, and, (iv) we discovered a novel post-transcriptional feedback architecture that efficiently suppresses noise to stabilize fate commitment. Most excitingly, and most relevant to this application, we (v) discovered noise- enhancer molecules that appear to substantially improve viral reactivation from latency and have been used by other labs to increase noise in diverse systems (e.g., circadian rhythm). The objective of this renewal is to identify molecular mechanisms of noise modulation in mammalian cell-fate circuits to enable therapeutic control of noise. Based on our findings and extensive preliminary evidence in embryonic stem cells (ESCs), our central hypothesis is that generalized `core' cellular mechanisms exist to tune expression noise and that these mechanisms can be pharmacologically perturbed. Our specific aims build off our unique tool of noise-enhancer molecules and will: (Aim 1) map the molecular mechanistic pathways of noise enhancer molecules to develop a mathematical model predictive of transcriptome-wide noise in mammalian cells; (Aim 2) map the molecular mechanisms of noise-suppressor molecules; and (Aim 3) to quantify relative contributions of stochastic vs. deterministic mechanisms underlying HIV latency in vivo and safety & efficacy of noise-modulating molecules in vivo. The proposed research has broad significance as it will determine core molecular mechanisms regulating expression in disparate fate-specification models, reveal genetic targets of noise enhancement and suppression that can lead to the development of new broad-spectrum noise modulators, and propel clinical translation of noise-modulating molecules. Ultimately, the knowledge gained will guide new therapeutic approaches to overcome barriers to precise cell-fate control across diverse mammalian systems.

项目概要 基因表达的随机波动在单细胞水平上是不可避免的，并影响着命运的决定 HIV到胚胎发育。然而，我们对机制的理解仍然存在根本差距 产生并调节哺乳动物细胞中的表达波动。解决这一知识差距的方法是 对于波动和异质性存在治疗障碍的系统中的治疗开发至关重要， 例如艾滋病毒、干细胞疗法和癌症。我们的长期目标是开发针对 细胞异质性机制，以克服精确控制细胞命运的障碍。 在过去的 5 年中，我们的工作确立了噪声和异质性的机制作用，表明 噪声是生物系统的一个特征，而不是一个缺陷，可以通过调节来达到治疗效果。 具体来说，我们：（i）阐明了一种利用噪音来调节 HIV 潜伏期的病毒转录反馈回路， (ii) 发现该电路通过进化进行了优化，可作为病毒式下注对冲电路，(iii) 做出了贡献 细胞生物学表明，转录波动通常会因核输出和翻译而放大， 并且，（iv）我们发现了一种新颖的转录后反馈架构，可以有效地抑制噪声 稳定命运的承诺。最令人兴奋且与该应用最相关的是，我们 (v) 发现了噪声- 增强剂分子似乎可以显着改善病毒潜伏期的再激活，并已被使用 其他实验室增加不同系统中的噪音（例如昼夜节律）。 此次更新的目的是确定哺乳动物细胞命运中噪声调节的分子机制 电路以实现噪声的治疗控制。根据我们的调查结果和广泛的初步证据 胚胎干细胞（ESC），我们的中心假设是存在广义的“核心”细胞机制来调节 表达噪音，并且这些机制可能在药理学上受到干扰。我们的具体目标建立在 我们独特的噪声增强剂分子工具将：（目标 1）绘制噪声的分子机制路径 增强子分子开发预测哺乳动物转录组范围噪音的数学模型 细胞； （目标 2）绘制噪声抑制分子的分子机制；和（目标 3）量化相对 HIV体内潜伏期和安全性背后的随机机制与确定性机制的贡献& 噪音调节分子在体内的功效。拟议的研究具有广泛的意义，因为它将决定 调节不同命运规范模型中表达的核心分子机制，揭示遗传目标 噪声增强和抑制的研究可以导致新的广谱噪声的发展 调节剂，并推动噪音调节分子的临床转化。最终，所获得的知识将 指导新的治疗方法，克服不同哺乳动物精确细胞命运控制的障碍 系统。