Modulating Stochastic Gene Expression for Cell-fate Control and Therapeutics

项目摘要 基因表达的随机波动在单细胞水平上是不可避免的，并影响细胞的命运决定。 艾滋病毒对胚胎发育的影响。然而，在我们对这些机制的理解方面， 在哺乳动物细胞中产生和调节表达波动。解决这一知识差距是 在波动和异质性造成治疗障碍的系统中， 例如在HIV、干细胞治疗和癌症中。我们的长期目标是开发针对 细胞异质性机制，以克服障碍，精确控制细胞命运。 在过去的5年里，我们的工作建立了噪音和异质性的机械作用，表明 噪声是生物系统的一个特征，而不是一个缺陷，它可以被调节以达到治疗效果。 具体来说，我们：（i）阐明了一个病毒转录反馈电路，利用噪音来调节HIV潜伏期， (ii)发现这个回路通过进化得到优化，以作为病毒性赌注对冲回路，（iii）做出了贡献 细胞生物学表明，转录波动，一般来说，放大核输出和翻译， 和，（iv）我们发现了一种新的转录后反馈结构，可以有效地抑制噪音， 稳定命运承诺。最令人兴奋的是，与此应用程序最相关的是，我们（v）发现了噪音- 增强子分子似乎显著改善了病毒从潜伏期的再活化， 以增加不同系统中的噪声（例如，昼夜节律）。 这次更新的目的是确定哺乳动物细胞命运中噪音调节的分子机制 电路以实现噪声的治疗控制。根据我们的发现和大量的初步证据， 胚胎干细胞（ESCs），我们的中心假设是，广义的“核心”细胞机制存在，以调整 表达噪音，这些机制可能会受到干扰。我们的具体目标是 我们独特的工具，噪音增强分子，并将：（目标1）地图的分子机制途径的噪音 增强子分子开发预测哺乳动物中转录组范围噪声的数学模型 （目的2）绘制噪声抑制分子的分子机制;（目的3）量化相对于噪声抑制的分子机制。 随机与确定性机制的贡献，这些机制是HIV在体内潜伏期和安全性的基础， 噪声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 核心分子机制调节表达在不同的命运规范模型，揭示遗传靶点 噪声增强和抑制，可能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翻译。最终，获得的知识将 指导新的治疗方法，以克服各种哺乳动物精确控制细胞命运的障碍 系统.

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.