Multiscale tools and approaches for understanding and engineering cell-fate transitions

用于理解和设计细胞命运转变的多尺度工具和方法

• 批准号: 10276773
• 负责人: Kate Elizabeth Galloway
• 金额: $ 38.78万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-01 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10276773
• 关键词: Affect; Behavior; Binding; Cell Fate Control; Cell Therapy; Cells; Chromatin; Chromatin Structure; DNA; Detection; Engineering; Enzymes; Epigenetic Process; Event; Foundations; Gene Expression; Genes; Genetic; Genetic Transcription; Human; Innate Immune Response; Length; Molecular; Mus; Oncogenes; Outcome; Performance; Phase; Process; Regenerative Medicine; Regulation; Regulator Genes; Role; Signal Transduction; Synthetic Genes; System; Systems Biology; Time; Transgenes; Work; Writing; biological systems; cellular engineering; design; genetic element; improved; insight; metaplastic cell transformation; pathogen; programs; quorum sensing; response; stem cell biology; synthetic biology; three dimensional structure; tool; transgene delivery; tumor

Project summary Synthetic biology aims to harness the power of biological systems to dynamically access information in the cell, enabling synthetic biomedical tasks such as tumor surveillance, pathogen identification, or cell-fate reprogramming. Such tasks in cellular engineering rely on robust mechanisms to regulate transgenes for the delivery of enzymes, genetic corrections, and cellular therapies. To unleash its full potential, mammalian synthetic biology requires foundational tools for implementing reliable control of gene expression in primary cells. For example, transgene silencing (e.g. loss of expression) remains a common challenge to effectively engineering primary cells. Layers of regulation across a range of length- and time-scales coordinate events from molecular binding to cell signaling regulate gene expression and thus cell fate. Multiscale approaches are needed to integrate the diverse processes that control cell-fate transitions. Cell-fate transitions represent pivotal events requiring coordination of multiple processes from epigenetic and cytoskeletal remodeling to proliferation and transcription. Understanding these transitions may illuminate how oncogenes coopt these processes to drive cellular transformation. Here, we propose a multiscale approach for understanding and engineering cell-fate transitions (e.g. reprogramming, differentiation). From our previous work to identify principles of cell-fate transitions, we identified systems-level constraints that limited reprogramming and developed a cocktail that increased reprograming 100-fold in mouse cells. Comparing the human and mouse response to reprogramming, we identified species-specific differences in proliferation, signaling, and the innate immune response during reprogramming that may contribute to lower reprogramming rates for human cells. We propose to examine these molecular correlates to determine how each impacts the reprogramming process and outcomes. We will use these insights to design genetic controllers to guide cells through reprogramming. Already we have identified a strategy to optimize reprogramming by inducing a transient “erase” phase followed by a “write” phase to establish the new cell fate. We propose to develop controllers capable of autonomously guiding cells through these competing objectives to enhance the efficiency of reprogramming. Genetic controllers are composed from synthetic gene circuits connected to native gene regulatory networks. While significant efforts have been devoted to the logical design of enhanced synthetic circuitry (e.g. circuits for synchronized quorum sensing, edge-detection), less is understood regarding how cellular hardware and the emergent three-dimensional structure of genetic elements affect circuits. Here, we propose to improve our understanding how transcription reshapes DNA and how it impacts the performance of gene circuits. Defining the role of chromatin structure in cellular identity will guide molecular engineering efforts to build genetic controllers capable of regulating behavior. We anticipate that the principles and tools we develop will be broadly applicable across cellular engineering applications as well as for investigating cell-fate transitions.

项目概要 合成生物学旨在利用生物系统的力量动态获取信息 细胞，实现合成生物医学任务，例如肿瘤监测、病原体识别或细胞命运 重新编程。细胞工程中的此类任务依赖于强大的机制来调节转基因 酶的输送、基因校正和细胞疗法。为了充分发挥其潜力，哺乳动物 合成生物学需要基础工具来实现对原代细胞中基因表达的可靠控制。 例如，转基因沉默（例如表达丧失）仍然是有效地解决这一问题的一个常见挑战。 工程原代细胞。跨越一系列长度和时间尺度的监管层协调事件 与细胞信号传导的分子结合调节基因表达，从而调节细胞命运。多尺度方法是 需要整合控制细胞命运转变的不同过程。细胞命运转变至关重要 需要协调从表观遗传和细胞骨架重塑到增殖的多个过程的事件 和转录。了解这些转变可能会阐明癌基因如何利用这些过程来驱动 细胞转化。在这里，我们提出了一种理解和改造细胞命运的多尺度方法 转变（例如重编程、分化）。 从我们之前确定细胞命运转变原理的工作中，我们确定了系统级 限制重编程的约束并开发了一种鸡尾酒，可以将小鼠的重编程提高 100 倍 细胞。比较人类和小鼠对重编程的反应，我们发现了物种特异性差异 重编程过程中的增殖、信号传导和先天免疫反应可能有助于降低 人类细胞的重编程率。我们建议检查这些分子相关性以确定每个分子如何 影响重编程过程和结果。我们将利用这些见解来设计遗传控制器 引导细胞进行重编程。我们已经确定了一种通过诱导来优化重编程的策略 短暂的“擦除”阶段，然后是“写入”阶段，以建立新的细胞命运。我们建议开发 控制器能够自主引导细胞完成这些相互竞争的目标，以提高效率 重新编程。遗传控制器由连接到天然基因的合成基因电路组成 监管网络。虽然人们在增强合成的逻辑设计上付出了巨大的努力 电路（例如用于同步群体感应、边缘检测的电路），关于如何实现的了解较少 细胞硬件和遗传元件的新兴三维结构影响电路。在这里，我们 提议提高我们对转录如何重塑 DNA 及其如何影响 DNA 性能的理解 基因电路。定义染色质结构在细胞身份中的作用将指导分子工程工作 建立能够调节行为的基因控制器。我们预计我们开发的原则和工具 将广泛适用于细胞工程应用以及研究细胞命运转变。