Synthetic toolkit for precision gene expression control and signal processing in mammalian cells

用于哺乳动物细胞中精确基因表达控制和信号处理的合成工具包

基本信息

批准号：
10584605
负责人：
Ahmad Samir Khalil
金额：
$ 67.5万
依托单位：
BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-05-01 至 2025-01-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10584605
关键词：
Address Adoption Advanced Development Autoimmunity Behavior Biochemical Biological Biological Process Biomedical Engineering Biomedical Research Cell Differentiation process Cell Reprogramming Cell Therapy Cells Cellular immunotherapy Chemicals Communities Complex Cues Custom Development Disease Dose Drug Design Enabling Factors Engineering FDA approved Fostering Gene Activation Gene Expression Generations Genes Genetic Transcription Goals Human Human Biology Human Engineering Immune Immunologist Ligands Malignant Neoplasms Mammalian Cell Methods Modeling Oncoproteins Organoids Output Pharmaceutical Preparations Physiology Play Process Property Publishing Regenerative Medicine Regulation Reporter Research Personnel Role Scheme Science Scientist Shapes Signal Transduction Specificity Stimulus System Technology Therapeutic Tissue Engineering Tissues Transcriptional Regulation Viral Vector Work Yeasts cell behavior cellular engineering combinatorial cytokine design flexibility gene product improved information processing interest notch protein novel novel diagnostics novel therapeutics programs response self assembly signal processing spatiotemporal synthetic biology therapy development tool transcription factor tumor

项目摘要

PROJECT SUMMARY/ABSTRACT Cells activate precise gene expression programs in response to multifactorial chemical and biological stimuli. The purposeful manipulation of this process is a principal goal of synthetic biology, and its application to human cells could lead to breakthroughs in our understanding of human biology and in the development of next-generation diagnostics and therapeutics that respond in sophisticated ways to disease. Unfortunately, tools to artificially control gene expression in mammalian cells have significant limitations, constraining our ability to study fundamental biological processes and design more effective cell-based therapies. The most widely-used tools are older generation technology, derived from bacterial transcriptional systems. These are greatly limited in number, which restricts the number of gene products that can be simultaneously controlled. Additionally and importantly, they use “simple” one-to-one regulatory interactions, imposing fundamental restrictions on the regulatory flexibility and sophistication of designer systems. As a consequence, researchers are unable to create sophisticated gene expression controllers that can flexibly sense and integrate biochemical signals (e.g. ligands, chemical inducers, disease cues), and tune or reshape corresponding gene activation profiles. Among the many biomedical applications that would be transformed by these precision gene expression controllers in mammalian cells is the development of cell-based therapeutics for cancer, auto- immunity, and regenerative medicine, which can suffer from issues related to over-activation and tissue specificity. We propose to overcome these barriers by developing a novel synthetic toolkit for gene expression control in mammalian cells. Inspired by the natural design of metazoan transcriptional systems, our framework is based on synthetic transcription factors (synTFs) that can be programmed to assemble cooperatively in multivalent complexes. Our previous work showed that cooperative synTFs enable construction of gene expression control circuits with greatly expanded signal processing behavior in yeast. Here we will develop and characterize mammalian self-assembling synTFs that have superior properties for installation into human cells relative to existing tools. We will use these tools to develop three classes of gene expression controllers, which we will demonstrate in human immune cells, chosen for their important role in human physiology and their potential for cellular therapy: (1) Inducible controllers regulated by orthogonal, FDA-approved drugs. (2) Cell- autonomous controllers that sense and process biological stimuli, including ligand recognition by synthetic Notch receptors and microenvironmental cues. (3) Signal integration controllers that can perceive and integrate multiple biological signals to activate transcriptional programs. We anticipate that this toolkit will be broadly used by researchers to enable precision gene expression control across mammalian systems, including in biomedical applications of synthetic biology, cell reprogramming, and cell-based therapeutics. We will make our tools and design framework freely available to the academic scientific community.

项目摘要/摘要细胞根据多因素化学和生物学刺激激活精度基因表达程序。对此过程的有目的操纵是合成生物学的主要目标，其应用于人类细胞可能会导致我们对人类生物学的理解和发展的突破下一代诊断和疗法以复杂的疾病方式反应。很遗憾，人为控制哺乳动物细胞中基因表达的工具具有重大局限性，控制了我们能够研究基本生物学过程和设计更有效的基于细胞的疗法。最多广泛使用的工具是老年一代技术，它来自细菌转录系统。这些都是数量极大的限制，这限制了可以简单控制的基因产品的数量。此外，重要的是，他们使用“简单”一对一的监管互动，施加基本对设计器系统的监管灵活性和复杂设计的限制。结果，研究人员无法创建可以灵活感知和集成的复杂基因表达控制器生化信号（例如配体，化学诱导剂，疾病提示）和调子或重塑相应的基因激活轮廓。在这些精度将转化的许多生物医学应用中哺乳动物细胞中的基因表达控制器是基于细胞的癌症治疗的发展免疫力和再生医学，可能遭受与过度激活和组织有关的问题特异性。我们建议通过开发一种用于基因表达的新型合成工具包来克服这些障碍控制哺乳动物细胞。受到后生动物转录系统的自然设计的启发，我们的框架是基于可以编程以合作组装的合成转录因子（syntfs）多价复合物。我们以前的工作表明，合作的同步能够构建基因酵母中具有大大扩展的信号处理行为的表达控制电路。在这里，我们将发展和表征具有在人类细胞中安装的较高特性的哺乳动物自组装的syntfs 相对于现有工具。我们将使用这些工具来开发三类的基因表达控制器，我们将在人类免疫核管中证明，以其在人类生理中的重要作用而被选中细胞疗法的潜力：（1）由正交，FDA批准的药物调节的诱导控制器。（2）细胞 - 感知和过程生物学刺激的自主控制器，包括合成的配体识别缺口受体和微环境提示。（3）可以感知和集成的信号集成控制器多个生物信号激活转录程序。我们预计这个工具包将广泛研究人员使用的合成生物学，细胞重编程和基于细胞的疗法的生物医学应用。我们会做的我们的工具和设计框架免费提供给学术科学界。

项目成果

期刊论文数量（6）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Human herpesvirus 8 ORF57 protein is able to reduce TDP-43 pathology: network analysis identifies interacting pathways.

人类疱疹病毒 8 ORF57 蛋白能够减少 TDP-43 病理：网络分析确定了相互作用的途径。

DOI：
10.1093/hmg/ddad122
发表时间：
2023
期刊：
Human molecular genetics
影响因子：
3.5
作者：
Webber,ChelseaJ;Murphy,CarolineN;Rondón-Ortiz,AlejandroN;vanderSpek,SophieJF;Kelly,ElenaX;Lampl,NoahM;Chiesa,Giulio;Khalil,AhmadS;Emili,Andrew;Wolozin,Benjamin
通讯作者：
Wolozin,Benjamin

Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics.