RNA circuits for cell state determination in mammalian cells in vitro and in vivo

用于体外和体内哺乳动物细胞状态测定的RNA电路

基本信息

批准号：
9106976
负责人：
RON WEISS
金额：
$ 63.96万
依托单位：
MASSACHUSETTS INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2016
资助国家：
美国
起止时间：
2016-03-01 至 2021-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9106976
关键词：
4T1 Algorithms Animals Behavior Behavioral Biological Biological Markers Biological Models Biology Breast Cancer Cell Breast Cancer Model Cancer Model Cancer cell line Cell physiology Cells Classification Climacteric Complex Computers DNA DNA Footprint Detection Diagnostic Diagnostic Imaging Disease Disease Marker Disease model Elements Engineering Environment Gene Expression Gene Expression Regulation Genetic Genetic Programming Goals In Vitro Individual Information Storage Libraries Life Location Logic Mammalian Cell Mammary gland Medical Messenger RNA Metabolic Methods MicroRNAs Molecular Molecular Motors Monitor Mus Mutation Nanostructures Nanotechnology Normal Cell Nucleotides Oligonucleotides Output Population Process RNA RNA Sequences RNA analysis Reading Regulation Sensory Specificity Staging State Interests Synthetic Genes Technology Testing Time Transcriptional Regulation Translations Work analog base cancer therapy cancer type cell determination cell free DNA cell type design digital improved in vivo in vivo Model information processing interest malignant breast neoplasm man molecular marker mouse model neoplastic cell operation programs promoter public health relevance sensor sensory input success tool transcription factor tumor progression

项目摘要

DESCRIPTION: Biology uses complex regulatory networks to sense and regulate cell state. Synthetic molecular circuits that can similarly control the timing and location of gene expression will have important applications in targeted disease therapy, cellular reprogramming, and beyond. However, a reliable, scalable, and general molecular technology for programmable gene expression has not yet been demonstrated. Here, we propose a paradigm shifting approach to this challenge: we will develop RNA strand displacement-based cellular bio computers. To date, strand displacement has primarily been demonstrated with DNA oligonucleotides in cell free settings. Strand displacement has been used effectively in cell-free DNA nanotechnology to build complex multi-input logic circuits, programmable nanostructures and molecular motors. Logic circuits made from hundreds of DNA oligonucleotides constitute the largest man-made molecular circuits built so far. In fact, there is currently no other engineering technology that supports de novo design of similarly complex, scalable and modular molecular circuitry, making this approach an intriguing candidate for performing biological computation in cells. Here we plan to bring strand displacement circuits to the cellular environment through the use of RNA instead of DNA, including sensors for endogenous RNA and RNA-based gene regulation. By foregoing the use of transcription factors and promoter regulation orthogonal with we can rapidly build more sophisticated circuits, cellular processes , which can be delivered more easily. We estimate that encoding of strand displacement circuits can be up to 10-fold more compact than genetic encoding of an equivalent circuit using transcriptional regulation. DNA serves as the information-storage medium, while transcribed RNA acts as the information- processing medium. Our RNA parts are engineered to interact with the cell milieu through specialized sensing and actuation components. We will demonstrate that, in principle, any endogenous cellular mRNA or miRNA can be an input, and that output gene expression can be regulated through RNA-RNA interactions. We will construct multi-input sensory circuits that provide high content information about cell state, and apply this for understanding biomarker levels and correlations for an in vitro and an in vivo 4T1 mouse breast cancer model. Importantly, our ability to encode highly sophisticated genetic programs with a much smaller DNA footprint will allow us to overcome current in vivo delivery limitations of complex circuitry. We initially focus on breast cancer as a model system but our technology can readily be adapted to other biomarkers, cancer types, and disease models. In fact, we believe that this adaptability, grounded in a rational design approach, is the key strength of the proposed technology. We expect that our technology will become relevant for many other applications that require sensing, analysis and control of cell state, including diagnostics and imaging applications, understanding of disease models, or programmed control of multi-stage differentiation.

描述：使用公司网络来感知和常规的细胞状态将deplater的生物计算机在无核核苷酸中。电路，使这种方法成为在细胞中执行生物学计算的有趣候选者。要估计，与等效的Sing转录调节的遗传编码相比，电路的编码可以高出10倍，DNA用作信息存储介质。细胞环境感应和致动成分，任何内源性细胞mRNA或miRNA都可以是输入，我们可以构建多输入的感觉电路，以提供有关细胞状态标记水平的高内容信息体内和体内4T1小鼠乳腺癌模型。实际上，我们认为这种适应性和合理的设计方法是拟议技术的关键优势。状态，包括诊断和成像应用，对疾病模型的理解或对多阶段区分的程序控制。