Center for Cell Circuits

描述（由申请人提供）：哺乳动物细胞中遗传和分子回路的系统性重建仍然是基因组学中一个重要的、大规模的和未解决的挑战。解决这一问题的紧迫性突出表现在相当数量的GWAS衍生疾病基因，其功能在很大程度上仍然不清楚，限制了我们对生物学理解和治疗干预的进展。在基因组规模上探测和操纵细胞电路的最新进展为电路重建的系统方法的发展开辟了道路。在这里，我们提出了一个细胞电路中心，以开发重建分子电路所需的试剂，技术，算法，协议和策略。我们的初步研究绘制了一条通往普遍战略的初步道路，我们将通过开发一个广泛和综合的实验和计算工具包来充分实施。我们将开发对不同电路层进行全面分析、遗传扰动和中尺度监测的方法（目标1）。与此同时，我们将开发一个计算框架来分析配置文件，推导临时模型，使用它们来确定扰动和监测的目标，并根据这些实验评估，改进和验证电路（目标2）。我们将开发，测试和完善这一战略的背景下，两个不同的和互补的哺乳动物电路。首先，我们将在树突状细胞（Aim 3）中产生对病原体的转录反应的集成多层电路，作为急性环境反应的一个例子。其次，我们将重建控制小鼠胚胎干细胞中染色质组织和基因表达的染色质因子和非编码RNA的电路（Aim 4），作为稳定细胞状态下电路的一个例子。这些详细的数据集和模型将揭示电路组织的一般原理，为这两个重要领域的科学家提供资源，并允许计算生物学家测试和开发算法。我们将向社区广泛传播我们的工具和方法，使研究人员能够以前所未有的细节解剖任何感兴趣的细胞回路。我们的工作将为重建人类疾病和个体的细胞回路开辟道路，以提高诊断和治疗的准确性。 相关性：虽然现在可以快速识别导致人类疾病的基因，但解释这些基因如何共同发挥正常功能或导致疾病仍然是一个重大挑战。我们建议开发一种通用的方法来发现基因如何在电路中一起工作，最终导致更好的诊断和治疗。

DESCRIPTION (provided by applicant): Systematic reconstruction of genetic and molecular circuits in mammalian cells remains a significant, large-scale and unsolved challenge in genomics. The urgency to address it is underscored by the sizeable number of GWAS-derived disease genes whose functions remain largely obscure, limiting our progress towards biological understanding and therapeutic intervention. Recent advances in probing and manipulating cellular circuits on a genomic scale open the way for the development of a systematic method for circuit reconstruction. Here, we propose a Center for Cell Circuits to develop the reagents, technologies, algorithms, protocols and strategies needed to reconstruct molecular circuits. Our preliminary studies chart an initial path towards a universal strategy, which we will fully implement by developing a broad and integrated experimental and computational toolkit. We will develop methods for comprehensive profiling, genetic perturbations and mesoscale monitoring of diverse circuit layers (Aim 1). In parallel, we will develop a computational framework to analyze profiles, derive provisional models, use them to determine targets for perturbation and monitoring, and evaluate, refine and validate circuits based on those experiments (Aim 2). We will develop, test and refine this strategy in the context of two distinct and complementary mammalian circuits. First, we will produce an integrated, multi-layer circuit of the transcriptional response to pathogens in dendritic cells (Aim 3) as an example ofan acute environmental response. Second, we will reconstruct the the circuit of chromatin factors and non-coding RNAs that control chromatin organization and gene expression in mouse embryonic stem cells (Aim 4) as an example of the circuitry underlying stable cell states. These detailed datasets and models will reveal general principles of circuit organization, provide a resource for scientists in these two important fields, and allow computational biologists to test and develop algorithms. We will broadly disseminate our tools and methods to the community, enabling researchers to dissect any cell circuit of interest at unprecedented detail. Our work will open the way for reconstructing cellular circuits in human disease and individuals, to improve the accuracy of both diagnosis and treatment. RELEVANCE: While it is now possible to rapidly identify genes that contribute to human disease, it is remains a major challenge to explain how these genes work together to carry out their normal functions or cause disease. We propose to develop a universal way to discover how genes work together in circuits, eventually leading to better diagnosis and therapy.