Reverse engineering of transcriptional networks in somatic cell reprogramming

描述（由申请人提供）：我们工作的广泛长期目标是确定诱导多能性的分子机制。在分化细胞中诱导多能性的能力已经彻底改变了干细胞生物学领域，并呈现出巨大的治疗应用潜力。然而，关于建立和维持多能性的机制，包括各种遗传、表观遗传和信号重编程因子如何与转录调控因子相互作用以诱导多能性，存在许多未回答的问题。重编程因子的高度相互关联和多维性质需要系统生物学方法，其中每个因子的作用在整个网络的背景下被考虑。提出了一种紧密结合的实验和统计建模方法来预测参与重编程网络的转录因子之间的连接。这一结果将为研究这一过程的机制提供有力的依据，并为提高重编程方法的安全性和效率提供信息。具体而言，该项目的目标是：1。为了产生一个大的数据集，包括转录和多能性反应下广泛的重编程线索; 2。使用贝叶斯网络分析方法预测介导重编程的转录控制机制; 3.以实验验证计算预测。我们令人兴奋的综合实验和计算方法应用系统生物学范式来解决干细胞生物学问题，并有望在一个重要问题上取得进展，直接影响干细胞在再生医学中的应用。最近，通过引入四种基因将成人皮肤细胞重编程为胚胎样干细胞的能力已经被发现。这项技术有可能彻底改变再生医学，但用于传递这四个基因的病毒载体对人类使用并不安全。通过研究这四个基因和其他重编程因子之间的相互作用网络，有可能确定在不使用病毒载体的情况下重编程细胞的方法。

DESCRIPTION (provided by applicant): The broad long-term objective of our work is to determine the molecular mechanism of induced pluripotency. The ability to induce pluripotency in differentiated cells has revolutionized the field of stem cell biology and presents great potential for therapeutic application. However, there are many unanswered questions regarding the mechanisms that establish and maintain pluripotency, including how the various genetic, epigenetic and signaling reprogramming factors interact with transcriptional regulators to induce pluripotency. The highly interconnected and multidimensional nature of the reprogramming factors necessitates a systems biology approach, where the role of each factor is considered within the context of the entire network. A tightly integrated experimental and statistical modeling approach is proposed to predict connections among transcription factors involved in the reprogramming network. The result will provide a strong basis for mechanistic investigation of this process and information for enhancing the safety and efficiency of reprogramming methods. Specifically, the aims of this project are: 1. To generate a large data set comprised of transcriptional and pluripotency responses under a broad range of reprogramming cues; 2. To use Bayesian network analysis methods to predict transcriptional control mechanisms that mediate reprogramming; and 3. To experimentally validate the computational predictions. Our exciting, integrated experimental and computational approach applies a systems biology paradigm to open questions in stem cell biology and promises to yield progress in an important problem with direct impact on the use of stem cells in regenerative medicine. Relevance Recently, the ability to reprogram adult skin cells into embryonic-like stem cells by the introduction of four genes has been discovered. This technology has the potential to revolutionize regenerative medicine, but the viral vectors used to deliver the four genes are not safe for human use. By studying the network of interactions between the four genes and other reprogramming factors, it may be possible to identify methods to reprogram cells without the use of viral vectors.