Reverse engineering of transcriptional networks in somatic cell reprogramming

描述(申请人提供)：我们工作的长期目标是确定诱导多能性的分子机制。在分化的细胞中诱导多能性的能力使干细胞生物学领域发生了革命性的变化，并展示了巨大的治疗应用潜力。然而，关于建立和维持多能性的机制仍有许多悬而未决的问题，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来诱导多能性。重新编程因素的高度相互关联和多维性质要求采用系统生物学方法，其中每个因素的作用都是在整个网络的背景下考虑的。提出了一种紧密结合的实验和统计建模方法，以预测参与重新编程网络的转录因子之间的联系。研究结果将为该过程的机械化研究提供有力的依据，为提高重编程方法的安全性和效率提供信息。具体地说，这个项目的目标是：1.产生一个由广泛的重新编程线索下的转录和多能性反应组成的大型数据集；2.使用贝叶斯网络分析方法来预测调节重新编程的转录控制机制；以及3.从实验上验证计算预测。我们令人兴奋的、集成的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中的问题，并有望在一个对干细胞在再生医学中的使用产生直接影响的重要问题上取得进展。相关性最近，通过引入四种基因，人们发现了将成人皮肤细胞重新编程为类似胚胎的干细胞的能力。这项技术有可能给再生医学带来革命性的变化，但用来传递这四种基因的病毒载体对人类来说并不安全。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，可能会找到无需使用病毒载体就能对细胞进行重编程的方法。

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.