间充质细胞聚集和图式形成机制的系统生物学及合成生物学研究

We aim to study mesenchymal cell pattern formation using genetic programming, quantitative manipulation/measurement and mathematical modeling. Epithelial-Mesenchymal transitions (EMT) and Mesenchymal-Epithelial transitions (MET) is critical in formation of animal body plan, organ genesis and repair. Their misregulation could also lead to fibrosis and cancer progression. A key element during MET is the coordinated motion of mesenchymal cell and formation of specific patterns, such as somite formation. Many of the molecular players involved in are well documented. However, due to the technical difficulty in observation and manipulation of such process in vivo, most of which is still poorly understood. In addition, pattern formations with mesenchymal cells in vitro are pursued in tissue engineering, where the quantitative control of the pattern formation process is especially important. We have identified a robust method of inducing mesenchymal cells to aggregate to form spots or net patterns.It might be a univerversal process. To answer this we need to find the critical physical interactions or chemical processes, and develop the capability to manipulate the genetic and environmental machineries to obtain predicted pattern formations. We have used similar approach to identify a new mechanism for sequential and periodic stripe formations. A thourough synthetic design, quantitative measurements and mathematic modeling not only unweil the mechanisms also provide a simple way to tune the pattern such as repeat numbers. Mesenchymal cells has much complex molecular machinaries for motion regulation. Therefore we will use genetic programmed circuit as a tool to probe the cells, followed by carefully designed quantitative experiments involving tracking motion of single cells. The key to success is to propose multiple mechanisms and mathematic models based on biological evidences. The models will be carefully studied to identify the experiments that models makde comflicted predictions. Thus we can effifiently rule out many mechanisms and identify the current one.

间充质细胞的运动及聚集在动物的发育，器官维持及癌变中起着关键的作用。科学家同时利用特殊来源的间充质细胞或间充质干细胞的聚集、图式形成来产生治疗用途的功能性组织如胰岛。虽然大量的研究集中于发现与特定间充质细胞聚集相关的基因，但是对于间充质细胞聚集及图式形成的运动机制缺乏系统和定量的研究。理论模型如Turing和Keller-Segel已经用于解释生物图式形成过程，然而还没有人系统地比较过多种理论模型的预言与实验结果,从而他们的结论都有一定的片面性。因此，我们拟通过控制细胞的微环境等实验条件，定量测量细胞的运动，系统地比较各种基于分子机制的可能的理论模型与定量实验结果从而确定间充质细胞在活体外聚集的机制。我们将进一步利用合成生物学方法导引如基因控制回路而定量调整间充质细胞的聚集及图式形成的动态过程。该研究利用新颖方法推动间充质细胞图式形成的基础研究，以及给相应的组织工程提供定量调控聚集的可行性

本研究在对间充质细胞自发形成团聚的研究中，改良了活细胞显微成像技术、细胞自动识别与跟踪的算法细胞，建立了独特的细胞间相互运动以及团聚的定量刻画指数，并通过结合定量实验测量和计算模型，首次发现了一种非图灵模型的生物自发图式形成原理，即细胞随机运动与粘附驱动的细胞聚集。根据实验观测结果将间充质细胞自发形成团聚分为三个步骤细胞延展与运动，细胞粘附以及细胞收缩，并据此对若干细胞因子进行了分类刻画，以便发现定量调控团聚的方法。我们建立起来的这个系统的定量研究方法对生理、病理的间充质细胞图式形成以及间充质干细胞组织工程研究提供了一个新的思路。