Eli and Edythe Broad CIRM Center, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California 90033-9080, United States.
Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089-0484, United States.
ACS Synth Biol. 2022 Apr 15;11(4):1417-1439. doi: 10.1021/acssynbio.0c00369. Epub 2022 Apr 1.
Synthetic development is a nascent field of research that uses the tools of synthetic biology to design genetic programs directing cellular patterning and morphogenesis in higher eukaryotic cells, such as mammalian cells. One specific example of such synthetic genetic programs was based on cell-cell contact-dependent signaling using synthetic Notch pathways and was shown to drive the formation of multilayered spheroids by modulating cell-cell adhesion differential expression of cadherin family proteins in a mouse fibroblast cell line (L929). The design method for these genetic programs relied on trial and error, which limited the number of possible circuits and parameter ranges that could be explored. Here, we build a parameterized computational framework that, given a cell-cell communication network driving changes in cell adhesion and initial conditions as inputs, predicts developmental trajectories. We first built a general computational framework where contact-dependent cell-cell signaling networks and changes in cell-cell adhesion could be designed in a modular fashion. We then used a set of available results (that we call the "training set" in analogy to similar pipelines in the machine learning field) to parameterize the computational model with values for adhesion and signaling. We then show that this parameterized model can qualitatively predict experimental results from a "testing set" of available data that varied the genetic network in terms of adhesion combinations, initial number of cells, and even changes to the network architecture. Finally, this parameterized model is used to recommend novel network implementation for the formation of a four-layered structure that has not been reported previously. The framework that we develop here could function as a testing ground to identify the reachable space of morphologies that can be obtained by controlling contact-dependent cell-cell communications and adhesion with these molecular tools and in this cellular system. Additionally, we discuss how the model could be expanded to include other forms of communication or effectors for the computational design of the next generation of synthetic developmental trajectories.
合成发展是一个新兴的研究领域,它利用合成生物学的工具来设计指导高等真核细胞(如哺乳动物细胞)中细胞模式和形态发生的遗传程序。这种合成遗传程序的一个具体例子是基于使用合成 Notch 途径的细胞-细胞接触依赖性信号,通过调节细胞-细胞黏附、在小鼠成纤维细胞系(L929)中差异表达钙黏蛋白家族蛋白,来驱动多层球体的形成。这些遗传程序的设计方法依赖于反复试验,这限制了可以探索的可能电路和参数范围的数量。在这里,我们构建了一个参数化的计算框架,该框架可以根据细胞-细胞通讯网络驱动细胞黏附变化和初始条件作为输入,预测发育轨迹。我们首先构建了一个通用的计算框架,其中可以以模块化的方式设计基于接触的细胞-细胞信号网络和细胞-细胞黏附的变化。然后,我们使用一组可用的结果(我们在机器学习领域类似的管道中称为“训练集”)来为计算模型的参数化提供黏附力和信号的数值。然后,我们表明,该参数化模型可以定性地预测来自“测试集”的实验结果,该“测试集”的可用数据中改变了遗传网络的黏附组合、初始细胞数量,甚至改变了网络结构。最后,该参数化模型用于推荐新颖的网络实现,以形成以前未报道过的四层结构。我们在这里开发的框架可以作为一个测试平台,以确定通过控制基于接触的细胞-细胞通讯和黏附来获得的形态的可到达空间,这些分子工具和在这个细胞系统中。此外,我们讨论了如何扩展模型以包括其他形式的通信或效应器,用于下一代合成发育轨迹的计算设计。