Synthetic development: dissection of morphogenetic programs via reconstructive and perturbative approaches

项目摘要 发育生物学中的一个基本问题涉及图案和形状的起源和控制， 也称为形态发生。在遗传网络中编码的多细胞信令网络是 胚胎的正常发育并驱动它们的形态发生。一个典型的例子是周期性的 脊椎动物发育过程中中胚层分裂成体节，体节是脊椎骨的前体。 基因、效应蛋白和细胞环境的变化可以导致胚胎发育的改变，如 见于先天性疾病。为了治愈疾病，我们需要了解基因是如何在多种情况下控制细胞的 规模以及细胞组如何形成连贯的、有功能的组织和器官。 在过去的几年里，单细胞测序在发育生物学方面的发现激增， 微流体、光学、计算能力的增加导致了前所未有的时空分辨率 形态发生系统的多尺度动力学，从分子到细胞再到整个胚胎。 虽然这些进展产生了在开发过程中精心策划的事件的详细路线图- 尽管如此，我们仍然缺乏关于哪些蜂窝网络驱动集体形态发生程序的清晰图景。这个 经典的正向和反向遗传微扰筛选，甚至现代的微扰工具，如 光遗传学方面，目前仍主要集中在基因(S)或单信号通路水平上。这就是它 在推断复杂的多细胞网络和发育转变之间的因果关系方面具有挑战性。 需要新的微扰工具来构建与在体内观察到的相似的复杂性。AS 体内这些复杂的网络都是基于细胞-细胞和细胞-环境的沟通途径，我们需要 这些通路的可控版本，我们可以(I)在复杂的合成网络中链接，(Ii)用来控制 内源性发育途径。这样的系统将能够引入精确和复杂的 在网络层面上的时空扰动，而不是基因(S)，最终带来了 理解复杂网络和由此产生的发展转变之间的关系。 在我们的实验室中，我们开发了合成的细胞-细胞和细胞-细胞外基质途径，将它们连接在网络中，并使用它们来 研究发育过程。在这里，我们建议(I)使用这些工具来研究 Notch信号在早熟患者信号波形成和传播中的作用 (Ii)在发育信号的启发下，开发细胞-细胞外基质通讯的新工具。我们 期待着进入一个由工具、测试、答案、新问题、新工具组成的循环。 这些研究将通过揭示发育生物学的行为和逻辑来推进发育生物学领域 多蜂窝系统以及复杂网络如何实现跨越空间和时间尺度的控制。收获 指导发育细胞群体的洞察力和工具将对治疗糖尿病具有广泛的相关性 发育缺陷和我们控制培养皿中组织和器官生长的能力。

Project Summary A fundamental question in developmental biology concerns the origin and control of patterns and shapes, also known as morphogenesis. Multicellular signaling networks, encoded in genetic networks, underlie the normal development of embryos and drive their morphogenesis. Paradigmatic example is the periodic segmentation of mesoderm into somites, the precursors of the vertebrae, during vertebrate development. Changes in genes, effector proteins, and cellular environments can lead to altered embryonic development as seen in congenital disorders. To cure diseases we need to understand how genes control cells at multiple scales and how groups of cells form coherent, functional tissues and organs. The last years have witnessed a boom in discoveries in developmental biology with single-cell sequencing, microfluidics, optics, increased computational power leading to unprecedented spatiotemporal resolution of the multiscale dynamics of morphogenetic systems, from molecules to cells to whole embryos. While these advancements have produced detailed roadmaps of the events orchestrated during develop- ment, we still lack a clear picture of which cellular networks drive collective morphogenetic programs. The classical forward and reverse genetic perturbative screenings, and even modern perturbative tools like optogenetics, still mainly focus at the level of the gene(s) or single signaling pathways. This makes it challenging to infer causal relationship between complex multicellular networks and developmental transitions. New perturbative tools are needed that could construct similar complexity as the ones observed in vivo. As these complex networks in vivo are based on cell-cell and cell-environment communication pathways, we need controllable versions of those pathways that we can (i) link in complex synthetic networks, (ii) use to control endogenous developmental pathways. Such a system would enable the introduction of precise and complex spatiotemporal perturbations at the level of the networks instead of the gene(s), ultimately delivering increased understanding of the relationship between complex networks and resulting developmental transitions. In our lab we develop synthetic cell-cell and cell-ECM pathways, connect them in networks, and use them to investigate developmental processes. Here we propose to (i) use these tools to investigate the mechanistic contribution of Notch signaling to the formation and propagation of signaling waves in the presomitic mesoderm and, (ii) develop new tools for cell-ECM communication, inspired by developmental signaling. We expect to enter a cycle of toolsàtestàanswersànew questionsànew tools. These studies will advance the field of developmental biology by shedding light on the behavior and logic of multicellular systems and how complex networks enable control across scales of space and time. Gaining insight and tools to direct developmental cell populations would have widespread relevance for the treatment of developmental defects and our capacity to control the growth of tissue and organs in a dish.