A model of repair: intercellular signaling and self-organization in plant regeneration

项目总结 植物具有在受伤后再生成年身体部位的特殊能力，提供了极好的 器官置换的概念模型。它们甚至可以迅速改造它们的成体干细胞壁龛 完全切除。我的实验室开创了研究植物再生的新系统和新技术。我们 利用转录和活体成像跟踪重编程细胞的细胞身份的开发方法 再生过程中的技术。在这项工作中，我领导了推出新的 单细胞rna-seq等技术应用于植物研究。使用这些和开发的其他技术 在NIGMS R01GM078279下，我们发现再生根似乎概括了胚胎程序 在器官再生过程中。这项工作使我们提出了这种高度自组织的模型 该系统协调了整个器官及其干细胞利基的再生。然而，虽然新的工具 就像在单细胞RNA-SEQ中一样，它提供了强大的方法来逐个细胞地分析发育程序， 他们在很大程度上对细胞间通讯在组织组装中的中介作用保持沉默。因此，我们的 目前的努力集中在开发新的办法来弥补这一差距。在一个提议的系统中，我们 以特定于细胞类型的方式诱导性地阻断共生(直接)通信通道，并使用单一- 细胞rna-seq以测试正常胚胎后对邻近和远处组织的影响 器官发生和再生(Block-Seq)。这类似于观察从 一个细胞连接到所有的邻居，而不是信号本身。植物中一种常见的信号模式是 转录因子在蛋白质水平上从一个细胞到其相邻细胞的运动。来跟踪蛋白质的运动 综上所述，我们正在开发一种点击化学方法，将标记的氨基酸结合到 特定的细胞类型，然后捕获和质谱分析相邻细胞中的移动蛋白 类型(Mobilome)。这种方法旨在揭示植物细胞用来 组织发展。总体而言，这些方法是由一个基本问题推动的，该问题支撑着 与医学相关的问题：位置信号如何产生一套规则，允许完美的 在再生中重建器官？

PROJECT SUMMARY Plants have exceptional capacity to regenerate adult body parts after injury, providing an excellent conceptual model for organ replacement. They can even rapidly reform their adult stem cell niches after complete excision. My lab has pioneered new systems and techniques to study plant regeneration. We developed methods for tracking cell identity of reprogramming cells using transcriptomic and live imaging techniques during regeneration. In connection with this work, I have led efforts to introduce new technologies like single-cell RNA-seq into plant research. Using these and other techniques developed under NIGMS R01GM078279, we found that regenerating roots appear to recapitulate embryonic programs during organ regeneration. The work has led to us to propose models of how this highly self-organizing system orchestrates the regeneration of an entire organ and its stem cell niche. However, while new tools like in single-cell RNA-seq provide powerful approaches to dissect developmental programs cell-by-cell, they are largely silent on the role of cell-cell communication in mediating tissue assembly. Hence, our current efforts are focused on developing new approaches to address this gap. In one proposed system, we inducibly block symplastic (direct) communication channels in a cell type-specific manner and use single- cell RNA-seq to test the consequences on neighboring and distant tissues during normal post-embryonic organogenesis and regeneration (Block-Seq). This is akin to observing the consequences of signaling from one cell to all its neighbors but not the signals themselves. One common mode of signaling in plants is the protein-level movement of transcription factors from one cell to its neighbors. To track protein movement comprehensively, we are developing a click chemistry approach to incorporate labeled amino acids in specific cell types followed by capture and mass spectrometry of the mobile proteins in neighboring cell types (the Mobilome). This approach is designed to reveal many of the signals that plant cells use to organize development. Overall, these approaches are motivated by a basic question that underpins a medically relevant question: how do positional signals generate a set of rules that allow the flawless reconstruction of organs in regeneration?