Volumetric spatial-genetic imaging with DNA microscopy

项目摘要/摘要 适应性免疫反应、大脑发育和肿瘤进展都显示出生理上的 取决于相互作用的细胞之间的体细胞突变和基因组重排。的确有 目前还没有广泛可用的工具来捕捉组织中三个核苷酸水平的变化. 维度上下文。在我的实验室里，我们正在开发空间遗传技术来弥合这一点 重大技术差距。 DNA显微镜，这是我开发的一种成像方式，用于生成 组织从头开始(Weinstein，Regev，Zhang，Cell 2019)为这项工作提供了关键基础。 DNA显微镜将细胞的空间位置和核苷酸水平差异编码到 DNA是独立化学反应的产物。这项技术通过首先标记来操作 单个DNA和RNA分子带有独特的DNA条形码，然后将这些条形码 分子进入互通网络：将条形码以 取决于原始分子之间的距离。在此过程中，DNA显微镜使用DNA 作为一种成像介质，由内而外有效地对标本成像。 我的实验室的研究有两个突破口。第一项研究的目的是利用DNA 显微镜图像捕获本质上是体积，并将其应用于深层组织三- 多维空间-遗传成像。我们研究的第二个主旨是利用 通过基因组突变和基因突变编码到增殖细胞DNA中的系统发育关系 其他形式的随机基因组重组，以便最终从它们的 基因组中有关细胞动态随时间变化的信息。我们的目标是利用DNA显微镜 能够联合解析细胞位置和细胞克隆关系以重建其 模式生物体发育中的时空动力学。我们的进一步目标是将这一点应用于 框架，以加深我们对肿瘤和免疫细胞基因组变异的理解 哺乳动物组织。在这项提案中，我描述了我们实现这两个目标的计划，以及 为将DNA显微镜用作空间遗传学的关键工具奠定基础 基础生物学和病理学的影像学。

Project Summary/Abstract Adaptive immune response, brain development, and tumor progression all display physiology that depends on somatic mutations and genomic rearrangements among interacting cells. There is currently no widely-available tool to capture nucleotide-level variation in a tissue’s three- dimensional context. In my lab, we are developing spatial-genetic technologies to bridge this major technological gap. DNA microscopy, an imaging modality that I developed for generating spatial-genetic maps of tissue de novo (Weinstein, Regev, Zhang, Cell 2019) provides a critical foundation for this work. DNA microscopy encodes the spatial positions and nucleotide-level differences of cells into the DNA products of a stand-alone chemical reaction. The technology operates by first tagging individual DNA and RNA molecules with unique DNA barcodes, and then turning these barcoded molecules into an intercommunicating network: linking barcodes to one another at rates that depend on the distance between the original molecules. In doing so, DNA microscopy uses DNA as an imaging medium, effectively imaging a specimen from the “inside-out”. My lab’s research has two thrusts. The first of these is aimed at exploiting the fact that DNA microscopy image-capture is intrinsically volumetric, and applying it to deep-tissue three- dimensional spatial-genetic imaging. The second thrust of our research is aimed at using the phylogenetic relationships encoded into the DNA of proliferating cells, via genomic mutations and other forms of stochastic genomic reorganization, in order to ultimately decode from their genomes information about cellular dynamics through time. Our goal is to use DNA microscopy’s capability to jointly resolve cellular positions and cell clonal relationships to reconstruct their spatial and temporal dynamics in model organism development. We further aim to apply this framework to deepen our understanding of genomic variability in tumors and immune cells in mammalian tissue. In this proposal, I describe our plan to achieve both of these goals, and to establish a foundation for DNA microscopy to be deployed as a critical tool for spatial-genetic imaging in both basic biology and pathology.