Volumetric spatial-genetic imaging with DNA microscopy

项目总结/摘要 适应性免疫反应，大脑发育和肿瘤进展都显示出生理学， 依赖于相互作用的细胞之间的体细胞突变和基因组重排。有 目前没有广泛可用的工具来捕获组织的三个- 维度语境在我的实验室里，我们正在开发空间遗传技术来连接这一点， 重大技术差距。 DNA显微镜，我开发的一种成像方式，用于生成空间遗传图谱， tissue de novo（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为 DNA是一种独立的化学反应产物。这项技术首先标记 每个DNA和RNA分子都有独特的DNA条形码，然后将这些条形码 将分子连接到相互通信的网络中：将条形码以 取决于原始分子之间的距离。在这样做的过程中，DNA显微镜使用DNA 作为成像介质，有效地从“由内而外”对样本进行成像。 我实验室的研究有两个重点。第一个目的是利用DNA 显微镜图像捕获本质上是体积的，并将其应用于深层组织三- 三维空间遗传成像我们研究的第二个重点是利用 通过基因组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，以便最终从他们的基因组中解码。 基因组信息的细胞动力学随着时间的推移。我们的目标是利用DNA显微镜 联合解析细胞位置和细胞克隆关系以重建其 模式生物发育的时空动态。我们进一步致力于应用这一点， 框架，以加深我们对肿瘤和免疫细胞基因组变异性的理解， 哺乳动物组织在这份提案中，我描述了我们实现这两个目标的计划， 为DNA显微镜作为空间遗传学的关键工具奠定了基础 基础生物学和病理学中的成像。

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.