Sui Xin, Lo Jennifer A, Luo Shuchen, He Yichun, Tang Zefang, Lin Zuwan, Zhou Yiming, Wang Wendy Xueyi, Liu Jia, Wang Xiao
Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
bioRxiv. 2024 Aug 8:2024.08.05.606553. doi: 10.1101/2024.08.05.606553.
Characterizing the transcriptional and translational gene expression patterns at the single-cell level within their three-dimensional (3D) tissue context is essential for revealing how genes shape tissue structure and function in health and disease. However, most existing spatial profiling techniques are limited to 5-20 μm thin tissue sections. Here, we developed Deep-STARmap and Deep-RIBOmap, which enable 3D quantification of thousands of gene transcripts and their corresponding translation activities, respectively, within 200-μm thick tissue blocks. This is achieved through scalable probe synthesis, hydrogel embedding with efficient probe anchoring, and robust cDNA crosslinking. We first utilized Deep-STARmap in combination with multicolor fluorescent protein imaging for simultaneous molecular cell typing and 3D neuron morphology tracing in the mouse brain. We also demonstrate that 3D spatial profiling facilitates comprehensive and quantitative analysis of tumor-immune interactions in human skin cancer.
在三维（3D）组织环境中对单细胞水平的转录和翻译基因表达模式进行表征，对于揭示基因如何在健康和疾病状态下塑造组织结构和功能至关重要。然而，大多数现有的空间分析技术仅限于5-20μm厚的组织切片。在此，我们开发了Deep-STARmap和Deep-RIBOmap，它们能够分别在200μm厚的组织块内对数千个基因转录本及其相应的翻译活性进行3D定量。这是通过可扩展的探针合成、具有高效探针锚定的水凝胶包埋以及稳健的cDNA交联实现的。我们首先将Deep-STARmap与多色荧光蛋白成像相结合，用于小鼠大脑中同时进行分子细胞分型和3D神经元形态追踪。我们还证明，3D空间分析有助于对人类皮肤癌中的肿瘤-免疫相互作用进行全面和定量分析。
