Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
Nat Biotechnol. 2022 Jan;40(1):74-85. doi: 10.1038/s41587-021-01006-2. Epub 2021 Sep 6.
Molecular profiling of single cells has advanced our knowledge of the molecular basis of development. However, current approaches mostly rely on dissociating cells from tissues, thereby losing the crucial spatial context of regulatory processes. Here, we apply an image-based single-cell transcriptomics method, sequential fluorescence in situ hybridization (seqFISH), to detect mRNAs for 387 target genes in tissue sections of mouse embryos at the 8-12 somite stage. By integrating spatial context and multiplexed transcriptional measurements with two single-cell transcriptome atlases, we characterize cell types across the embryo and demonstrate that spatially resolved expression of genes not profiled by seqFISH can be imputed. We use this high-resolution spatial map to characterize fundamental steps in the patterning of the midbrain-hindbrain boundary (MHB) and the developing gut tube. We uncover axes of cell differentiation that are not apparent from single-cell RNA-sequencing (scRNA-seq) data, such as early dorsal-ventral separation of esophageal and tracheal progenitor populations in the gut tube. Our method provides an approach for studying cell fate decisions in complex tissues and development.
单细胞的分子谱分析提高了我们对发育分子基础的认识。然而，目前的方法大多依赖于将细胞从组织中分离出来，从而失去了调控过程的关键空间背景。在这里，我们应用基于图像的单细胞转录组学方法——顺序荧光原位杂交（seqFISH），在 8-12 体节阶段的小鼠胚胎组织切片中检测 387 个靶基因的 mRNA。通过整合空间背景和带有两个单细胞转录组图谱的多路转录测量，我们对胚胎中的细胞类型进行了描述，并证明了可以对 seqFISH 未分析的基因的空间表达进行推断。我们使用这个高分辨率的空间图谱来描述中脑-后脑边界（MHB）和发育中的肠道管的图案形成的基本步骤。我们揭示了一些从单细胞 RNA 测序（scRNA-seq）数据中不明显的细胞分化轴，例如肠道管中食管和气管祖细胞群体的早期背腹分离。我们的方法为研究复杂组织和发育中的细胞命运决定提供了一种方法。
