Abstract
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.
Highlights
Lineage priming, cell fate specification and tissue patterning during early mammalian development are complex processes involving signals from surrounding tissues, mechanical constraints, and transcriptional and epigenetic changes, which together prompt the adoption of unique cell fates[1,2,3,4,5,6,7]
We have combined cutting-edge experimental approaches with advanced computational analyses to generate a comprehensive map of how gene expression varies in space across sagittal sections of an entire mouse embryo at the 8–12 ss of development
Previous studies using scRNA-seq have computationally reconstructed developmental trajectories based on gene expression, but, in the absence of cell-specific spatial information, it has been impossible to define how cell states are correlated with the position of cells within the embryo or to understand how the local signaling environment to which they are exposed might impact their molecular signature and their ultimate fate
Summary
Cell fate specification and tissue patterning during early mammalian development are complex processes involving signals from surrounding tissues, mechanical constraints, and transcriptional and epigenetic changes, which together prompt the adoption of unique cell fates[1,2,3,4,5,6,7]. ScRNA-seq and other single-cell genomic approaches have been used to investigate how the molecular landscape of cells within the mouse embryo changes during early development These methods have provided insights into how symmetry breaking of the epiblast population leads to commitment to different fates as the embryo passes through gastrulation and on to organogenesis[1,2,3,6,7,8,9,10,11,12,13,14]. Technological advances have enabled scRNA-seq to be performed alongside CRISPR–Cas[9] scarring, simultaneously documenting a cell’s molecular state and lineage Such approaches have been applied to track zebrafish development[15,16,17] and more recently mouse embryogenesis[9,18]. Our spatial data revealed that these two clusters were exclusively located on either the dorsal or ventral side of the gut tube, with corresponding transcriptional differences indicating that the dorsal cells give rise to the esophagus, while the ventral cells give rise to the lung and trachea
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
