Journal
GENOME BIOLOGY
Volume 19, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/s13059-018-1416-2
Keywords
Single-cell RNA-seq; Organogenesis; Interactions between mesenchyme and epithelium; Epithelial/mesenchymal hybrid state
Funding
- National Natural Science Foundation of China [81561138005, 31322037]
- Foundation for Innovative Research Groups of the National Natural Science Foundation of China [81521002]
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Background: Organogenesis is crucial for proper organ formation during mammalian embryonic development. However, the similarities and shared features between different organs and the cellular heterogeneity during this process at single-cell resolution remain elusive. Results: We perform single-cell RNA sequencing analysis of 1916 individual cells from eight organs and tissues of E9.5 to E11.5 mouse embryos, namely, the forebrain, hindbrain, skin, heart, somite, lung, liver, and intestine. Based on the regulatory activities rather than the expression patterns, all cells analyzed can be well classified into four major groups with epithelial, mesodermal, hematopoietic, and neuronal identities. For different organs within the same group, the similarities and differences of their features and developmental paths are revealed and reconstructed. Conclusions: We identify mutual interactions between epithelial and mesenchymal cells and detect epithelial cells with prevalent mesenchymal features during organogenesis, which are similar to the features of intermediate epithelial/mesenchymal cells during tumorigenesis. The comprehensive transcriptome at single-cell resolution profiled in our study paves the way for future mechanistic studies of the gene-regulatory networks governing mammalian organogenesis.
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